Starting phenix.real_space_refine
on Fri Aug 22 20:14:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yty_34095/08_2025/7yty_34095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yty_34095/08_2025/7yty_34095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yty_34095/08_2025/7yty_34095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yty_34095/08_2025/7yty_34095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yty_34095/08_2025/7yty_34095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yty_34095/08_2025/7yty_34095.cif"
  }
  resolution = 3.5
  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=   0.032
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      62      5.16       5
     C    4990      2.51       5
     N    1224      2.21       5
     O    1332      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7608
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 501, 3804
          Classifications: {'peptide': 501}
          Link IDs: {'PTRANS': 33, 'TRANS': 467}
          Chain breaks: 2
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.32, per 1000 atoms: 0.30
  Number of scatterers: 7608
  At special positions: 0
  Unit cell: (89.38, 107.42, 78.72, 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      62     16.00
     O    1332      8.00
     N    1224      7.00
     C    4990      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  78 " - pdb=" SG  CYS B 136 " distance=2.03

  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: 0.62
  Conformation dependent library (CDL) restraints added in 294.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1804

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 2 sheets defined
      71.7% alpha, 0.8% 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 51 through 67
      removed outlier: 3.507A  pdb=" N   GLY A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 77
      removed outlier: 4.122A  pdb=" N   PHE A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 108
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 3.629A  pdb=" N   ALA A 125 " --> pdb=" O   PHE A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 152 through 180
      removed outlier: 3.775A  pdb=" N   TRP A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 182 through 190
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 3.543A  pdb=" N   VAL A 195 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 206 through 215
    Processing helix  chain 'A' and resid 217 through 233
    Processing helix  chain 'A' and resid 262 through 281
      removed outlier: 3.761A  pdb=" N   LEU A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 301
      removed outlier: 3.831A  pdb=" N   ALA A 295 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   THR A 297 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ASP A 298 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ARG A 300 " --> pdb=" O   THR A 297 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY A 301 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.535A  pdb=" N   ILE A 306 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 354
      removed outlier: 3.542A  pdb=" N   GLY A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY A 354 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 381
    Processing helix  chain 'A' and resid 389 through 399
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.725A  pdb=" N   ALA A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 429
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.553A  pdb=" N   LEU A 435 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 485
      removed outlier: 3.540A  pdb=" N   LEU A 465 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      Proline residue:  A 479  - end of helix
    Processing helix  chain 'A' and resid 493 through 506
    Processing helix  chain 'A' and resid 506 through 522
      removed outlier: 3.706A  pdb=" N   GLY A 511 " --> pdb=" O   GLU A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 534
      removed outlier: 3.853A  pdb=" N   GLN A 533 " --> pdb=" O   GLY A 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 67
      removed outlier: 3.508A  pdb=" N   GLY B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 77
      removed outlier: 4.123A  pdb=" N   PHE B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU B  72 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 108
    Processing helix  chain 'B' and resid 121 through 129
      removed outlier: 3.629A  pdb=" N   ALA B 125 " --> pdb=" O   PHE B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 143
    Processing helix  chain 'B' and resid 152 through 180
      removed outlier: 3.774A  pdb=" N   TRP B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
      Proline residue:  B 158  - end of helix
    Processing helix  chain 'B' and resid 182 through 190
    Processing helix  chain 'B' and resid 191 through 204
      removed outlier: 3.543A  pdb=" N   VAL B 195 " --> pdb=" O   GLY B 191 " (cutoff:3.500A)
      Proline residue:  B 197  - end of helix
    Processing helix  chain 'B' and resid 206 through 215
    Processing helix  chain 'B' and resid 217 through 233
    Processing helix  chain 'B' and resid 262 through 281
      removed outlier: 3.760A  pdb=" N   LEU B 266 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 301
      removed outlier: 3.831A  pdb=" N   ALA B 295 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   THR B 297 " --> pdb=" O   GLN B 294 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ASP B 298 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ARG B 300 " --> pdb=" O   THR B 297 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY B 301 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 307
      removed outlier: 3.535A  pdb=" N   ILE B 306 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 354
      removed outlier: 3.542A  pdb=" N   GLY B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY B 354 " --> pdb=" O   ALA B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 381
    Processing helix  chain 'B' and resid 389 through 399
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 3.725A  pdb=" N   ALA B 419 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 429
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.553A  pdb=" N   LEU B 435 " --> pdb=" O   PRO B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 485
      removed outlier: 3.540A  pdb=" N   LEU B 465 " --> pdb=" O   SER B 461 " (cutoff:3.500A)
      Proline residue:  B 479  - end of helix
    Processing helix  chain 'B' and resid 493 through 506
    Processing helix  chain 'B' and resid 506 through 522
      removed outlier: 3.706A  pdb=" N   GLY B 511 " --> pdb=" O   GLU B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 534
      removed outlier: 3.853A  pdb=" N   GLN B 533 " --> pdb=" O   GLY B 530 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 117
    Processing sheet with id=AA2, first strand: chain 'B' and resid 115 through 117

    486 hydrogen bonds defined for protein.
    1434 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: 0.95

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1999
        1.33 -     1.45: 1465
        1.45 -     1.57: 4244
        1.57 -     1.69: 0
        1.69 -     1.81: 96
  Bond restraints: 7804
  Sorted by residual:
  bond pdb=" C   LEU A 182 "
       pdb=" N   PRO A 183 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 2.34e-02 1.83e+03 7.91e+00
  bond pdb=" C   LEU B 182 "
       pdb=" N   PRO B 183 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 2.34e-02 1.83e+03 7.91e+00
  bond pdb=" CB  PRO B 479 "
       pdb=" CG  PRO B 479 "
    ideal  model  delta    sigma   weight residual
    1.492  1.382  0.110 5.00e-02 4.00e+02 4.86e+00
  bond pdb=" CB  PRO A 479 "
       pdb=" CG  PRO A 479 "
    ideal  model  delta    sigma   weight residual
    1.492  1.383  0.109 5.00e-02 4.00e+02 4.78e+00
  bond pdb=" CA  ARG B 300 "
       pdb=" CB  ARG B 300 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.064 3.28e-02 9.30e+02 3.84e+00
  ... (remaining 7799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 10253
        2.67 -     5.34: 322
        5.34 -     8.00: 63
        8.00 -    10.67: 12
       10.67 -    13.34: 4
  Bond angle restraints: 10654
  Sorted by residual:
  angle pdb=" N   GLY A 330 "
        pdb=" CA  GLY A 330 "
        pdb=" C   GLY A 330 "
      ideal   model   delta    sigma   weight residual
     112.73  106.95    5.78 1.20e+00 6.94e-01 2.32e+01
  angle pdb=" N   GLY B 330 "
        pdb=" CA  GLY B 330 "
        pdb=" C   GLY B 330 "
      ideal   model   delta    sigma   weight residual
     112.73  107.02    5.71 1.20e+00 6.94e-01 2.27e+01
  angle pdb=" CB  MET A 445 "
        pdb=" CG  MET A 445 "
        pdb=" SD  MET A 445 "
      ideal   model   delta    sigma   weight residual
     112.70  126.04  -13.34 3.00e+00 1.11e-01 1.98e+01
  angle pdb=" CB  MET B 445 "
        pdb=" CG  MET B 445 "
        pdb=" SD  MET B 445 "
      ideal   model   delta    sigma   weight residual
     112.70  126.03  -13.33 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" CG  ARG A 236 "
        pdb=" CD  ARG A 236 "
        pdb=" NE  ARG A 236 "
      ideal   model   delta    sigma   weight residual
     112.00  121.07   -9.07 2.20e+00 2.07e-01 1.70e+01
  ... (remaining 10649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.76: 4038
       15.76 -    31.51: 404
       31.51 -    47.27: 92
       47.27 -    63.02: 10
       63.02 -    78.78: 4
  Dihedral angle restraints: 4548
    sinusoidal: 1720
      harmonic: 2828
  Sorted by residual:
  dihedral pdb=" CB  CYS B  78 "
           pdb=" SG  CYS B  78 "
           pdb=" SG  CYS B 136 "
           pdb=" CB  CYS B 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.24  -45.76     1      1.00e+01 1.00e-02 2.90e+01
  dihedral pdb=" CB  CYS A  78 "
           pdb=" SG  CYS A  78 "
           pdb=" SG  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.24  -45.76     1      1.00e+01 1.00e-02 2.90e+01
  dihedral pdb=" CA  LEU B 476 "
           pdb=" C   LEU B 476 "
           pdb=" N   THR B 477 "
           pdb=" CA  THR B 477 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.98  -21.02     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 4545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 866
       0.058 -    0.116: 297
       0.116 -    0.175: 84
       0.175 -    0.233: 11
       0.233 -    0.291: 4
  Chirality restraints: 1262
  Sorted by residual:
  chirality pdb=" CB  ILE B 312 "
            pdb=" CA  ILE B 312 "
            pdb=" CG1 ILE B 312 "
            pdb=" CG2 ILE B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.94   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  ILE A 312 "
            pdb=" CA  ILE A 312 "
            pdb=" CG1 ILE A 312 "
            pdb=" CG2 ILE A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CA  PRO A 183 "
            pdb=" N   PRO A 183 "
            pdb=" C   PRO A 183 "
            pdb=" CB  PRO A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1259 not shown)

  Planarity restraints: 1328
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 553 "    0.054 5.00e-02 4.00e+02   8.04e-02 1.03e+01
        pdb=" N   PRO A 554 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 554 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 554 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 553 "   -0.053 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO B 554 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 554 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 554 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 182 "    0.051 5.00e-02 4.00e+02   7.65e-02 9.38e+00
        pdb=" N   PRO B 183 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 183 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 183 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1325 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1542
        2.76 -     3.30: 7947
        3.30 -     3.83: 13628
        3.83 -     4.37: 15585
        4.37 -     4.90: 26138
  Nonbonded interactions: 64840
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 167 "
            pdb=" OG  SER B 171 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ILE A 167 "
            pdb=" OG  SER A 171 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE2 GLU A 341 "
            pdb=" OG1 THR A 387 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OE2 GLU B 341 "
            pdb=" OG1 THR B 387 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   THR B 501 "
            pdb=" OG1 THR B 505 "
     model   vdw
     2.245 3.040
  ... (remaining 64835 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.480
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.000
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
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      :  0.009   0.110   7806  Z= 0.398
  Angle     :  1.177  13.340  10658  Z= 0.618
  Chirality :  0.064   0.291   1262
  Planarity :  0.009   0.080   1328
  Dihedral  : 13.286  78.778   2738
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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 aren not related in a simple way.
  whole: -1.66 (0.26), residues: 990
  helix: -1.11 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop : -0.68 (0.38), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B 236 
 TYR   0.017   0.002   TYR B 291 
 PHE   0.051   0.004   PHE A  94 
 TRP   0.043   0.003   TRP A  48 
 HIS   0.007   0.002   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00938 ( 7804)
  covalent geometry    : angle       1.17643 (10654)
  SS BOND              : bond        0.00444 (    2)
  SS BOND              : angle       2.22977 (    4)
  hydrogen bonds       : bond        0.14819 (  486)
  hydrogen bonds       : angle       7.22136 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 MET cc_start: 0.6878 (tpp) cc_final: 0.5758 (mtt)
REVERT: A  497 ASP cc_start: 0.7620 (t0) cc_final: 0.7391 (t0)
REVERT: B  445 MET cc_start: 0.6890 (tpp) cc_final: 0.5755 (mtt)
REVERT: B  497 ASP cc_start: 0.7629 (t0) cc_final: 0.7392 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0830
  time to fit residues: 12.8123
Evaluate side-chains
  88 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.0070
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN
B 384 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.214533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.190686 restraints weight = 8004.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.194505 restraints weight = 4921.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.197126 restraints weight = 3539.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.198942 restraints weight = 2817.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.199984 restraints weight = 2410.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7806  Z= 0.169
  Angle     :  0.660   6.862  10658  Z= 0.339
  Chirality :  0.044   0.165   1262
  Planarity :  0.006   0.057   1328
  Dihedral  :  5.251  21.189   1062
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.36 %
    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 aren not related in a simple way.
  whole: -0.27 (0.27), residues: 990
  helix:  0.00 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.26 (0.42), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  81 
 TYR   0.010   0.001   TYR B 291 
 PHE   0.020   0.002   PHE B 427 
 TRP   0.020   0.002   TRP B  48 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7804)
  covalent geometry    : angle       0.65999 (10654)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       0.99941 (    4)
  hydrogen bonds       : bond        0.05583 (  486)
  hydrogen bonds       : angle       5.18918 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   66 THR cc_start: 0.8291 (t) cc_final: 0.8085 (m)
REVERT: A  445 MET cc_start: 0.7249 (tpp) cc_final: 0.6118 (mtt)
REVERT: A  497 ASP cc_start: 0.7623 (t0) cc_final: 0.7324 (t0)
REVERT: B   66 THR cc_start: 0.8291 (t) cc_final: 0.8085 (m)
REVERT: B  445 MET cc_start: 0.7255 (tpp) cc_final: 0.6102 (mtt)
REVERT: B  497 ASP cc_start: 0.7667 (t0) cc_final: 0.7362 (t0)
  outliers start: 10
  outliers final: 10
  residues processed: 106
  average time/residue: 0.0749
  time to fit residues: 11.1298
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0270
   chunk 54 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.223108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.199770 restraints weight = 7962.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.203144 restraints weight = 5342.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.205312 restraints weight = 4057.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.207027 restraints weight = 3350.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.207662 restraints weight = 2939.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7806  Z= 0.164
  Angle     :  0.625   6.783  10658  Z= 0.320
  Chirality :  0.044   0.169   1262
  Planarity :  0.005   0.051   1328
  Dihedral  :  4.821  19.316   1062
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.46 %
    Favored  : 84.10 %
  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 aren not related in a simple way.
  whole:  0.30 (0.28), residues: 990
  helix:  0.42 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.00 (0.43), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 529 
 TYR   0.015   0.002   TYR B  49 
 PHE   0.017   0.002   PHE B 427 
 TRP   0.017   0.001   TRP B  48 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 7804)
  covalent geometry    : angle       0.62462 (10654)
  SS BOND              : bond        0.00366 (    2)
  SS BOND              : angle       0.80906 (    4)
  hydrogen bonds       : bond        0.05156 (  486)
  hydrogen bonds       : angle       4.86938 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  445 MET cc_start: 0.7239 (tpp) cc_final: 0.6257 (mtt)
REVERT: A  497 ASP cc_start: 0.7807 (t0) cc_final: 0.7488 (t0)
REVERT: B  445 MET cc_start: 0.7246 (tpp) cc_final: 0.6245 (mtt)
REVERT: B  497 ASP cc_start: 0.7827 (t0) cc_final: 0.7495 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0700
  time to fit residues: 10.4628
Evaluate side-chains
  98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  532 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 71 optimal weight:    0.4980
   chunk 77 optimal weight:    0.6980
   chunk 98 optimal weight:    0.4980
   chunk 82 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.223100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.198568 restraints weight = 7996.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.202732 restraints weight = 5484.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.205026 restraints weight = 4208.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.205924 restraints weight = 3470.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.207396 restraints weight = 3139.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7806  Z= 0.164
  Angle     :  0.606   6.669  10658  Z= 0.311
  Chirality :  0.044   0.164   1262
  Planarity :  0.005   0.049   1328
  Dihedral  :  4.653  17.886   1062
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.86 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.29), residues: 990
  helix:  0.57 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.01 (0.43), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 529 
 TYR   0.023   0.002   TYR A 346 
 PHE   0.013   0.002   PHE B 427 
 TRP   0.014   0.001   TRP B  48 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7804)
  covalent geometry    : angle       0.60565 (10654)
  SS BOND              : bond        0.00312 (    2)
  SS BOND              : angle       0.73642 (    4)
  hydrogen bonds       : bond        0.05007 (  486)
  hydrogen bonds       : angle       4.75703 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  445 MET cc_start: 0.7212 (tpp) cc_final: 0.6341 (mtt)
REVERT: A  497 ASP cc_start: 0.7796 (t0) cc_final: 0.7498 (t0)
REVERT: B  445 MET cc_start: 0.7217 (tpp) cc_final: 0.6334 (mtt)
REVERT: B  497 ASP cc_start: 0.7811 (t0) cc_final: 0.7502 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 108
  average time/residue: 0.0777
  time to fit residues: 11.8572
Evaluate side-chains
  100 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0030
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.220320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.196983 restraints weight = 7878.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.199793 restraints weight = 5285.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.201907 restraints weight = 4112.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.203381 restraints weight = 3502.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.204070 restraints weight = 3100.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7806  Z= 0.170
  Angle     :  0.604   6.788  10658  Z= 0.309
  Chirality :  0.044   0.169   1262
  Planarity :  0.005   0.047   1328
  Dihedral  :  4.536  18.061   1062
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.39 %
    Favored  : 80.96 %
  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 aren not related in a simple way.
  whole:  0.53 (0.29), residues: 990
  helix:  0.68 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.17 (0.42), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  81 
 TYR   0.015   0.002   TYR A 346 
 PHE   0.015   0.002   PHE B 456 
 TRP   0.013   0.001   TRP B  48 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 7804)
  covalent geometry    : angle       0.60390 (10654)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       0.90038 (    4)
  hydrogen bonds       : bond        0.04968 (  486)
  hydrogen bonds       : angle       4.71106 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7823 (t) cc_final: 0.7182 (p)
REVERT: A  445 MET cc_start: 0.7202 (tpp) cc_final: 0.6407 (mtt)
REVERT: A  497 ASP cc_start: 0.7825 (t0) cc_final: 0.7520 (t0)
REVERT: B  205 SER cc_start: 0.7833 (t) cc_final: 0.7201 (p)
REVERT: B  445 MET cc_start: 0.7203 (tpp) cc_final: 0.6408 (mtt)
REVERT: B  497 ASP cc_start: 0.7839 (t0) cc_final: 0.7526 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0741
  time to fit residues: 11.0382
Evaluate side-chains
  106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0040
   chunk 40 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 ASN
B  58 HIS
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 384 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.221397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.198134 restraints weight = 7987.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.200756 restraints weight = 5241.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.203092 restraints weight = 4095.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.204363 restraints weight = 3470.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.204963 restraints weight = 3107.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7806  Z= 0.160
  Angle     :  0.591   6.954  10658  Z= 0.300
  Chirality :  0.044   0.166   1262
  Planarity :  0.005   0.046   1328
  Dihedral  :  4.417  18.098   1062
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.90 %
    Favored  : 81.20 %
  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 aren not related in a simple way.
  whole:  0.60 (0.28), residues: 990
  helix:  0.73 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.14 (0.42), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.015   0.001   TYR A 346 
 PHE   0.013   0.002   PHE B 456 
 TRP   0.010   0.001   TRP B  48 
 HIS   0.002   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 7804)
  covalent geometry    : angle       0.59071 (10654)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       0.69492 (    4)
  hydrogen bonds       : bond        0.04888 (  486)
  hydrogen bonds       : angle       4.63029 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7765 (t) cc_final: 0.7168 (p)
REVERT: A  445 MET cc_start: 0.7129 (tpp) cc_final: 0.6393 (mtt)
REVERT: A  497 ASP cc_start: 0.7822 (t0) cc_final: 0.7535 (t0)
REVERT: B  205 SER cc_start: 0.7775 (t) cc_final: 0.7186 (p)
REVERT: B  445 MET cc_start: 0.7137 (tpp) cc_final: 0.6394 (mtt)
REVERT: B  497 ASP cc_start: 0.7829 (t0) cc_final: 0.7533 (t0)
  outliers start: 24
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0797
  time to fit residues: 12.7634
Evaluate side-chains
  114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 ASN
A 480 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 384 ASN
B 480 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.218888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.194439 restraints weight = 7988.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.197884 restraints weight = 5477.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.199897 restraints weight = 4262.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.201632 restraints weight = 3595.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.202435 restraints weight = 3195.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7806  Z= 0.180
  Angle     :  0.637  12.204  10658  Z= 0.316
  Chirality :  0.044   0.169   1262
  Planarity :  0.005   0.046   1328
  Dihedral  :  4.451  18.264   1062
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.39 %
    Favored  : 80.48 %
  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 aren not related in a simple way.
  whole:  0.53 (0.28), residues: 990
  helix:  0.67 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.16 (0.42), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.013   0.001   TYR A 346 
 PHE   0.013   0.002   PHE A 456 
 TRP   0.011   0.001   TRP B  48 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7804)
  covalent geometry    : angle       0.63680 (10654)
  SS BOND              : bond        0.00392 (    2)
  SS BOND              : angle       0.97445 (    4)
  hydrogen bonds       : bond        0.05014 (  486)
  hydrogen bonds       : angle       4.69034 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7843 (t) cc_final: 0.7276 (p)
REVERT: A  445 MET cc_start: 0.7191 (tpp) cc_final: 0.6455 (mtt)
REVERT: A  497 ASP cc_start: 0.7827 (t0) cc_final: 0.7564 (t0)
REVERT: A  503 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7354 (mt)
REVERT: B  205 SER cc_start: 0.7849 (t) cc_final: 0.7291 (p)
REVERT: B  445 MET cc_start: 0.7174 (tpp) cc_final: 0.6487 (mtt)
REVERT: B  459 MET cc_start: 0.7725 (mtp) cc_final: 0.7523 (mtp)
REVERT: B  497 ASP cc_start: 0.7840 (t0) cc_final: 0.7567 (t0)
REVERT: B  503 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7361 (mt)
  outliers start: 26
  outliers final: 20
  residues processed: 118
  average time/residue: 0.0760
  time to fit residues: 12.9889
Evaluate side-chains
  116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.220434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.196132 restraints weight = 7902.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.199683 restraints weight = 5377.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.201799 restraints weight = 4140.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.203518 restraints weight = 3464.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.204444 restraints weight = 3063.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7806  Z= 0.160
  Angle     :  0.602   7.614  10658  Z= 0.302
  Chirality :  0.044   0.177   1262
  Planarity :  0.005   0.045   1328
  Dihedral  :  4.392  18.244   1062
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.87 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.29), residues: 990
  helix:  0.69 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.01 (0.44), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  81 
 TYR   0.013   0.001   TYR B 346 
 PHE   0.012   0.001   PHE B 456 
 TRP   0.010   0.001   TRP B  48 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7804)
  covalent geometry    : angle       0.60206 (10654)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       0.69963 (    4)
  hydrogen bonds       : bond        0.04867 (  486)
  hydrogen bonds       : angle       4.61072 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7807 (t) cc_final: 0.7250 (p)
REVERT: A  445 MET cc_start: 0.7164 (tpp) cc_final: 0.6442 (mtt)
REVERT: A  497 ASP cc_start: 0.7820 (t0) cc_final: 0.7561 (t0)
REVERT: A  503 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7349 (mt)
REVERT: B  205 SER cc_start: 0.7809 (t) cc_final: 0.7271 (p)
REVERT: B  445 MET cc_start: 0.7164 (tpp) cc_final: 0.6428 (mtt)
REVERT: B  459 MET cc_start: 0.7679 (mtp) cc_final: 0.7477 (mtp)
REVERT: B  497 ASP cc_start: 0.7824 (t0) cc_final: 0.7563 (t0)
REVERT: B  503 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7357 (mt)
  outliers start: 24
  outliers final: 22
  residues processed: 112
  average time/residue: 0.0546
  time to fit residues: 9.0369
Evaluate side-chains
  116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0050
   chunk 12 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.3372

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

Flipped N/Q/H residues before XYZ refinement:
A 485 ASN
B 485 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.224158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.200028 restraints weight = 7904.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.203580 restraints weight = 5375.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.205898 restraints weight = 4144.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.207305 restraints weight = 3465.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.208371 restraints weight = 3061.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7806  Z= 0.139
  Angle     :  0.585   7.779  10658  Z= 0.293
  Chirality :  0.043   0.181   1262
  Planarity :  0.005   0.045   1328
  Dihedral  :  4.305  18.143   1062
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.71 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.29), residues: 990
  helix:  0.85 (0.21), residues: 694
  sheet:  None (None), residues: 0
  loop :  0.08 (0.44), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.014   0.001   TYR A 346 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.009   0.001   TRP B  48 
 HIS   0.002   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7804)
  covalent geometry    : angle       0.58512 (10654)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.50000 (    4)
  hydrogen bonds       : bond        0.04654 (  486)
  hydrogen bonds       : angle       4.50656 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  193 LEU cc_start: 0.7593 (mt) cc_final: 0.7335 (mt)
REVERT: A  205 SER cc_start: 0.7641 (t) cc_final: 0.7093 (p)
REVERT: A  445 MET cc_start: 0.7088 (tpp) cc_final: 0.6429 (mtt)
REVERT: A  497 ASP cc_start: 0.7804 (t0) cc_final: 0.7496 (t0)
REVERT: A  503 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7333 (mt)
REVERT: B  193 LEU cc_start: 0.7556 (mt) cc_final: 0.7294 (mt)
REVERT: B  205 SER cc_start: 0.7649 (t) cc_final: 0.7124 (p)
REVERT: B  445 MET cc_start: 0.7094 (tpp) cc_final: 0.6377 (mtt)
REVERT: B  459 MET cc_start: 0.7583 (mtp) cc_final: 0.7371 (mtp)
REVERT: B  497 ASP cc_start: 0.7815 (t0) cc_final: 0.7497 (t0)
REVERT: B  503 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7345 (mt)
  outliers start: 24
  outliers final: 22
  residues processed: 112
  average time/residue: 0.0585
  time to fit residues: 9.7956
Evaluate side-chains
  116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.220302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.195932 restraints weight = 7872.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.199362 restraints weight = 5429.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.201538 restraints weight = 4222.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.202821 restraints weight = 3561.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.204107 restraints weight = 3174.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7806  Z= 0.175
  Angle     :  0.616   8.181  10658  Z= 0.308
  Chirality :  0.044   0.184   1262
  Planarity :  0.005   0.046   1328
  Dihedral  :  4.361  17.952   1062
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.71 %
    Favored  : 78.80 %
  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 aren not related in a simple way.
  whole:  0.71 (0.29), residues: 990
  helix:  0.76 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop :  0.07 (0.43), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.012   0.001   TYR B 346 
 PHE   0.012   0.002   PHE A 466 
 TRP   0.010   0.001   TRP B  48 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7804)
  covalent geometry    : angle       0.61617 (10654)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       0.76851 (    4)
  hydrogen bonds       : bond        0.04888 (  486)
  hydrogen bonds       : angle       4.61044 ( 1434)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7770 (t) cc_final: 0.7221 (p)
REVERT: A  445 MET cc_start: 0.7149 (tpp) cc_final: 0.6435 (mtt)
REVERT: A  497 ASP cc_start: 0.7831 (t0) cc_final: 0.7523 (t0)
REVERT: A  503 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7351 (mt)
REVERT: B  205 SER cc_start: 0.7781 (t) cc_final: 0.7251 (p)
REVERT: B  445 MET cc_start: 0.7139 (tpp) cc_final: 0.6402 (mtt)
REVERT: B  459 MET cc_start: 0.7684 (mtp) cc_final: 0.7481 (mtp)
REVERT: B  497 ASP cc_start: 0.7837 (t0) cc_final: 0.7526 (t0)
REVERT: B  503 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7367 (mt)
  outliers start: 29
  outliers final: 25
  residues processed: 112
  average time/residue: 0.0606
  time to fit residues: 10.3088
Evaluate side-chains
  117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0670
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.176974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.148772 restraints weight = 7885.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153067 restraints weight = 4506.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.155958 restraints weight = 3115.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158078 restraints weight = 2431.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159409 restraints weight = 2033.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7806  Z= 0.160
  Angle     :  0.606   8.102  10658  Z= 0.303
  Chirality :  0.044   0.188   1262
  Planarity :  0.005   0.045   1328
  Dihedral  :  4.345  18.037   1062
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.47 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.29), residues: 990
  helix:  0.77 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.01 (0.43), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.013   0.001   TYR B 346 
 PHE   0.021   0.002   PHE A 466 
 TRP   0.011   0.001   TRP A 318 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7804)
  covalent geometry    : angle       0.60576 (10654)
  SS BOND              : bond        0.00318 (    2)
  SS BOND              : angle       0.73481 (    4)
  hydrogen bonds       : bond        0.04828 (  486)
  hydrogen bonds       : angle       4.59238 ( 1434)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1286.59 seconds
wall clock time: 23 minutes 1.09 seconds (1381.09 seconds total)