Starting phenix.real_space_refine
on Wed Mar 12 08:38:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yty_34095/03_2025/7yty_34095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yty_34095/03_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_34095/03_2025/7yty_34095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yty_34095/03_2025/7yty_34095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yty_34095/03_2025/7yty_34095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yty_34095/03_2025/7yty_34095.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.38, per 1000 atoms: 0.97
  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: 1.75
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.66
  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: 2.12

  Time building geometry restraints manager: 2.11 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: 0.04
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:             3.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.020
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.950
-------------------------------------------------------------------------------
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   7804  Z= 0.621
  Angle     :  1.176  13.340  10654  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (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
 TRP   0.043   0.003   TRP A  48 
 HIS   0.007   0.002   HIS A  58 
 PHE   0.051   0.004   PHE A  94 
 TYR   0.017   0.002   TYR B 291 
 ARG   0.019   0.001   ARG B 236 

*********************** 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  : 0.841 
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: 0.2112
  time to fit residues: 32.7530
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  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.0770
   chunk 75 optimal weight:    0.4980
   chunk 42 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.3736

-------------------------------------------------------------------------------
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 = 0.4403 r_free = 0.4403 target = 0.219066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.194404 restraints weight = 7978.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.198457 restraints weight = 4981.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.200828 restraints weight = 3601.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7804  Z= 0.226
  Angle     :  0.646   6.763  10654  Z= 0.333
  Chirality :  0.044   0.162   1262
  Planarity :  0.006   0.058   1328
  Dihedral  :  5.243  21.046   1062
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.84 %
    Favored  : 88.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.28), residues: 990
  helix:  0.06 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.18 (0.42), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  48 
 HIS   0.003   0.001   HIS B  58 
 PHE   0.021   0.002   PHE B 427 
 TYR   0.010   0.001   TYR B 291 
 ARG   0.004   0.001   ARG A  81 

*********************** 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
  110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A  445 MET cc_start: 0.7225 (tpp) cc_final: 0.6107 (mtt)
REVERT: A  497 ASP cc_start: 0.7646 (t0) cc_final: 0.7362 (t0)
REVERT: B  445 MET cc_start: 0.7233 (tpp) cc_final: 0.6101 (mtt)
REVERT: B  497 ASP cc_start: 0.7652 (t0) cc_final: 0.7376 (t0)
  outliers start: 8
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1868
  time to fit residues: 26.9722
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  : 0.746 
-------------------------------------------------------------------------------
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  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  493 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0050
   chunk 41 optimal weight:    0.1980
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0170
   chunk 11 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.3432

-------------------------------------------------------------------------------
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 = 0.4481 r_free = 0.4481 target = 0.227252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.204352 restraints weight = 8011.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.207936 restraints weight = 5303.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.209976 restraints weight = 3993.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7804  Z= 0.213
  Angle     :  0.608   6.613  10654  Z= 0.312
  Chirality :  0.043   0.165   1262
  Planarity :  0.005   0.051   1328
  Dihedral  :  4.737  19.513   1062
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.28), residues: 990
  helix:  0.56 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop :  0.02 (0.43), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  48 
 HIS   0.002   0.001   HIS B  58 
 PHE   0.017   0.002   PHE B 427 
 TYR   0.015   0.001   TYR B  49 
 ARG   0.004   0.000   ARG B 529 

*********************** 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
  98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  445 MET cc_start: 0.7181 (tpp) cc_final: 0.6182 (mtt)
REVERT: A  497 ASP cc_start: 0.7807 (t0) cc_final: 0.7493 (t0)
REVERT: B  445 MET cc_start: 0.7190 (tpp) cc_final: 0.6175 (mtt)
REVERT: B  497 ASP cc_start: 0.7818 (t0) cc_final: 0.7498 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1544
  time to fit residues: 21.4315
Evaluate side-chains
  94 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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 B residue  407 VAL
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  493 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0060
   chunk 5 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0770
   chunk 47 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.3754

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.228796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.205852 restraints weight = 7886.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.209279 restraints weight = 5407.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.211184 restraints weight = 4180.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7804  Z= 0.216
  Angle     :  0.582   6.536  10654  Z= 0.299
  Chirality :  0.043   0.162   1262
  Planarity :  0.005   0.050   1328
  Dihedral  :  4.536  17.544   1062
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.30 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.28), residues: 990
  helix:  0.71 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop :  0.04 (0.43), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  48 
 HIS   0.002   0.001   HIS B  58 
 PHE   0.013   0.001   PHE B 427 
 TYR   0.024   0.002   TYR A 346 
 ARG   0.002   0.000   ARG B 404 

*********************** 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
  99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A  445 MET cc_start: 0.7137 (tpp) cc_final: 0.6273 (mtt)
REVERT: A  497 ASP cc_start: 0.7781 (t0) cc_final: 0.7478 (t0)
REVERT: B  445 MET cc_start: 0.7145 (tpp) cc_final: 0.6268 (mtt)
REVERT: B  497 ASP cc_start: 0.7811 (t0) cc_final: 0.7495 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1350
  time to fit residues: 19.8164
Evaluate side-chains
  94 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  417 LEU
Chi-restraints excluded: chain A residue  493 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  417 LEU
Chi-restraints excluded: chain B residue  493 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 18 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 84 optimal weight:    0.2980
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 480 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 480 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.222245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.199333 restraints weight = 7844.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.201531 restraints weight = 5327.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.204309 restraints weight = 4178.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7804  Z= 0.285
  Angle     :  0.635  10.273  10654  Z= 0.321
  Chirality :  0.044   0.168   1262
  Planarity :  0.005   0.047   1328
  Dihedral  :  4.527  17.767   1062
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.75 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 990
  helix:  0.65 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.15 (0.42), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.015   0.002   PHE A 456 
 TYR   0.031   0.002   TYR A 346 
 ARG   0.003   0.000   ARG B 529 

*********************** 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
  117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  445 MET cc_start: 0.7235 (tpp) cc_final: 0.6392 (mtt)
REVERT: A  497 ASP cc_start: 0.7835 (t0) cc_final: 0.7545 (t0)
REVERT: B  445 MET cc_start: 0.7237 (tpp) cc_final: 0.6401 (mtt)
REVERT: B  497 ASP cc_start: 0.7859 (t0) cc_final: 0.7550 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1634
  time to fit residues: 26.0158
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  417 LEU
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  335 THR
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
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 42 optimal weight:    0.0980
   chunk 94 optimal weight:    0.4980
   chunk 21 optimal weight:    0.0570
   chunk 56 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
A 384 ASN
B 294 GLN
B 384 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.226260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.202376 restraints weight = 7856.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.205910 restraints weight = 5318.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.208169 restraints weight = 4079.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7804  Z= 0.213
  Angle     :  0.584   8.015  10654  Z= 0.295
  Chirality :  0.043   0.164   1262
  Planarity :  0.005   0.045   1328
  Dihedral  :  4.377  18.114   1062
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.23 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.28), residues: 990
  helix:  0.78 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.01 (0.42), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  48 
 HIS   0.002   0.001   HIS B  58 
 PHE   0.012   0.001   PHE B 466 
 TYR   0.025   0.002   TYR A 346 
 ARG   0.004   0.000   ARG A  81 

*********************** 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
  112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7566 (t) cc_final: 0.6935 (p)
REVERT: A  445 MET cc_start: 0.7067 (tpp) cc_final: 0.6338 (mtt)
REVERT: A  497 ASP cc_start: 0.7798 (t0) cc_final: 0.7520 (t0)
REVERT: B  205 SER cc_start: 0.7588 (t) cc_final: 0.6951 (p)
REVERT: B  445 MET cc_start: 0.7067 (tpp) cc_final: 0.6330 (mtt)
REVERT: B  497 ASP cc_start: 0.7813 (t0) cc_final: 0.7528 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1720
  time to fit residues: 26.5949
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
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  493 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   89 LEU
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  493 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 75 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0870
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 384 ASN
B 384 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.220431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.194620 restraints weight = 7844.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.198475 restraints weight = 5205.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.200983 restraints weight = 3945.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7804  Z= 0.292
  Angle     :  0.625   7.390  10654  Z= 0.315
  Chirality :  0.044   0.168   1262
  Planarity :  0.005   0.047   1328
  Dihedral  :  4.424  17.951   1062
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.47 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.28), residues: 990
  helix:  0.64 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -0.13 (0.42), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.015   0.002   PHE A 456 
 TYR   0.024   0.002   TYR A 346 
 ARG   0.004   0.000   ARG B  81 

*********************** 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
  113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7768 (t) cc_final: 0.7200 (p)
REVERT: A  445 MET cc_start: 0.7163 (tpp) cc_final: 0.6472 (mtt)
REVERT: A  497 ASP cc_start: 0.7846 (t0) cc_final: 0.7591 (t0)
REVERT: B  205 SER cc_start: 0.7772 (t) cc_final: 0.7222 (p)
REVERT: B  445 MET cc_start: 0.7164 (tpp) cc_final: 0.6472 (mtt)
REVERT: B  497 ASP cc_start: 0.7857 (t0) cc_final: 0.7591 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1741
  time to fit residues: 26.4637
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  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0980
   chunk 54 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   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
B  58 HIS
B 294 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.222242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.197677 restraints weight = 7957.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.201144 restraints weight = 5472.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.203082 restraints weight = 4251.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7804  Z= 0.285
  Angle     :  0.616   7.828  10654  Z= 0.311
  Chirality :  0.044   0.171   1262
  Planarity :  0.005   0.045   1328
  Dihedral  :  4.426  18.139   1062
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.35 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.28), residues: 990
  helix:  0.60 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.05 (0.43), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 318 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.014   0.002   PHE A 456 
 TYR   0.021   0.002   TYR A 346 
 ARG   0.004   0.000   ARG A  81 

*********************** 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
  112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7781 (t) cc_final: 0.7227 (p)
REVERT: A  445 MET cc_start: 0.7160 (tpp) cc_final: 0.6427 (mtt)
REVERT: A  497 ASP cc_start: 0.7844 (t0) cc_final: 0.7606 (t0)
REVERT: B  205 SER cc_start: 0.7790 (t) cc_final: 0.7249 (p)
REVERT: B  445 MET cc_start: 0.7160 (tpp) cc_final: 0.6423 (mtt)
REVERT: B  497 ASP cc_start: 0.7855 (t0) cc_final: 0.7611 (t0)
  outliers start: 22
  outliers final: 20
  residues processed: 106
  average time/residue: 0.1674
  time to fit residues: 25.2684
Evaluate side-chains
  110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.218948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.195278 restraints weight = 7932.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.198840 restraints weight = 5257.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.200762 restraints weight = 3981.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7804  Z= 0.256
  Angle     :  0.604   8.009  10654  Z= 0.304
  Chirality :  0.044   0.178   1262
  Planarity :  0.005   0.046   1328
  Dihedral  :  4.384  18.253   1062
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.11 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.28), residues: 990
  helix:  0.68 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.00 (0.42), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.020   0.002   PHE B 466 
 TYR   0.021   0.002   TYR A 346 
 ARG   0.004   0.000   ARG B  81 

*********************** 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
  119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7751 (t) cc_final: 0.7190 (p)
REVERT: A  445 MET cc_start: 0.7186 (tpp) cc_final: 0.6429 (mtt)
REVERT: A  497 ASP cc_start: 0.7824 (t0) cc_final: 0.7520 (t0)
REVERT: A  503 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7367 (mt)
REVERT: B  205 SER cc_start: 0.7748 (t) cc_final: 0.7197 (p)
REVERT: B  445 MET cc_start: 0.7190 (tpp) cc_final: 0.6424 (mtt)
REVERT: B  497 ASP cc_start: 0.7828 (t0) cc_final: 0.7515 (t0)
REVERT: B  503 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7375 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 113
  average time/residue: 0.1696
  time to fit residues: 27.3668
Evaluate side-chains
  116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 49 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
A 485 ASN
B 294 GLN
B 485 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.221416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.195688 restraints weight = 7969.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.199612 restraints weight = 5270.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.202127 restraints weight = 3972.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7804  Z= 0.290
  Angle     :  0.621   8.293  10654  Z= 0.313
  Chirality :  0.045   0.177   1262
  Planarity :  0.005   0.046   1328
  Dihedral  :  4.415  18.051   1062
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.23 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 990
  helix:  0.63 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.05 (0.43), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  48 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.014   0.002   PHE B 456 
 TYR   0.020   0.002   TYR B 346 
 ARG   0.004   0.000   ARG A  81 

********************** 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
  119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  205 SER cc_start: 0.7791 (t) cc_final: 0.7252 (p)
REVERT: A  445 MET cc_start: 0.7167 (tpp) cc_final: 0.6454 (mtt)
REVERT: A  497 ASP cc_start: 0.7842 (t0) cc_final: 0.7574 (t0)
REVERT: A  503 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7410 (mt)
REVERT: B  205 SER cc_start: 0.7794 (t) cc_final: 0.7262 (p)
REVERT: B  445 MET cc_start: 0.7172 (tpp) cc_final: 0.6443 (mtt)
REVERT: B  459 MET cc_start: 0.7785 (mtp) cc_final: 0.7582 (mtp)
REVERT: B  497 ASP cc_start: 0.7850 (t0) cc_final: 0.7569 (t0)
REVERT: B  503 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7428 (mt)
  outliers start: 26
  outliers final: 23
  residues processed: 111
  average time/residue: 0.1680
  time to fit residues: 26.6259
Evaluate side-chains
  118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
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  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  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 89 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0970
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** B 115 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 = 0.4427 r_free = 0.4427 target = 0.219225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.195654 restraints weight = 7845.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.199205 restraints weight = 5230.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.201347 restraints weight = 3985.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7804  Z= 0.257
  Angle     :  0.607   8.117  10654  Z= 0.306
  Chirality :  0.044   0.185   1262
  Planarity :  0.005   0.045   1328
  Dihedral  :  4.366  18.141   1062
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.71 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 990
  helix:  0.74 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop :  0.10 (0.43), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 318 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.014   0.002   PHE B 456 
 TYR   0.020   0.001   TYR A 346 
 ARG   0.004   0.000   ARG A  81 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2450.10 seconds
wall clock time: 43 minutes 16.50 seconds (2596.50 seconds total)