Starting phenix.real_space_refine
on Wed Feb 12 04:25:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8efd_28080/02_2025/8efd_28080.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8efd_28080/02_2025/8efd_28080.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8efd_28080/02_2025/8efd_28080.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8efd_28080/02_2025/8efd_28080.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8efd_28080/02_2025/8efd_28080.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8efd_28080/02_2025/8efd_28080.cif"
  }
  resolution = 3.8
  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=   0.001
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      40      5.16       5
     C    4524      2.51       5
     N    1210      2.21       5
     O    1333      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7107
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 5967
          Classifications: {'peptide': 740}
          Link IDs: {'PTRANS': 28, 'TRANS': 711}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1140
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 142}
  Time building chain proxies: 5.72, per 1000 atoms: 0.80
  Number of scatterers: 7107
  At special positions: 0
  Unit cell: (86.24, 127.204, 117.502, 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      40     16.00
     O    1333      8.00
     N    1210      7.00
     C    4524      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1658

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      57.2% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 11
      removed outlier: 6.202A  pdb=" N   ALA A  11 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 17
      removed outlier: 3.524A  pdb=" N   LEU A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.759A  pdb=" N   THR A  28 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 97 through 111
      removed outlier: 3.675A  pdb=" N   LEU A 102 " --> pdb=" O   GLU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 134
      removed outlier: 4.436A  pdb=" N   TYR A 134 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 131 through 134'
    Processing helix  chain 'A' and resid 135 through 143
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 183 through 197
    Processing helix  chain 'A' and resid 217 through 231
      Proline residue:  A 225  - end of helix
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 283 through 290
      removed outlier: 4.434A  pdb=" N   TYR A 287 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
    Processing helix  chain 'A' and resid 306 through 309
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 324 through 338
    Processing helix  chain 'A' and resid 343 through 359
      removed outlier: 3.577A  pdb=" N   ASN A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
    Processing helix  chain 'A' and resid 391 through 401
    Processing helix  chain 'A' and resid 416 through 448
    Processing helix  chain 'A' and resid 472 through 504
    Processing helix  chain 'A' and resid 513 through 526
      removed outlier: 3.709A  pdb=" N   LEU A 517 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA A 519 " --> pdb=" O   MET A 515 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   CYS A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 540
      removed outlier: 3.551A  pdb=" N   CYS A 538 " --> pdb=" O   LEU A 534 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   MET A 539 " --> pdb=" O   GLU A 535 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE A 540 " --> pdb=" O   GLU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 557
    Processing helix  chain 'A' and resid 592 through 598
      removed outlier: 3.971A  pdb=" N   LYS A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 611
    Processing helix  chain 'A' and resid 615 through 620
    Processing helix  chain 'A' and resid 647 through 664
      removed outlier: 3.913A  pdb=" N   SER A 664 " --> pdb=" O   THR A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 696
    Processing helix  chain 'A' and resid 697 through 707
    Processing helix  chain 'A' and resid 715 through 723
      removed outlier: 3.506A  pdb=" N   ARG A 723 " --> pdb=" O   ARG A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 749
    Processing helix  chain 'A' and resid 752 through 754
      No H-bonds generated for 'chain 'A' and resid 752 through 754'
    Processing helix  chain 'A' and resid 766 through 796
      removed outlier: 3.915A  pdb=" N   LEU A 770 " --> pdb=" O   LYS A 766 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 57
    Processing helix  chain 'B' and resid 65 through 75
      removed outlier: 3.962A  pdb=" N   VAL B  69 " --> pdb=" O   THR B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 103 through 116
      Proline residue:  B 109  - end of helix
      removed outlier: 3.655A  pdb=" N   ASN B 116 " --> pdb=" O   GLN B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 132
      removed outlier: 3.547A  pdb=" N   VAL B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 153
    Processing helix  chain 'B' and resid 158 through 166
    Processing helix  chain 'B' and resid 178 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118
      removed outlier: 4.053A  pdb=" N   PHE A 121 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 266
      removed outlier: 6.691A  pdb=" N   LYS A 246 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   LEU A 460 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE A 248 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   GLY A 458 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE A 250 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   PHE A 456 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLN A 172 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 406
    Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 581
      removed outlier: 3.726A  pdb=" N   PHE A 577 " --> pdb=" O   TYR A 588 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 714
    Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 142
      removed outlier: 3.630A  pdb=" N   VAL B 141 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1032 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: 2.28

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2344
        1.34 -     1.46: 1365
        1.46 -     1.58: 3466
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 7245
  Sorted by residual:
  bond pdb=" CG  GLU A 775 "
       pdb=" CD  GLU A 775 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.11e+00
  bond pdb=" C   GLU A 374 "
       pdb=" O   GLU A 374 "
    ideal  model  delta    sigma   weight residual
    1.245  1.229  0.016 1.53e-02 4.27e+03 1.08e+00
  bond pdb=" CG1 ILE A 289 "
       pdb=" CD1 ILE A 289 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.80e-01
  bond pdb=" N   LYS A 570 "
       pdb=" CA  LYS A 570 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.011 1.29e-02 6.01e+03 7.48e-01
  bond pdb=" C   GLU A 374 "
       pdb=" N   PRO A 375 "
    ideal  model  delta    sigma   weight residual
    1.330  1.339 -0.009 1.22e-02 6.72e+03 5.83e-01
  ... (remaining 7240 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 9335
        1.03 -     2.06: 330
        2.06 -     3.09: 57
        3.09 -     4.11: 27
        4.11 -     5.14: 5
  Bond angle restraints: 9754
  Sorted by residual:
  angle pdb=" N   GLU A 775 "
        pdb=" CA  GLU A 775 "
        pdb=" CB  GLU A 775 "
      ideal   model   delta    sigma   weight residual
     110.28  115.42   -5.14 1.55e+00 4.16e-01 1.10e+01
  angle pdb=" C   GLU A 774 "
        pdb=" N   GLU A 775 "
        pdb=" CA  GLU A 775 "
      ideal   model   delta    sigma   weight residual
     120.31  115.74    4.57 1.52e+00 4.33e-01 9.04e+00
  angle pdb=" CA  GLU A 775 "
        pdb=" CB  GLU A 775 "
        pdb=" CG  GLU A 775 "
      ideal   model   delta    sigma   weight residual
     114.10  118.94   -4.84 2.00e+00 2.50e-01 5.85e+00
  angle pdb=" CA  PRO A 375 "
        pdb=" C   PRO A 375 "
        pdb=" O   PRO A 375 "
      ideal   model   delta    sigma   weight residual
     122.08  119.30    2.78 1.28e+00 6.10e-01 4.73e+00
  angle pdb=" N   PHE A 364 "
        pdb=" CA  PHE A 364 "
        pdb=" C   PHE A 364 "
      ideal   model   delta    sigma   weight residual
     110.91  113.33   -2.42 1.17e+00 7.31e-01 4.26e+00
  ... (remaining 9749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3959
       17.91 -    35.81: 365
       35.81 -    53.72: 61
       53.72 -    71.63: 6
       71.63 -    89.53: 9
  Dihedral angle restraints: 4400
    sinusoidal: 1829
      harmonic: 2571
  Sorted by residual:
  dihedral pdb=" CB  GLU A 328 "
           pdb=" CG  GLU A 328 "
           pdb=" CD  GLU A 328 "
           pdb=" OE1 GLU A 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.53   89.53     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A  98 "
           pdb=" CG  GLU A  98 "
           pdb=" CD  GLU A  98 "
           pdb=" OE1 GLU A  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.09   88.09     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CA  ARG A 706 "
           pdb=" CB  ARG A 706 "
           pdb=" CG  ARG A 706 "
           pdb=" CD  ARG A 706 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.94   50.94     3      1.50e+01 4.44e-03 8.96e+00
  ... (remaining 4397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 682
       0.027 -    0.055: 248
       0.055 -    0.082: 75
       0.082 -    0.109: 38
       0.109 -    0.136: 17
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" CA  VAL A 459 "
            pdb=" N   VAL A 459 "
            pdb=" C   VAL A 459 "
            pdb=" CB  VAL A 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ILE A 674 "
            pdb=" N   ILE A 674 "
            pdb=" C   ILE A 674 "
            pdb=" CB  ILE A 674 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  PRO A 710 "
            pdb=" N   PRO A 710 "
            pdb=" C   PRO A 710 "
            pdb=" CB  PRO A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 1057 not shown)

  Planarity restraints: 1269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 224 "   -0.016 5.00e-02 4.00e+02   2.46e-02 9.65e-01
        pdb=" N   PRO A 225 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 225 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 225 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 609 "    0.006 2.00e-02 2.50e+03   6.55e-03 8.57e-01
        pdb=" CG  TYR A 609 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 609 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 609 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 609 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 609 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 609 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 609 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 709 "    0.015 5.00e-02 4.00e+02   2.22e-02 7.85e-01
        pdb=" N   PRO A 710 "   -0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO A 710 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 710 "    0.012 5.00e-02 4.00e+02
  ... (remaining 1266 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 117
        2.62 -     3.19: 6966
        3.19 -     3.76: 11311
        3.76 -     4.33: 14687
        4.33 -     4.90: 24028
  Nonbonded interactions: 57109
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 235 "
            pdb=" O   ASN A 238 "
     model   vdw
     2.048 3.040
  nonbonded pdb=" O   THR A 449 "
            pdb=" NH2 ARG A 453 "
     model   vdw
     2.086 3.120
  nonbonded pdb=" O   ALA A 141 "
            pdb=" NZ  LYS A 145 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" OG1 THR A  94 "
            pdb=" O   ALA A 767 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   LEU A 166 "
            pdb=" NH1 ARG A 169 "
     model   vdw
     2.119 3.120
  ... (remaining 57104 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             4.400
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.130
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
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      :  0.002   0.039   7245  Z= 0.144
  Angle     :  0.492   5.144   9754  Z= 0.272
  Chirality :  0.037   0.136   1060
  Planarity :  0.002   0.025   1269
  Dihedral  : 14.097  89.535   2742
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.39 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.81 (0.29), residues: 876
  helix:  1.91 (0.25), residues: 446
  sheet: -1.37 (0.62), residues: 82
  loop : -0.78 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 130 
 HIS   0.006   0.001   HIS B 148 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.016   0.001   TYR A 609 
 ARG   0.002   0.000   ARG A 108 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  165 MET cc_start: 0.8946 (tmm) cc_final: 0.8712 (tmm)
REVERT: A  388 MET cc_start: 0.8990 (mpp) cc_final: 0.8761 (mpp)
REVERT: A  439 MET cc_start: 0.9109 (mpp) cc_final: 0.8881 (mpp)
REVERT: A  546 MET cc_start: 0.8837 (tpt) cc_final: 0.8613 (tpp)
REVERT: A  776 MET cc_start: 0.9460 (mmp) cc_final: 0.9223 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1639
  time to fit residues: 14.2541
Evaluate side-chains
  45 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0870
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
A 691 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.050487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.040384 restraints weight = 60958.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.041382 restraints weight = 33035.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.042003 restraints weight = 21261.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.181
  Angle     :  0.552   5.754   9754  Z= 0.290
  Chirality :  0.040   0.143   1060
  Planarity :  0.004   0.039   1269
  Dihedral  :  3.838  16.530    954
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.15 %
    Favored  : 91.81 %
  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:  0.74 (0.29), residues: 876
  helix:  1.81 (0.25), residues: 452
  sheet: -1.29 (0.61), residues: 82
  loop : -0.82 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 593 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.027   0.001   PHE B 181 
 TYR   0.017   0.001   TYR A 609 
 ARG   0.004   0.001   ARG A 453 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A    6 MET cc_start: 0.7827 (tmm) cc_final: 0.7580 (tmm)
REVERT: A  388 MET cc_start: 0.8985 (mpp) cc_final: 0.8434 (mpp)
REVERT: A  546 MET cc_start: 0.8488 (tpt) cc_final: 0.8248 (tpp)
REVERT: A  776 MET cc_start: 0.9470 (mmp) cc_final: 0.9259 (mmm)
REVERT: B   97 MET cc_start: 0.4949 (ptt) cc_final: 0.3815 (tpt)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 0.1781
  time to fit residues: 13.7153
Evaluate side-chains
  48 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 71 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0270
   chunk 21 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.050807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.040741 restraints weight = 62438.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.041697 restraints weight = 33669.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.042358 restraints weight = 21616.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7245  Z= 0.145
  Angle     :  0.506   5.553   9754  Z= 0.266
  Chirality :  0.039   0.132   1060
  Planarity :  0.003   0.030   1269
  Dihedral  :  3.761  16.626    954
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.23 %
    Favored  : 89.47 %
  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:  0.63 (0.29), residues: 876
  helix:  1.59 (0.25), residues: 461
  sheet: -1.20 (0.61), residues: 82
  loop : -0.77 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 112 
 HIS   0.001   0.000   HIS A 492 
 PHE   0.010   0.001   PHE A 669 
 TYR   0.048   0.001   TYR A 609 
 ARG   0.002   0.000   ARG A 453 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.7826 (tmm) cc_final: 0.7552 (tmm)
REVERT: A  113 MET cc_start: 0.6921 (ttm) cc_final: 0.6519 (ttm)
REVERT: A  546 MET cc_start: 0.8476 (tpt) cc_final: 0.8242 (tpp)
REVERT: A  609 TYR cc_start: 0.8574 (m-80) cc_final: 0.8355 (m-80)
REVERT: B   97 MET cc_start: 0.5265 (ptt) cc_final: 0.4395 (tpt)
  outliers start: 10
  outliers final: 4
  residues processed: 53
  average time/residue: 0.1799
  time to fit residues: 14.5102
Evaluate side-chains
  47 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
A 171 ASN
A 711 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.049576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.039682 restraints weight = 62131.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.040662 restraints weight = 33262.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.041282 restraints weight = 21134.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.217
  Angle     :  0.554   8.130   9754  Z= 0.288
  Chirality :  0.040   0.162   1060
  Planarity :  0.003   0.037   1269
  Dihedral  :  3.990  21.111    954
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.09 %
    Favored  : 86.35 %
  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:  0.59 (0.29), residues: 876
  helix:  1.55 (0.25), residues: 453
  sheet: -1.30 (0.61), residues: 82
  loop : -0.70 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 508 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.019   0.001   PHE B 181 
 TYR   0.036   0.001   TYR A 609 
 ARG   0.002   0.000   ARG B  58 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.7042 (ttm) cc_final: 0.6585 (ttm)
REVERT: A  195 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7983 (m-80)
REVERT: A  300 MET cc_start: 0.8802 (ppp) cc_final: 0.8591 (ppp)
REVERT: A  546 MET cc_start: 0.8509 (tpt) cc_final: 0.8259 (tpp)
REVERT: A  609 TYR cc_start: 0.8643 (m-80) cc_final: 0.8342 (m-80)
REVERT: B   97 MET cc_start: 0.5270 (ptt) cc_final: 0.4409 (tpt)
  outliers start: 12
  outliers final: 5
  residues processed: 50
  average time/residue: 0.1576
  time to fit residues: 12.2917
Evaluate side-chains
  49 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
B 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.049100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.039128 restraints weight = 60729.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.040100 restraints weight = 33239.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.040731 restraints weight = 21434.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7245  Z= 0.199
  Angle     :  0.544   9.000   9754  Z= 0.282
  Chirality :  0.040   0.152   1060
  Planarity :  0.003   0.036   1269
  Dihedral  :  4.056  18.981    954
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.13 %
    Favored  : 85.31 %
  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 (0.29), residues: 876
  helix:  1.51 (0.25), residues: 457
  sheet: -1.40 (0.60), residues: 82
  loop : -0.77 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 508 
 HIS   0.002   0.001   HIS A 651 
 PHE   0.014   0.001   PHE B 104 
 TYR   0.032   0.001   TYR A 609 
 ARG   0.002   0.000   ARG A 780 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.7008 (ttm) cc_final: 0.6504 (ttm)
REVERT: A  195 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8021 (m-80)
REVERT: A  300 MET cc_start: 0.8767 (ppp) cc_final: 0.8565 (ppp)
REVERT: A  546 MET cc_start: 0.8525 (tpt) cc_final: 0.8275 (tpp)
REVERT: A  609 TYR cc_start: 0.8684 (m-80) cc_final: 0.8259 (m-80)
REVERT: B   97 MET cc_start: 0.5471 (ptt) cc_final: 0.4761 (tpt)
  outliers start: 12
  outliers final: 8
  residues processed: 51
  average time/residue: 0.1567
  time to fit residues: 12.0035
Evaluate side-chains
  52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0980
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.049603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.039736 restraints weight = 60867.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.040717 restraints weight = 32411.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.041340 restraints weight = 20665.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7245  Z= 0.167
  Angle     :  0.552  11.829   9754  Z= 0.276
  Chirality :  0.039   0.161   1060
  Planarity :  0.003   0.034   1269
  Dihedral  :  3.975  19.549    954
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.17 %
    Favored  : 84.01 %
  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 (0.29), residues: 876
  helix:  1.54 (0.25), residues: 457
  sheet: -1.36 (0.61), residues: 82
  loop : -0.81 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 508 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.010   0.001   PHE B 104 
 TYR   0.028   0.001   TYR A 609 
 ARG   0.002   0.000   ARG A 453 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7884 (m-80)
REVERT: A  300 MET cc_start: 0.8794 (ppp) cc_final: 0.8580 (ppp)
REVERT: A  546 MET cc_start: 0.8585 (tpt) cc_final: 0.8324 (tpp)
REVERT: A  609 TYR cc_start: 0.8678 (m-80) cc_final: 0.8271 (m-80)
REVERT: B   97 MET cc_start: 0.5522 (ptt) cc_final: 0.4935 (tpt)
  outliers start: 14
  outliers final: 7
  residues processed: 55
  average time/residue: 0.1633
  time to fit residues: 13.8428
Evaluate side-chains
  52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0770
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.049646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.039783 restraints weight = 60262.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.040781 restraints weight = 32433.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.041405 restraints weight = 20638.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7245  Z= 0.162
  Angle     :  0.580  11.160   9754  Z= 0.287
  Chirality :  0.039   0.181   1060
  Planarity :  0.003   0.031   1269
  Dihedral  :  3.966  17.535    954
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.60 %
    Favored  : 82.70 %
  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 (0.29), residues: 876
  helix:  1.52 (0.25), residues: 457
  sheet: -1.35 (0.62), residues: 82
  loop : -0.85 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 508 
 HIS   0.002   0.001   HIS A 491 
 PHE   0.023   0.001   PHE B 181 
 TYR   0.027   0.001   TYR A 609 
 ARG   0.001   0.000   ARG A 453 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7839 (m-80)
REVERT: A  546 MET cc_start: 0.8552 (tpt) cc_final: 0.8301 (tpp)
REVERT: A  609 TYR cc_start: 0.8684 (m-80) cc_final: 0.8286 (m-80)
REVERT: B   97 MET cc_start: 0.5503 (ptt) cc_final: 0.4960 (tpt)
  outliers start: 13
  outliers final: 6
  residues processed: 54
  average time/residue: 0.1647
  time to fit residues: 13.6607
Evaluate side-chains
  51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0010
   chunk 5 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0980
   overall best weight:    0.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.049997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.040056 restraints weight = 60692.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.041051 restraints weight = 32406.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.041685 restraints weight = 20578.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7245  Z= 0.148
  Angle     :  0.581  11.237   9754  Z= 0.284
  Chirality :  0.039   0.183   1060
  Planarity :  0.003   0.031   1269
  Dihedral  :  3.884  17.204    954
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.25 %
    Favored  : 82.31 %
  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:  0.59 (0.29), residues: 876
  helix:  1.59 (0.25), residues: 452
  sheet: -1.35 (0.62), residues: 82
  loop : -0.75 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 508 
 HIS   0.001   0.000   HIS A 651 
 PHE   0.008   0.001   PHE A 669 
 TYR   0.025   0.001   TYR A 609 
 ARG   0.002   0.000   ARG A 777 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7621 (pmm) cc_final: 0.7011 (ptm)
REVERT: A  195 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7845 (m-80)
REVERT: A  358 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.6214 (t-90)
REVERT: A  546 MET cc_start: 0.8495 (tpt) cc_final: 0.8244 (tpp)
REVERT: A  609 TYR cc_start: 0.8715 (m-80) cc_final: 0.8381 (m-80)
REVERT: B   97 MET cc_start: 0.5652 (ptt) cc_final: 0.5119 (tpt)
  outliers start: 11
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1528
  time to fit residues: 12.1869
Evaluate side-chains
  50 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.049004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.039014 restraints weight = 63067.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.040017 restraints weight = 33927.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.040637 restraints weight = 21608.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7245  Z= 0.207
  Angle     :  0.613  12.008   9754  Z= 0.303
  Chirality :  0.040   0.189   1060
  Planarity :  0.003   0.035   1269
  Dihedral  :  4.071  17.509    954
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.51 %
    Favored  : 81.92 %
  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:  0.41 (0.29), residues: 876
  helix:  1.53 (0.25), residues: 451
  sheet: -1.49 (0.61), residues: 82
  loop : -0.94 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 491 
 PHE   0.014   0.001   PHE B 181 
 TYR   0.024   0.001   TYR A 609 
 ARG   0.005   0.000   ARG A 780 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7887 (pmm) cc_final: 0.7094 (ptm)
REVERT: A  104 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (t0)
REVERT: A  195 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7932 (m-80)
REVERT: A  358 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6299 (t-90)
REVERT: A  609 TYR cc_start: 0.8663 (m-80) cc_final: 0.8429 (m-80)
REVERT: B   97 MET cc_start: 0.5543 (ptt) cc_final: 0.4984 (tpt)
  outliers start: 12
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1550
  time to fit residues: 11.6998
Evaluate side-chains
  50 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASN
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.049013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.039087 restraints weight = 63259.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.040084 restraints weight = 34172.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.040715 restraints weight = 21744.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7245  Z= 0.191
  Angle     :  0.638  12.583   9754  Z= 0.311
  Chirality :  0.040   0.196   1060
  Planarity :  0.003   0.029   1269
  Dihedral  :  4.121  16.970    954
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.78 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.43 (0.29), residues: 876
  helix:  1.55 (0.25), residues: 447
  sheet: -1.45 (0.62), residues: 82
  loop : -0.93 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 508 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.016   0.001   PHE B 107 
 TYR   0.024   0.001   TYR A 609 
 ARG   0.003   0.000   ARG A 108 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7877 (pmm) cc_final: 0.7108 (ptm)
REVERT: A  113 MET cc_start: 0.6798 (ttm) cc_final: 0.6461 (ttm)
REVERT: A  142 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7229 (t80)
REVERT: A  195 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7939 (m-80)
REVERT: A  358 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6303 (t-90)
REVERT: A  435 MET cc_start: 0.8783 (tpt) cc_final: 0.8376 (tpt)
REVERT: B   97 MET cc_start: 0.5647 (ptt) cc_final: 0.5143 (tpt)
  outliers start: 13
  outliers final: 7
  residues processed: 51
  average time/residue: 0.1527
  time to fit residues: 12.0479
Evaluate side-chains
  51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 TYR
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0980
   chunk 83 optimal weight:    0.0040
   chunk 80 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0970
   overall best weight:    0.0766

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.050124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.040280 restraints weight = 59310.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.041294 restraints weight = 32346.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.041975 restraints weight = 20682.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7245  Z= 0.140
  Angle     :  0.629  12.722   9754  Z= 0.304
  Chirality :  0.040   0.189   1060
  Planarity :  0.003   0.031   1269
  Dihedral  :  3.890  16.673    954
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.30 %
    Favored  : 81.27 %
  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:  0.64 (0.29), residues: 876
  helix:  1.69 (0.25), residues: 442
  sheet: -1.35 (0.62), residues: 82
  loop : -0.73 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 508 
 HIS   0.001   0.000   HIS A 581 
 PHE   0.014   0.001   PHE B 107 
 TYR   0.025   0.001   TYR A 609 
 ARG   0.003   0.000   ARG A 108 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2433.90 seconds
wall clock time: 44 minutes 44.20 seconds (2684.20 seconds total)