Starting phenix.real_space_refine
on Tue Feb 11 08:16:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w9f_32366/02_2025/7w9f_32366.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w9f_32366/02_2025/7w9f_32366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w9f_32366/02_2025/7w9f_32366.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w9f_32366/02_2025/7w9f_32366.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w9f_32366/02_2025/7w9f_32366.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w9f_32366/02_2025/7w9f_32366.cif"
  }
  resolution = 3.6
  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=   0.002 sd=   0.033
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      22      5.16       5
     C    3066      2.51       5
     N     807      2.21       5
     O     961      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 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: 4856
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1671
          Classifications: {'peptide': 220}
          Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 202}
    Chain: "B"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1643
          Classifications: {'peptide': 211}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 200}
    Chain: "E"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1542
          Classifications: {'peptide': 194}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
  Time building chain proxies: 3.44, per 1000 atoms: 0.71
  Number of scatterers: 4856
  At special positions: 0
  Unit cell: (63.394, 92.905, 137.718, 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      22     16.00
     O     961      8.00
     N     807      7.00
     C    3066      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 147 " - pdb=" SG  CYS A 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.04

  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: 1.14
  Conformation dependent library (CDL) restraints added in 535.2 milliseconds
  

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 13 sheets defined
      7.7% alpha, 31.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 65
      removed outlier: 4.070A  pdb=" N   LYS A  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 65'
    Processing helix  chain 'A' and resid 87 through 90
      removed outlier: 3.627A  pdb=" N   ASP A  90 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 90'
    Processing helix  chain 'A' and resid 100 through 104
      removed outlier: 3.627A  pdb=" N   TYR A 104 " --> pdb=" O   TYR A 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.796A  pdb=" N   LEU B  83 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
    Processing helix  chain 'B' and resid 182 through 187
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 4.003A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 370
      removed outlier: 3.733A  pdb=" N   TYR E 369 " --> pdb=" O   TYR E 365 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.759A  pdb=" N   VAL A  18 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS A  22 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA A  79 " --> pdb=" O   CYS A  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.558A  pdb=" N   GLU A  10 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A 117 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A  49 " --> pdb=" O   TRP A  36 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LYS A  38 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   TRP A  47 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER A  40 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU A  45 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLY A  50 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A  59 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130
      removed outlier: 3.657A  pdb=" N   VAL A 143 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL A 188 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS A 147 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 186 " --> pdb=" O   CYS A 147 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 184 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   TYR A 182 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130
      removed outlier: 3.657A  pdb=" N   VAL A 143 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL A 188 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS A 147 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 186 " --> pdb=" O   CYS A 147 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 184 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   TYR A 182 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 161
      removed outlier: 3.663A  pdb=" N   THR A 211 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 6
      removed outlier: 3.675A  pdb=" N   PHE B  71 " --> pdb=" O   CYS B  23 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR B  72 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 49
      removed outlier: 6.729A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   TYR B  49 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118
      removed outlier: 3.841A  pdb=" N   ASN B 137 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   TYR B 173 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154
      removed outlier: 3.792A  pdb=" N   ASN B 145 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS B 149 " --> pdb=" O   THR B 193 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR B 193 " --> pdb=" O   LYS B 149 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.966A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LYS E 356 " --> pdb=" O   ALA E 397 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA E 397 " --> pdb=" O   LYS E 356 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS E 378 " --> pdb=" O   VAL E 433 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR E 376 " --> pdb=" O   ALA E 435 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AB4, first strand: chain 'E' and resid 473 through 474

    125 hydrogen bonds defined for protein.
    303 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.34 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: 1538
        1.34 -     1.46: 1249
        1.46 -     1.58: 2167
        1.58 -     1.70: 0
        1.70 -     1.81: 28
  Bond restraints: 4982
  Sorted by residual:
  bond pdb=" CA  PRO A 133 "
       pdb=" C   PRO A 133 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 1.42e-02 4.96e+03 2.55e+00
  bond pdb=" N   THR B  51 "
       pdb=" CA  THR B  51 "
    ideal  model  delta    sigma   weight residual
    1.462  1.484 -0.022 1.48e-02 4.57e+03 2.22e+00
  bond pdb=" C   PRO A 133 "
       pdb=" N   GLY A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.40e-02 5.10e+03 2.07e+00
  bond pdb=" C   TYR A 101 "
       pdb=" N   PRO A 102 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.45e+00
  bond pdb=" CB  LYS E 458 "
       pdb=" CG  LYS E 458 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.21e+00
  ... (remaining 4977 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 6628
        2.14 -     4.27: 135
        4.27 -     6.41: 16
        6.41 -     8.54: 5
        8.54 -    10.68: 1
  Bond angle restraints: 6785
  Sorted by residual:
  angle pdb=" C   PRO A 133 "
        pdb=" N   GLY A 134 "
        pdb=" CA  GLY A 134 "
      ideal   model   delta    sigma   weight residual
     121.70  132.38  -10.68 1.80e+00 3.09e-01 3.52e+01
  angle pdb=" C   SER B  50 "
        pdb=" N   THR B  51 "
        pdb=" CA  THR B  51 "
      ideal   model   delta    sigma   weight residual
     122.61  129.74   -7.13 1.56e+00 4.11e-01 2.09e+01
  angle pdb=" CA  PRO A 133 "
        pdb=" C   PRO A 133 "
        pdb=" N   GLY A 134 "
      ideal   model   delta    sigma   weight residual
     117.98  123.82   -5.84 1.43e+00 4.89e-01 1.67e+01
  angle pdb=" N   PRO A 133 "
        pdb=" CA  PRO A 133 "
        pdb=" C   PRO A 133 "
      ideal   model   delta    sigma   weight residual
     113.40  118.54   -5.14 1.34e+00 5.57e-01 1.47e+01
  angle pdb=" C   GLY A 100 "
        pdb=" N   TYR A 101 "
        pdb=" CA  TYR A 101 "
      ideal   model   delta    sigma   weight residual
     120.09  123.38   -3.29 1.25e+00 6.40e-01 6.95e+00
  ... (remaining 6780 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 2672
       17.92 -    35.83: 239
       35.83 -    53.75: 36
       53.75 -    71.66: 8
       71.66 -    89.58: 4
  Dihedral angle restraints: 2959
    sinusoidal: 1136
      harmonic: 1823
  Sorted by residual:
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.74  -50.74     1      1.00e+01 1.00e-02 3.52e+01
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.42  -47.42     1      1.00e+01 1.00e-02 3.10e+01
  dihedral pdb=" CA  TYR A 105 "
           pdb=" C   TYR A 105 "
           pdb=" N   ALA A 106 "
           pdb=" CA  ALA A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 2956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 585
       0.058 -    0.116: 133
       0.116 -    0.174: 19
       0.174 -    0.232: 3
       0.232 -    0.289: 2
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CB  ILE E 468 "
            pdb=" CA  ILE E 468 "
            pdb=" CG1 ILE E 468 "
            pdb=" CG2 ILE E 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CA  PRO A 133 "
            pdb=" N   PRO A 133 "
            pdb=" C   PRO A 133 "
            pdb=" CB  PRO A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CB  ILE A  51 "
            pdb=" CA  ILE A  51 "
            pdb=" CG1 ILE A  51 "
            pdb=" CG2 ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 739 not shown)

  Planarity restraints: 874
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 155 "    0.032 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO A 156 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 156 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 156 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 101 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO A 102 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO E 463 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 871 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1574
        2.82 -     3.34: 3720
        3.34 -     3.86: 7775
        3.86 -     4.38: 8405
        4.38 -     4.90: 14864
  Nonbonded interactions: 36338
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  82 "
            pdb=" OH  TYR B  86 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   SER A 179 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   ILE B 150 "
            pdb=" OG  SER B 153 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   SER B 171 "
            pdb=" OG  SER B 171 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OH  TYR B  36 "
            pdb=" OE1 GLN B  89 "
     model   vdw
     2.354 3.040
  ... (remaining 36333 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:             0.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     15.300
  Find NCS groups from input model:        0.090
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
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      :  0.003   0.034   4982  Z= 0.226
  Angle     :  0.729  10.679   6785  Z= 0.395
  Chirality :  0.051   0.289    742
  Planarity :  0.006   0.048    874
  Dihedral  : 13.990  89.579   1775
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -3.66 (0.28), residues: 619
  helix: -5.15 (0.17), residues: 28
  sheet: -1.84 (0.29), residues: 249
  loop : -2.69 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 195 
 HIS   0.002   0.001   HIS B 189 
 PHE   0.013   0.001   PHE E 400 
 TYR   0.010   0.001   TYR B  49 
 ARG   0.005   0.000   ARG B  61 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.6403 (ttm) cc_final: 0.5698 (tpp)
REVERT: A   81 MET cc_start: 0.8461 (ttp) cc_final: 0.8202 (ttm)
REVERT: A   95 TYR cc_start: 0.8091 (m-80) cc_final: 0.7569 (m-80)
REVERT: A  129 TYR cc_start: 0.7631 (m-80) cc_final: 0.7320 (m-80)
REVERT: A  142 MET cc_start: 0.8006 (mtm) cc_final: 0.7625 (mmt)
REVERT: B   11 MET cc_start: 0.7820 (mtm) cc_final: 0.7580 (mtt)
REVERT: B  107 LYS cc_start: 0.8695 (mttt) cc_final: 0.8449 (ttmm)
REVERT: B  108 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7795 (ttt-90)
REVERT: E  360 ASN cc_start: 0.7111 (t0) cc_final: 0.6814 (t0)
REVERT: E  414 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8211 (mp10)
REVERT: E  505 TYR cc_start: 0.7385 (t80) cc_final: 0.7136 (t80)
REVERT: E  508 TYR cc_start: 0.7257 (m-80) cc_final: 0.6949 (m-80)
REVERT: E  511 VAL cc_start: 0.8341 (t) cc_final: 0.8047 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1641
  time to fit residues: 28.8833
Evaluate side-chains
  130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
A 140 ASN
B   8 GLN
B 124 GLN
B 138 ASN
B 190 ASN
E 460 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.134381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.121989 restraints weight = 7658.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125934 restraints weight = 3779.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.128323 restraints weight = 2133.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4982  Z= 0.265
  Angle     :  0.584   6.935   6785  Z= 0.311
  Chirality :  0.044   0.177    742
  Planarity :  0.005   0.060    874
  Dihedral  :  4.603  29.607    685
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.27 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -2.74 (0.30), residues: 619
  helix: -4.77 (0.22), residues: 33
  sheet: -1.14 (0.30), residues: 248
  loop : -2.04 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 436 
 HIS   0.002   0.001   HIS E 519 
 PHE   0.015   0.002   PHE E 347 
 TYR   0.021   0.002   TYR E 351 
 ARG   0.004   0.000   ARG A  98 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.6316 (ttm) cc_final: 0.5729 (tpp)
REVERT: A  115 SER cc_start: 0.7751 (t) cc_final: 0.7253 (p)
REVERT: A  129 TYR cc_start: 0.7730 (m-80) cc_final: 0.7492 (m-80)
REVERT: A  142 MET cc_start: 0.7898 (mtm) cc_final: 0.7682 (mmt)
REVERT: A  186 SER cc_start: 0.8581 (m) cc_final: 0.8334 (p)
REVERT: B    9 LYS cc_start: 0.7787 (mttt) cc_final: 0.7509 (mttt)
REVERT: B   11 MET cc_start: 0.7744 (mtm) cc_final: 0.7515 (mtt)
REVERT: B  108 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7898 (ttt-90)
REVERT: B  206 VAL cc_start: 0.7331 (t) cc_final: 0.7006 (p)
REVERT: E  341 VAL cc_start: 0.8286 (m) cc_final: 0.8063 (t)
REVERT: E  360 ASN cc_start: 0.7557 (t0) cc_final: 0.7233 (t0)
REVERT: E  394 ASN cc_start: 0.8522 (p0) cc_final: 0.8195 (p0)
REVERT: E  414 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8108 (mp10)
REVERT: E  508 TYR cc_start: 0.7234 (m-80) cc_final: 0.6933 (m-80)
REVERT: E  512 VAL cc_start: 0.7703 (t) cc_final: 0.7486 (p)
  outliers start: 10
  outliers final: 7
  residues processed: 138
  average time/residue: 0.1509
  time to fit residues: 27.3598
Evaluate side-chains
  140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0870
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 GLN
** E 501 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.135092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.122676 restraints weight = 7688.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126600 restraints weight = 3832.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.129078 restraints weight = 2194.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4982  Z= 0.179
  Angle     :  0.550   6.851   6785  Z= 0.287
  Chirality :  0.043   0.170    742
  Planarity :  0.004   0.062    874
  Dihedral  :  4.286  24.595    685
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.30 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -2.18 (0.32), residues: 619
  helix: -4.32 (0.38), residues: 33
  sheet: -0.77 (0.31), residues: 252
  loop : -1.66 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 519 
 PHE   0.011   0.001   PHE E 347 
 TYR   0.024   0.002   TYR B 140 
 ARG   0.003   0.000   ARG E 357 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.7808 (t) cc_final: 0.7336 (p)
REVERT: A  129 TYR cc_start: 0.7706 (m-80) cc_final: 0.7441 (m-80)
REVERT: A  142 MET cc_start: 0.7820 (mtm) cc_final: 0.7616 (mmp)
REVERT: A  186 SER cc_start: 0.8533 (m) cc_final: 0.8264 (p)
REVERT: B    9 LYS cc_start: 0.7710 (mttt) cc_final: 0.7459 (mttt)
REVERT: B   53 TYR cc_start: 0.8126 (m-10) cc_final: 0.7905 (m-10)
REVERT: B  107 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8230 (mttp)
REVERT: B  108 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7749 (ttt-90)
REVERT: E  341 VAL cc_start: 0.8301 (m) cc_final: 0.8050 (t)
REVERT: E  360 ASN cc_start: 0.7532 (t0) cc_final: 0.7165 (t0)
REVERT: E  365 TYR cc_start: 0.8211 (m-10) cc_final: 0.7819 (m-10)
REVERT: E  394 ASN cc_start: 0.8758 (p0) cc_final: 0.8313 (p0)
REVERT: E  414 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8073 (mp10)
REVERT: E  508 TYR cc_start: 0.7279 (m-80) cc_final: 0.6984 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 143
  average time/residue: 0.1587
  time to fit residues: 29.4054
Evaluate side-chains
  149 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 501 ASN ** 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 = 0.3763 r_free = 0.3763 target = 0.134382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.121927 restraints weight = 7884.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.125882 restraints weight = 3903.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.128378 restraints weight = 2222.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4982  Z= 0.203
  Angle     :  0.553   7.428   6785  Z= 0.287
  Chirality :  0.043   0.169    742
  Planarity :  0.004   0.064    874
  Dihedral  :  4.298  24.754    685
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.40 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.84 (0.32), residues: 619
  helix: -3.97 (0.49), residues: 34
  sheet: -0.58 (0.31), residues: 252
  loop : -1.40 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 436 
 HIS   0.002   0.000   HIS E 519 
 PHE   0.009   0.001   PHE E 374 
 TYR   0.025   0.002   TYR B 140 
 ARG   0.003   0.000   ARG E 357 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.7818 (t) cc_final: 0.7334 (p)
REVERT: A  129 TYR cc_start: 0.7772 (m-80) cc_final: 0.7544 (m-80)
REVERT: A  142 MET cc_start: 0.7781 (mtm) cc_final: 0.7476 (mmp)
REVERT: A  186 SER cc_start: 0.8545 (m) cc_final: 0.8262 (p)
REVERT: B    9 LYS cc_start: 0.7737 (mttt) cc_final: 0.7485 (mttt)
REVERT: B  107 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8240 (mttp)
REVERT: B  108 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7765 (ttt-90)
REVERT: E  341 VAL cc_start: 0.8352 (m) cc_final: 0.8086 (t)
REVERT: E  360 ASN cc_start: 0.7688 (t0) cc_final: 0.7312 (t0)
REVERT: E  365 TYR cc_start: 0.8077 (m-10) cc_final: 0.7729 (m-10)
REVERT: E  398 ASP cc_start: 0.6535 (m-30) cc_final: 0.6179 (m-30)
REVERT: E  406 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6945 (mp0)
REVERT: E  414 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8080 (mp10)
REVERT: E  508 TYR cc_start: 0.7281 (m-80) cc_final: 0.7002 (m-80)
REVERT: E  511 VAL cc_start: 0.8421 (t) cc_final: 0.8184 (m)
  outliers start: 15
  outliers final: 13
  residues processed: 145
  average time/residue: 0.1582
  time to fit residues: 29.4342
Evaluate side-chains
  151 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 501 ASN ** 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 = 0.3732 r_free = 0.3732 target = 0.131986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.119906 restraints weight = 7700.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.123758 restraints weight = 3808.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126196 restraints weight = 2171.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4982  Z= 0.290
  Angle     :  0.592   7.035   6785  Z= 0.308
  Chirality :  0.044   0.174    742
  Planarity :  0.004   0.064    874
  Dihedral  :  4.615  28.397    685
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.05 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.81 (0.32), residues: 619
  helix: -3.60 (0.60), residues: 33
  sheet: -0.47 (0.32), residues: 250
  loop : -1.52 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 109 
 PHE   0.010   0.001   PHE E 400 
 TYR   0.027   0.002   TYR B 140 
 ARG   0.003   0.000   ARG A  98 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.7863 (t) cc_final: 0.7339 (p)
REVERT: A  129 TYR cc_start: 0.7862 (m-80) cc_final: 0.7625 (m-80)
REVERT: A  142 MET cc_start: 0.7745 (mtm) cc_final: 0.7493 (mmp)
REVERT: A  186 SER cc_start: 0.8644 (m) cc_final: 0.8372 (p)
REVERT: B    4 MET cc_start: 0.7281 (mmm) cc_final: 0.7049 (ttt)
REVERT: B    9 LYS cc_start: 0.7759 (mttt) cc_final: 0.7508 (mttt)
REVERT: B  107 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8261 (mttp)
REVERT: B  108 ARG cc_start: 0.8212 (ttt-90) cc_final: 0.7976 (ttt-90)
REVERT: B  206 VAL cc_start: 0.7427 (t) cc_final: 0.7128 (p)
REVERT: E  341 VAL cc_start: 0.8475 (m) cc_final: 0.8229 (t)
REVERT: E  360 ASN cc_start: 0.7839 (t0) cc_final: 0.7411 (t0)
REVERT: E  365 TYR cc_start: 0.8064 (m-10) cc_final: 0.7816 (m-10)
REVERT: E  377 PHE cc_start: 0.7611 (t80) cc_final: 0.7332 (t80)
REVERT: E  398 ASP cc_start: 0.6522 (m-30) cc_final: 0.6209 (m-30)
REVERT: E  414 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8015 (mp10)
REVERT: E  508 TYR cc_start: 0.7265 (m-80) cc_final: 0.6963 (m-80)
REVERT: E  511 VAL cc_start: 0.8547 (t) cc_final: 0.8176 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 138
  average time/residue: 0.1490
  time to fit residues: 27.0255
Evaluate side-chains
  142 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0970
   chunk 58 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 501 ASN ** 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 = 0.3748 r_free = 0.3748 target = 0.133182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120971 restraints weight = 7736.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124903 restraints weight = 3839.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.127358 restraints weight = 2178.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4982  Z= 0.190
  Angle     :  0.552   6.713   6785  Z= 0.286
  Chirality :  0.043   0.167    742
  Planarity :  0.004   0.065    874
  Dihedral  :  4.383  23.562    685
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.96 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.60 (0.33), residues: 619
  helix: -3.53 (0.62), residues: 34
  sheet: -0.36 (0.32), residues: 250
  loop : -1.32 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 436 
 HIS   0.001   0.000   HIS E 519 
 PHE   0.008   0.001   PHE E 400 
 TYR   0.028   0.002   TYR B 140 
 ARG   0.002   0.000   ARG A  98 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.7854 (t) cc_final: 0.7352 (p)
REVERT: A  142 MET cc_start: 0.7731 (mtm) cc_final: 0.7462 (mmp)
REVERT: A  186 SER cc_start: 0.8509 (m) cc_final: 0.8240 (p)
REVERT: B    4 MET cc_start: 0.7285 (mmm) cc_final: 0.6936 (tpp)
REVERT: B    9 LYS cc_start: 0.7718 (mttt) cc_final: 0.7503 (mttt)
REVERT: B  107 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8258 (mttp)
REVERT: B  108 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7941 (ttt-90)
REVERT: B  123 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8290 (mp0)
REVERT: B  175 MET cc_start: 0.7416 (ttp) cc_final: 0.7116 (ttt)
REVERT: E  341 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8198 (t)
REVERT: E  360 ASN cc_start: 0.7810 (t0) cc_final: 0.7371 (t0)
REVERT: E  398 ASP cc_start: 0.6477 (m-30) cc_final: 0.6154 (m-30)
REVERT: E  414 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7953 (mp10)
REVERT: E  433 VAL cc_start: 0.7947 (p) cc_final: 0.7661 (m)
REVERT: E  508 TYR cc_start: 0.7243 (m-80) cc_final: 0.6936 (m-80)
REVERT: E  511 VAL cc_start: 0.8520 (t) cc_final: 0.8128 (m)
  outliers start: 12
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1455
  time to fit residues: 26.4660
Evaluate side-chains
  143 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0670
   chunk 22 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 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 = 0.3756 r_free = 0.3756 target = 0.133439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120977 restraints weight = 7696.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.124881 restraints weight = 3816.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.127389 restraints weight = 2190.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4982  Z= 0.152
  Angle     :  0.531   6.539   6785  Z= 0.277
  Chirality :  0.042   0.164    742
  Planarity :  0.004   0.064    874
  Dihedral  :  4.175  19.740    685
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.78 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.42 (0.33), residues: 619
  helix: -3.44 (0.64), residues: 34
  sheet: -0.26 (0.32), residues: 250
  loop : -1.17 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 110 
 HIS   0.001   0.000   HIS E 519 
 PHE   0.009   0.001   PHE E 377 
 TYR   0.025   0.002   TYR A 129 
 ARG   0.002   0.000   ARG A  98 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7855 (t) cc_final: 0.7364 (p)
REVERT: A  142 MET cc_start: 0.7713 (mtm) cc_final: 0.7395 (mmp)
REVERT: A  186 SER cc_start: 0.8478 (m) cc_final: 0.8199 (p)
REVERT: B    4 MET cc_start: 0.7255 (mmm) cc_final: 0.6982 (tpp)
REVERT: B    9 LYS cc_start: 0.7714 (mttt) cc_final: 0.7486 (mttt)
REVERT: B  107 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8259 (mttp)
REVERT: B  108 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7951 (ttt-90)
REVERT: B  123 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8284 (mp0)
REVERT: B  175 MET cc_start: 0.7333 (ttp) cc_final: 0.7083 (ttt)
REVERT: E  341 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8190 (t)
REVERT: E  360 ASN cc_start: 0.7794 (t0) cc_final: 0.7338 (t0)
REVERT: E  398 ASP cc_start: 0.6524 (m-30) cc_final: 0.6231 (m-30)
REVERT: E  406 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7183 (mt-10)
REVERT: E  414 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7878 (mp10)
REVERT: E  433 VAL cc_start: 0.7936 (p) cc_final: 0.7686 (m)
REVERT: E  508 TYR cc_start: 0.7219 (m-80) cc_final: 0.6973 (m-80)
REVERT: E  511 VAL cc_start: 0.8498 (t) cc_final: 0.8075 (m)
  outliers start: 12
  outliers final: 10
  residues processed: 139
  average time/residue: 0.1375
  time to fit residues: 25.1572
Evaluate side-chains
  143 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 4 optimal weight:    0.0000
   chunk 56 optimal weight:    0.0060
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0980
   chunk 48 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.3200

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 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 = 0.3773 r_free = 0.3773 target = 0.134672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.121987 restraints weight = 7804.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125983 restraints weight = 3869.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.128520 restraints weight = 2215.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4982  Z= 0.141
  Angle     :  0.533   6.489   6785  Z= 0.278
  Chirality :  0.042   0.163    742
  Planarity :  0.004   0.065    874
  Dihedral  :  4.059  17.065    685
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 20.88 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.22 (0.33), residues: 619
  helix: -3.44 (0.63), residues: 34
  sheet: -0.20 (0.33), residues: 242
  loop : -0.94 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 110 
 HIS   0.001   0.000   HIS E 519 
 PHE   0.008   0.001   PHE E 377 
 TYR   0.030   0.001   TYR B 140 
 ARG   0.008   0.000   ARG E 357 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  110 TRP cc_start: 0.7662 (m100) cc_final: 0.7178 (m100)
REVERT: A  115 SER cc_start: 0.7854 (t) cc_final: 0.7344 (p)
REVERT: A  142 MET cc_start: 0.7689 (mtm) cc_final: 0.7369 (mmp)
REVERT: A  186 SER cc_start: 0.8461 (m) cc_final: 0.8152 (p)
REVERT: B    9 LYS cc_start: 0.7708 (mttt) cc_final: 0.7476 (mttt)
REVERT: B  108 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7913 (ttt-90)
REVERT: B  123 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8264 (mp0)
REVERT: E  341 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (t)
REVERT: E  360 ASN cc_start: 0.7800 (t0) cc_final: 0.7332 (t0)
REVERT: E  394 ASN cc_start: 0.8544 (p0) cc_final: 0.8040 (p0)
REVERT: E  406 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7174 (mt-10)
REVERT: E  414 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7849 (mp10)
REVERT: E  508 TYR cc_start: 0.7220 (m-80) cc_final: 0.6960 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 139
  average time/residue: 0.1340
  time to fit residues: 24.7351
Evaluate side-chains
  143 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 501 ASN ** 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 = 0.3750 r_free = 0.3750 target = 0.132907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120511 restraints weight = 7755.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124465 restraints weight = 3838.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.126968 restraints weight = 2197.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4982  Z= 0.196
  Angle     :  0.568   6.606   6785  Z= 0.293
  Chirality :  0.043   0.171    742
  Planarity :  0.004   0.065    874
  Dihedral  :  4.248  21.493    685
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 21.25 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.12 (0.34), residues: 619
  helix: -3.29 (0.67), residues: 34
  sheet: -0.10 (0.33), residues: 249
  loop : -0.92 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 110 
 HIS   0.001   0.001   HIS B 198 
 PHE   0.009   0.001   PHE E 377 
 TYR   0.020   0.001   TYR E 351 
 ARG   0.006   0.000   ARG E 357 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7727 (t) cc_final: 0.7243 (p)
REVERT: A  142 MET cc_start: 0.7653 (mtm) cc_final: 0.7410 (mmp)
REVERT: A  186 SER cc_start: 0.8616 (m) cc_final: 0.8305 (p)
REVERT: B    9 LYS cc_start: 0.7736 (mttt) cc_final: 0.7503 (mttt)
REVERT: B  123 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8271 (mp0)
REVERT: E  341 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (t)
REVERT: E  360 ASN cc_start: 0.7881 (t0) cc_final: 0.7431 (t0)
REVERT: E  394 ASN cc_start: 0.8616 (p0) cc_final: 0.8164 (p0)
REVERT: E  406 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7179 (mt-10)
REVERT: E  414 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7734 (mp10)
REVERT: E  433 VAL cc_start: 0.7988 (p) cc_final: 0.7700 (m)
REVERT: E  508 TYR cc_start: 0.7204 (m-80) cc_final: 0.6941 (m-80)
REVERT: E  511 VAL cc_start: 0.8568 (t) cc_final: 0.8124 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 141
  average time/residue: 0.1393
  time to fit residues: 26.2502
Evaluate side-chains
  145 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 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 = 0.3756 r_free = 0.3756 target = 0.133488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121092 restraints weight = 7778.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.125049 restraints weight = 3854.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127564 restraints weight = 2201.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4982  Z= 0.177
  Angle     :  0.565   6.498   6785  Z= 0.293
  Chirality :  0.043   0.183    742
  Planarity :  0.004   0.065    874
  Dihedral  :  4.395  32.213    685
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 20.88 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.20 (0.34), residues: 619
  helix: -3.47 (0.58), residues: 40
  sheet: -0.10 (0.33), residues: 249
  loop : -0.95 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 110 
 HIS   0.002   0.001   HIS B 198 
 PHE   0.018   0.001   PHE E 377 
 TYR   0.020   0.001   TYR E 351 
 ARG   0.002   0.000   ARG E 357 

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  110 TRP cc_start: 0.7731 (m100) cc_final: 0.7323 (m100)
REVERT: A  115 SER cc_start: 0.7866 (t) cc_final: 0.7355 (p)
REVERT: A  142 MET cc_start: 0.7649 (mtm) cc_final: 0.7388 (mmp)
REVERT: A  186 SER cc_start: 0.8619 (m) cc_final: 0.8304 (p)
REVERT: B    9 LYS cc_start: 0.7702 (mttt) cc_final: 0.7482 (mttt)
REVERT: B  123 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8243 (mp0)
REVERT: E  341 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8205 (t)
REVERT: E  360 ASN cc_start: 0.7854 (t0) cc_final: 0.7396 (t0)
REVERT: E  394 ASN cc_start: 0.8519 (p0) cc_final: 0.8096 (p0)
REVERT: E  414 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7744 (mp10)
REVERT: E  433 VAL cc_start: 0.7931 (p) cc_final: 0.7686 (m)
REVERT: E  508 TYR cc_start: 0.7196 (m-80) cc_final: 0.6897 (m-80)
REVERT: E  511 VAL cc_start: 0.8555 (t) cc_final: 0.8106 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1447
  time to fit residues: 27.5120
Evaluate side-chains
  145 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 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 = 0.3755 r_free = 0.3755 target = 0.133285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121123 restraints weight = 7642.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.124990 restraints weight = 3766.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.127460 restraints weight = 2140.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4982  Z= 0.192
  Angle     :  0.585   8.213   6785  Z= 0.300
  Chirality :  0.044   0.210    742
  Planarity :  0.004   0.064    874
  Dihedral  :  4.464  32.214    685
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.43 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.71 %
    Cis-general     : 0.51 %
    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: -1.19 (0.34), residues: 619
  helix: -3.23 (0.68), residues: 34
  sheet: -0.11 (0.33), residues: 250
  loop : -1.01 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 110 
 HIS   0.001   0.000   HIS A 109 
 PHE   0.014   0.001   PHE E 377 
 TYR   0.020   0.001   TYR E 351 
 ARG   0.002   0.000   ARG A  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1780.01 seconds
wall clock time: 32 minutes 42.77 seconds (1962.77 seconds total)