Starting phenix.real_space_refine
on Wed Jun  4 17:47:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5t_37303/06_2025/8w5t_37303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5t_37303/06_2025/8w5t_37303.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/8w5t_37303/06_2025/8w5t_37303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5t_37303/06_2025/8w5t_37303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5t_37303/06_2025/8w5t_37303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5t_37303/06_2025/8w5t_37303.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=   0.009 sd=   0.086
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      16      5.16       5
     C    2273      2.51       5
     N     614      2.21       5
     O     721      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3624
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 920
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "A"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 969
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 8, 'TRANS': 119}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 957
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 8, 'TRANS': 118}
          Chain breaks: 1
  Time building chain proxies: 2.91, per 1000 atoms: 0.80
  Number of scatterers: 3624
  At special positions: 0
  Unit cell: (80.52, 85.8, 91.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     721      8.00
     N     614      7.00
     C    2273      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 474.1 milliseconds
  

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  886

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      13.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'H' and resid 56 through 59
      removed outlier: 4.299A  pdb=" N   SER H  59 " --> pdb=" O   THR H  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 56 through 59'
    Processing helix  chain 'H' and resid 77 through 79
      No H-bonds generated for 'chain 'H' and resid 77 through 79'
    Processing helix  chain 'A' and resid 101 through 116
      removed outlier: 3.664A  pdb=" N   ARG A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 127
      removed outlier: 3.640A  pdb=" N   GLN A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 45
    Processing helix  chain 'B' and resid 101 through 116
      removed outlier: 3.911A  pdb=" N   ARG B 105 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 128
    Processing sheet with id=AA1, first strand: chain 'L' and resid 22 through 23
      removed outlier: 4.559A  pdb=" N   VAL L  22 " --> pdb=" O   ILE L  77 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 49
      removed outlier: 3.523A  pdb=" N   GLN L  39 " --> pdb=" O   ARG L  47 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LEU L  49 " --> pdb=" O   TRP L  37 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 49
      removed outlier: 3.523A  pdb=" N   GLN L  39 " --> pdb=" O   ARG L  47 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LEU L  49 " --> pdb=" O   TRP L  37 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR L  34 " --> pdb=" O   TRP L  93 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TRP L  93 " --> pdb=" O   TYR L  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 7
      removed outlier: 3.664A  pdb=" N   LEU H  82 " --> pdb=" O   CYS H  25 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASP H  76 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   THR H  72 " --> pdb=" O   GLN H  85 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 62
      removed outlier: 3.502A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   THR H  53 " --> pdb=" O   MET H  37 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   MET H  37 " --> pdb=" O   THR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 6 through 7
      removed outlier: 6.119A  pdb=" N   SER A  34 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 47 through 52
      removed outlier: 4.176A  pdb=" N   VAL A  64 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   VAL B  64 " --> pdb=" O   PHE B  94 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LYS B  63 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 7 through 11
      removed outlier: 3.926A  pdb=" N   ASN B  10 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   GLN B  17 " --> pdb=" O   ASN B  10 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 74
      removed outlier: 7.214A  pdb=" N   THR B  72 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS B  74 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER B  83 " --> pdb=" O   CYS B  74 " (cutoff:3.500A)

    105 hydrogen bonds defined for protein.
    270 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.81

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1179
        1.34 -     1.46: 838
        1.46 -     1.58: 1651
        1.58 -     1.70: 1
        1.70 -     1.82: 24
  Bond restraints: 3693
  Sorted by residual:
  bond pdb=" CB  PRO A  28 "
       pdb=" CG  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.29e+00
  bond pdb=" CG  PRO A  28 "
       pdb=" CD  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.503  1.539 -0.036 3.40e-02 8.65e+02 1.13e+00
  bond pdb=" C   PRO L  97 "
       pdb=" N   PRO L  98 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.025 2.34e-02 1.83e+03 1.10e+00
  bond pdb=" CB  LYS A  60 "
       pdb=" CG  LYS A  60 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CB  MET L  41 "
       pdb=" CG  MET L  41 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.75e-01
  ... (remaining 3688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 4925
        2.80 -     5.61: 87
        5.61 -     8.41: 11
        8.41 -    11.21: 1
       11.21 -    14.01: 1
  Bond angle restraints: 5025
  Sorted by residual:
  angle pdb=" CB  MET L  41 "
        pdb=" CG  MET L  41 "
        pdb=" SD  MET L  41 "
      ideal   model   delta    sigma   weight residual
     112.70  126.71  -14.01 3.00e+00 1.11e-01 2.18e+01
  angle pdb=" C   GLU L  83 "
        pdb=" CA  GLU L  83 "
        pdb=" CB  GLU L  83 "
      ideal   model   delta    sigma   weight residual
     110.42  118.33   -7.91 1.99e+00 2.53e-01 1.58e+01
  angle pdb=" C   TRP H 108 "
        pdb=" N   TYR H 109 "
        pdb=" CA  TYR H 109 "
      ideal   model   delta    sigma   weight residual
     121.54  129.05   -7.51 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" N   TYR H 109 "
        pdb=" CA  TYR H 109 "
        pdb=" CB  TYR H 109 "
      ideal   model   delta    sigma   weight residual
     110.49  117.04   -6.55 1.69e+00 3.50e-01 1.50e+01
  angle pdb=" CA  TYR H 109 "
        pdb=" CB  TYR H 109 "
        pdb=" CG  TYR H 109 "
      ideal   model   delta    sigma   weight residual
     113.90  120.76   -6.86 1.80e+00 3.09e-01 1.45e+01
  ... (remaining 5020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 1941
       15.05 -    30.11: 235
       30.11 -    45.16: 46
       45.16 -    60.21: 5
       60.21 -    75.26: 1
  Dihedral angle restraints: 2228
    sinusoidal: 849
      harmonic: 1379
  Sorted by residual:
  dihedral pdb=" CA  VAL H 105 "
           pdb=" C   VAL H 105 "
           pdb=" N   PRO H 106 "
           pdb=" CA  PRO H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.12   50.88     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  TYR L  96 "
           pdb=" C   TYR L  96 "
           pdb=" N   PRO L  97 "
           pdb=" CA  PRO L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.30  -28.70     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  PRO L  97 "
           pdb=" C   PRO L  97 "
           pdb=" N   PRO L  98 "
           pdb=" CA  PRO L  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.97  -21.03     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 2225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 388
       0.035 -    0.070: 110
       0.070 -    0.105: 56
       0.105 -    0.140: 26
       0.140 -    0.175: 3
  Chirality restraints: 583
  Sorted by residual:
  chirality pdb=" CA  GLU L  20 "
            pdb=" N   GLU L  20 "
            pdb=" C   GLU L  20 "
            pdb=" CB  GLU L  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  GLU L  83 "
            pdb=" N   GLU L  83 "
            pdb=" C   GLU L  83 "
            pdb=" CB  GLU L  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  PRO L  97 "
            pdb=" N   PRO L  97 "
            pdb=" C   PRO L  97 "
            pdb=" CB  PRO L  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.77e-01
  ... (remaining 580 not shown)

  Planarity restraints: 645
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 105 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO H 106 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO H 106 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO H 106 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  27 "   -0.041 5.00e-02 4.00e+02   6.26e-02 6.27e+00
        pdb=" N   PRO B  28 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B  28 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  28 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  96 "   -0.039 5.00e-02 4.00e+02   5.89e-02 5.56e+00
        pdb=" N   PRO L  97 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO L  97 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO L  97 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 642 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 188
        2.71 -     3.26: 3680
        3.26 -     3.80: 5484
        3.80 -     4.35: 6248
        4.35 -     4.90: 10950
  Nonbonded interactions: 26550
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H 111 "
            pdb=" N   VAL H 112 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" OG1 THR A  93 "
            pdb=" OD1 ASP B  91 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" NE1 TRP H  50 "
            pdb=" OG1 THR H  53 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" N   SER L  67 "
            pdb=" OG  SER L  74 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OG  SER L  69 "
            pdb=" O   SER L  72 "
     model   vdw
     2.320 3.040
  ... (remaining 26545 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 131)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.050
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
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      :  0.004   0.091   3693  Z= 0.158
  Angle     :  0.847  14.013   5025  Z= 0.423
  Chirality :  0.046   0.175    583
  Planarity :  0.007   0.080    645
  Dihedral  : 13.149  75.262   1342
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  : 11.85 %
    Favored  : 87.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.65 (0.40), residues: 464
  helix:  0.40 (0.73), residues: 46
  sheet: -0.71 (0.42), residues: 173
  loop : -1.68 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  37 
 PHE   0.009   0.001   PHE H  32 
 TYR   0.015   0.001   TYR H 107 
 ARG   0.010   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24296 (  104)
  hydrogen bonds       : angle       9.58414 (  270)
  covalent geometry    : bond        0.00392 ( 3693)
  covalent geometry    : angle       0.84653 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLN cc_start: 0.8677 (tp40) cc_final: 0.8225 (tp40)
REVERT: H    7 LEU cc_start: 0.9108 (tp) cc_final: 0.8518 (tp)
REVERT: H    8 VAL cc_start: 0.8388 (p) cc_final: 0.8157 (p)
REVERT: H   14 LEU cc_start: 0.9124 (pt) cc_final: 0.8861 (pt)
REVERT: H   21 LEU cc_start: 0.8449 (pt) cc_final: 0.8181 (pt)
REVERT: H   85 GLN cc_start: 0.9333 (tp-100) cc_final: 0.8817 (tp-100)
REVERT: H   93 ASP cc_start: 0.8942 (m-30) cc_final: 0.8670 (m-30)
REVERT: H   96 MET cc_start: 0.8149 (ppp) cc_final: 0.7650 (ppp)
REVERT: H  108 TRP cc_start: 0.8632 (p90) cc_final: 0.8325 (p90)
REVERT: A   14 ASP cc_start: 0.8696 (p0) cc_final: 0.7877 (p0)
REVERT: A   37 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8517 (tm-30)
REVERT: A   44 LEU cc_start: 0.8920 (mm) cc_final: 0.8600 (tt)
REVERT: A   46 LYS cc_start: 0.8760 (mppt) cc_final: 0.8319 (mppt)
REVERT: A   68 ILE cc_start: 0.9056 (tt) cc_final: 0.8651 (tt)
REVERT: A  104 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: A  111 GLU cc_start: 0.9344 (tt0) cc_final: 0.9073 (tt0)
REVERT: A  116 LEU cc_start: 0.9608 (mm) cc_final: 0.9277 (mm)
REVERT: A  123 ASP cc_start: 0.9183 (t0) cc_final: 0.8512 (t0)
REVERT: B    8 LEU cc_start: 0.8496 (mm) cc_final: 0.8288 (mm)
REVERT: B   10 ASN cc_start: 0.8877 (m110) cc_final: 0.8648 (m110)
REVERT: B   14 ASP cc_start: 0.9070 (p0) cc_final: 0.8446 (p0)
REVERT: B   47 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8328 (mtp85)
REVERT: B   60 LYS cc_start: 0.9021 (ptpp) cc_final: 0.8688 (ptpp)
REVERT: B   86 ARG cc_start: 0.8164 (ptt-90) cc_final: 0.7655 (ptt90)
REVERT: B  123 ASP cc_start: 0.8080 (t0) cc_final: 0.7719 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2089
  time to fit residues: 41.3998
Evaluate side-chains
  139 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0470
   chunk 40 optimal weight:   30.0000
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.9482

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

Flipped N/Q/H residues before XYZ refinement:
L  55 ASN
B  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.095362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.076115 restraints weight = 9392.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.079158 restraints weight = 4774.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.081260 restraints weight = 3062.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3693  Z= 0.161
  Angle     :  0.805   8.134   5025  Z= 0.404
  Chirality :  0.048   0.155    583
  Planarity :  0.006   0.073    645
  Dihedral  :  5.268  51.081    515
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.78 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.08 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.54 (0.40), residues: 464
  helix:  0.43 (0.74), residues: 48
  sheet: -0.66 (0.41), residues: 173
  loop : -1.59 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 113 
 PHE   0.006   0.001   PHE A 107 
 TYR   0.027   0.002   TYR H 109 
 ARG   0.008   0.001   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03628 (  104)
  hydrogen bonds       : angle       6.67555 (  270)
  covalent geometry    : bond        0.00380 ( 3693)
  covalent geometry    : angle       0.80546 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: L   80 MET cc_start: 0.8815 (tmm) cc_final: 0.8581 (tmm)
REVERT: H    6 GLN cc_start: 0.8406 (tp40) cc_final: 0.7889 (tp40)
REVERT: H    7 LEU cc_start: 0.8742 (tp) cc_final: 0.8235 (tp)
REVERT: H   21 LEU cc_start: 0.7799 (pt) cc_final: 0.7493 (pt)
REVERT: H   85 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8151 (tp-100)
REVERT: H   96 MET cc_start: 0.7690 (ppp) cc_final: 0.7235 (ppp)
REVERT: H  111 ASP cc_start: 0.8917 (t0) cc_final: 0.7608 (p0)
REVERT: A   37 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8504 (tm-30)
REVERT: A   46 LYS cc_start: 0.8544 (mppt) cc_final: 0.8204 (mppt)
REVERT: A  104 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: A  116 LEU cc_start: 0.9378 (mm) cc_final: 0.9054 (mm)
REVERT: A  123 ASP cc_start: 0.8971 (t0) cc_final: 0.8093 (t0)
REVERT: A  129 ASN cc_start: 0.8135 (m110) cc_final: 0.7528 (m110)
REVERT: B   14 ASP cc_start: 0.8814 (p0) cc_final: 0.8586 (p0)
REVERT: B   34 SER cc_start: 0.8243 (t) cc_final: 0.7812 (p)
REVERT: B   37 GLN cc_start: 0.8530 (tt0) cc_final: 0.8323 (tt0)
REVERT: B   59 ARG cc_start: 0.9009 (ttp-110) cc_final: 0.8686 (ttp-110)
REVERT: B   60 LYS cc_start: 0.8851 (ptpp) cc_final: 0.8494 (ptpp)
REVERT: B   86 ARG cc_start: 0.7682 (ptt-90) cc_final: 0.7381 (ptt90)
REVERT: B  123 ASP cc_start: 0.8048 (t0) cc_final: 0.7658 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 154
  average time/residue: 0.2052
  time to fit residues: 36.6236
Evaluate side-chains
  140 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0010
   chunk 33 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    1.9590

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

Flipped N/Q/H residues before XYZ refinement:
L  55 ASN
B  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.095334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.075906 restraints weight = 9249.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.078903 restraints weight = 4732.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.081033 restraints weight = 3065.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3693  Z= 0.156
  Angle     :  0.781   9.727   5025  Z= 0.395
  Chirality :  0.047   0.168    583
  Planarity :  0.005   0.072    645
  Dihedral  :  5.247  50.775    515
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.13 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 22.03 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.62 (0.40), residues: 464
  helix:  0.34 (0.72), residues: 48
  sheet: -0.94 (0.40), residues: 180
  loop : -1.42 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 113 
 PHE   0.005   0.001   PHE A  96 
 TYR   0.023   0.002   TYR H 109 
 ARG   0.008   0.001   ARG B  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03173 (  104)
  hydrogen bonds       : angle       6.14837 (  270)
  covalent geometry    : bond        0.00367 ( 3693)
  covalent geometry    : angle       0.78099 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: L   80 MET cc_start: 0.8773 (tmm) cc_final: 0.8457 (tmm)
REVERT: H    6 GLN cc_start: 0.8310 (tp40) cc_final: 0.7951 (tp40)
REVERT: H    7 LEU cc_start: 0.8681 (tp) cc_final: 0.8346 (tp)
REVERT: H   42 GLN cc_start: 0.8811 (tt0) cc_final: 0.8264 (tp40)
REVERT: H   85 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8267 (tm-30)
REVERT: H  111 ASP cc_start: 0.9066 (t0) cc_final: 0.7844 (p0)
REVERT: A   37 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8329 (tm-30)
REVERT: A   46 LYS cc_start: 0.8488 (mppt) cc_final: 0.8268 (mppt)
REVERT: A   86 ARG cc_start: 0.8115 (ptt90) cc_final: 0.7228 (ptt90)
REVERT: A   98 GLN cc_start: 0.8974 (pt0) cc_final: 0.7697 (tp40)
REVERT: A  116 LEU cc_start: 0.9347 (mm) cc_final: 0.9084 (mm)
REVERT: A  123 ASP cc_start: 0.8912 (t0) cc_final: 0.8029 (t0)
REVERT: A  129 ASN cc_start: 0.8117 (m110) cc_final: 0.7495 (m110)
REVERT: B   14 ASP cc_start: 0.8857 (p0) cc_final: 0.8532 (p0)
REVERT: B   34 SER cc_start: 0.8031 (t) cc_final: 0.7555 (p)
REVERT: B   54 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8518 (mm-40)
REVERT: B   59 ARG cc_start: 0.9048 (ttp-110) cc_final: 0.8432 (mtm110)
REVERT: B   60 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8539 (ptpp)
REVERT: B  102 ASP cc_start: 0.8649 (p0) cc_final: 0.8437 (p0)
REVERT: B  111 GLU cc_start: 0.9313 (pt0) cc_final: 0.8949 (pp20)
REVERT: B  123 ASP cc_start: 0.8016 (t0) cc_final: 0.7693 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 153
  average time/residue: 0.1963
  time to fit residues: 34.9575
Evaluate side-chains
  148 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
B  10 ASN
** B  27 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 = 0.3508 r_free = 0.3508 target = 0.092432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.072733 restraints weight = 9611.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075721 restraints weight = 4873.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.077827 restraints weight = 3154.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3693  Z= 0.208
  Angle     :  0.801   8.165   5025  Z= 0.406
  Chirality :  0.047   0.166    583
  Planarity :  0.006   0.076    645
  Dihedral  :  5.475  50.904    515
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  : 11.21 %
    Favored  : 87.93 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 23.76 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.65 (0.40), residues: 464
  helix:  0.29 (0.72), residues: 48
  sheet: -0.94 (0.40), residues: 180
  loop : -1.47 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 113 
 PHE   0.008   0.002   PHE A  96 
 TYR   0.024   0.002   TYR H 109 
 ARG   0.010   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  104)
  hydrogen bonds       : angle       6.15322 (  270)
  covalent geometry    : bond        0.00490 ( 3693)
  covalent geometry    : angle       0.80078 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   80 MET cc_start: 0.8800 (tmm) cc_final: 0.8088 (tmm)
REVERT: L   91 GLN cc_start: 0.7952 (tp40) cc_final: 0.7720 (tp40)
REVERT: H    6 GLN cc_start: 0.8314 (tp40) cc_final: 0.7950 (tp40)
REVERT: H    7 LEU cc_start: 0.8698 (tp) cc_final: 0.8356 (tp)
REVERT: H   85 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8125 (tm-30)
REVERT: H  103 PHE cc_start: 0.9106 (m-80) cc_final: 0.8706 (m-10)
REVERT: A    2 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.5228 (mmtt)
REVERT: A   37 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8965 (tm-30)
REVERT: A   46 LYS cc_start: 0.8385 (mppt) cc_final: 0.7969 (mppt)
REVERT: A   74 CYS cc_start: 0.8676 (t) cc_final: 0.8393 (p)
REVERT: A   86 ARG cc_start: 0.8162 (ptt90) cc_final: 0.7360 (ptt90)
REVERT: A   98 GLN cc_start: 0.8983 (pt0) cc_final: 0.7716 (tp40)
REVERT: A  123 ASP cc_start: 0.8835 (t0) cc_final: 0.7963 (t0)
REVERT: A  129 ASN cc_start: 0.8274 (m110) cc_final: 0.7645 (m110)
REVERT: B   11 ILE cc_start: 0.8490 (mm) cc_final: 0.8208 (mm)
REVERT: B   14 ASP cc_start: 0.8815 (p0) cc_final: 0.8548 (p0)
REVERT: B   34 SER cc_start: 0.7989 (t) cc_final: 0.7552 (p)
REVERT: B   54 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8726 (mm-40)
REVERT: B   60 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8566 (ptpp)
REVERT: B   87 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8037 (mm-40)
REVERT: B  102 ASP cc_start: 0.8708 (p0) cc_final: 0.8500 (p0)
  outliers start: 20
  outliers final: 13
  residues processed: 156
  average time/residue: 0.1988
  time to fit residues: 36.1766
Evaluate side-chains
  151 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  125 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 40 optimal weight:   30.0000
   chunk 42 optimal weight:    0.0070
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
B  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.097114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.077132 restraints weight = 9538.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.080285 restraints weight = 4771.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.082484 restraints weight = 3049.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3693  Z= 0.148
  Angle     :  0.831  10.603   5025  Z= 0.414
  Chirality :  0.047   0.186    583
  Planarity :  0.005   0.072    645
  Dihedral  :  5.296  50.176    515
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  1.29 %
    Allowed  :  9.27 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.47 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.40), residues: 464
  helix:  0.25 (0.71), residues: 49
  sheet: -0.93 (0.40), residues: 180
  loop : -1.49 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 PHE   0.007   0.001   PHE H  71 
 TYR   0.022   0.002   TYR H 109 
 ARG   0.009   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02860 (  104)
  hydrogen bonds       : angle       5.94153 (  270)
  covalent geometry    : bond        0.00348 ( 3693)
  covalent geometry    : angle       0.83059 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.9051 (tpp) cc_final: 0.8393 (mmp)
REVERT: L   80 MET cc_start: 0.8814 (tmm) cc_final: 0.7972 (tmm)
REVERT: H    6 GLN cc_start: 0.8101 (tp40) cc_final: 0.7630 (tp40)
REVERT: H    7 LEU cc_start: 0.8573 (tp) cc_final: 0.8217 (tp)
REVERT: H   41 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8139 (ttp80)
REVERT: H   42 GLN cc_start: 0.8675 (tt0) cc_final: 0.8228 (tp40)
REVERT: H   85 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8135 (tm-30)
REVERT: H  111 ASP cc_start: 0.9059 (t0) cc_final: 0.8785 (t70)
REVERT: A   37 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9030 (tm-30)
REVERT: A   46 LYS cc_start: 0.8224 (mppt) cc_final: 0.7908 (mppt)
REVERT: A   86 ARG cc_start: 0.8016 (ptt90) cc_final: 0.7158 (ptt90)
REVERT: A   98 GLN cc_start: 0.8958 (pt0) cc_final: 0.7745 (tp40)
REVERT: A  111 GLU cc_start: 0.9288 (tt0) cc_final: 0.9010 (tt0)
REVERT: A  123 ASP cc_start: 0.8784 (t0) cc_final: 0.7943 (t0)
REVERT: A  129 ASN cc_start: 0.8021 (m110) cc_final: 0.7412 (m110)
REVERT: B   11 ILE cc_start: 0.8381 (mm) cc_final: 0.8152 (mm)
REVERT: B   14 ASP cc_start: 0.8814 (p0) cc_final: 0.8525 (p0)
REVERT: B   34 SER cc_start: 0.7750 (t) cc_final: 0.7237 (p)
REVERT: B   37 GLN cc_start: 0.8465 (tt0) cc_final: 0.7703 (pt0)
REVERT: B   54 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8690 (mm-40)
REVERT: B   59 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8382 (mtm180)
REVERT: B   60 LYS cc_start: 0.8906 (ptpp) cc_final: 0.8515 (ptpp)
REVERT: B   86 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7721 (ptt90)
REVERT: B   87 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7775 (mm-40)
REVERT: B  116 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (mm)
  outliers start: 13
  outliers final: 11
  residues processed: 161
  average time/residue: 0.2107
  time to fit residues: 39.3313
Evaluate side-chains
  157 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 145
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   90 LYS
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  116 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0070
   chunk 13 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.5604

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.098910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.078615 restraints weight = 9495.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.081846 restraints weight = 4699.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.084067 restraints weight = 2986.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3693  Z= 0.159
  Angle     :  0.854  10.463   5025  Z= 0.427
  Chirality :  0.047   0.177    583
  Planarity :  0.005   0.072    645
  Dihedral  :  5.270  49.901    515
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  1.29 %
    Allowed  : 10.13 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 26.24 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.56 (0.40), residues: 464
  helix:  0.31 (0.70), residues: 49
  sheet: -0.83 (0.41), residues: 180
  loop : -1.44 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 PHE   0.007   0.001   PHE H  71 
 TYR   0.022   0.001   TYR H 109 
 ARG   0.008   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03045 (  104)
  hydrogen bonds       : angle       5.89749 (  270)
  covalent geometry    : bond        0.00379 ( 3693)
  covalent geometry    : angle       0.85371 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 TYR cc_start: 0.8697 (m-80) cc_final: 0.7658 (m-10)
REVERT: L   41 MET cc_start: 0.9034 (tpp) cc_final: 0.8424 (mmp)
REVERT: L   80 MET cc_start: 0.8786 (tmm) cc_final: 0.7937 (tmm)
REVERT: L   91 GLN cc_start: 0.7613 (tp40) cc_final: 0.7355 (tp40)
REVERT: H    6 GLN cc_start: 0.8061 (tp40) cc_final: 0.7593 (tp40)
REVERT: H    7 LEU cc_start: 0.8537 (tp) cc_final: 0.8172 (tp)
REVERT: H   85 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8154 (tm-30)
REVERT: H  111 ASP cc_start: 0.9078 (t0) cc_final: 0.8016 (p0)
REVERT: A   37 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8842 (tm-30)
REVERT: A   46 LYS cc_start: 0.8338 (mppt) cc_final: 0.8016 (mppt)
REVERT: A   86 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7180 (ptt90)
REVERT: A   98 GLN cc_start: 0.8918 (pt0) cc_final: 0.7563 (tp40)
REVERT: A  123 ASP cc_start: 0.8770 (t0) cc_final: 0.7868 (t0)
REVERT: A  129 ASN cc_start: 0.8111 (m110) cc_final: 0.7461 (m110)
REVERT: B   11 ILE cc_start: 0.8340 (mm) cc_final: 0.8087 (mm)
REVERT: B   14 ASP cc_start: 0.8800 (p0) cc_final: 0.8513 (p0)
REVERT: B   34 SER cc_start: 0.7698 (t) cc_final: 0.7064 (p)
REVERT: B   37 GLN cc_start: 0.8498 (tt0) cc_final: 0.7765 (pt0)
REVERT: B   54 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8302 (mm-40)
REVERT: B   59 ARG cc_start: 0.9176 (ttp-110) cc_final: 0.8599 (mtm180)
REVERT: B   60 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8528 (ptpp)
REVERT: B   86 ARG cc_start: 0.8055 (ptt90) cc_final: 0.7378 (ptt90)
REVERT: B   87 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7920 (mm-40)
REVERT: B  116 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (mm)
  outliers start: 23
  outliers final: 18
  residues processed: 164
  average time/residue: 0.2035
  time to fit residues: 38.6742
Evaluate side-chains
  166 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   90 LYS
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  116 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.093219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.073661 restraints weight = 9556.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.076698 restraints weight = 4957.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.078796 restraints weight = 3240.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3693  Z= 0.180
  Angle     :  0.862  11.850   5025  Z= 0.435
  Chirality :  0.048   0.188    583
  Planarity :  0.005   0.073    645
  Dihedral  :  5.411  50.702    515
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.56 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 26.98 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.58 (0.40), residues: 464
  helix:  0.28 (0.72), residues: 49
  sheet: -0.92 (0.42), residues: 168
  loop : -1.38 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 113 
 PHE   0.013   0.002   PHE L 101 
 TYR   0.022   0.002   TYR H 109 
 ARG   0.008   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03008 (  104)
  hydrogen bonds       : angle       5.99652 (  270)
  covalent geometry    : bond        0.00429 ( 3693)
  covalent geometry    : angle       0.86171 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.9020 (tpp) cc_final: 0.8422 (mmp)
REVERT: L   80 MET cc_start: 0.8789 (tmm) cc_final: 0.7916 (tmm)
REVERT: L   91 GLN cc_start: 0.7803 (tp40) cc_final: 0.7404 (tp40)
REVERT: H    6 GLN cc_start: 0.8193 (tp40) cc_final: 0.7686 (tp40)
REVERT: H    7 LEU cc_start: 0.8690 (tp) cc_final: 0.8326 (tp)
REVERT: H   85 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8169 (tm-30)
REVERT: H  111 ASP cc_start: 0.9180 (t0) cc_final: 0.8069 (p0)
REVERT: A   37 GLN cc_start: 0.9384 (tm-30) cc_final: 0.8837 (tm-30)
REVERT: A   46 LYS cc_start: 0.8412 (mppt) cc_final: 0.8075 (mppt)
REVERT: A   86 ARG cc_start: 0.8216 (ptt90) cc_final: 0.7422 (ptt90)
REVERT: A   98 GLN cc_start: 0.8948 (pt0) cc_final: 0.7737 (tp40)
REVERT: A  123 ASP cc_start: 0.8873 (t0) cc_final: 0.7959 (t0)
REVERT: A  129 ASN cc_start: 0.8256 (m110) cc_final: 0.7589 (m110)
REVERT: B   14 ASP cc_start: 0.8865 (p0) cc_final: 0.8618 (p0)
REVERT: B   34 SER cc_start: 0.7823 (t) cc_final: 0.7158 (p)
REVERT: B   37 GLN cc_start: 0.8653 (tt0) cc_final: 0.7592 (pt0)
REVERT: B   54 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8528 (mm-40)
REVERT: B   60 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8675 (ptpp)
REVERT: B   87 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7927 (mm-40)
REVERT: B  116 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8882 (mm)
  outliers start: 22
  outliers final: 16
  residues processed: 156
  average time/residue: 0.1971
  time to fit residues: 35.8363
Evaluate side-chains
  156 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   90 LYS
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  116 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0370
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   overall best weight:    2.5864

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.091535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.071738 restraints weight = 9826.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.074843 restraints weight = 5060.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076968 restraints weight = 3295.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3693  Z= 0.185
  Angle     :  0.885  10.969   5025  Z= 0.444
  Chirality :  0.049   0.196    583
  Planarity :  0.005   0.073    645
  Dihedral  :  5.451  51.156    515
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.99 %
    Favored  : 87.93 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 27.23 %
    Favored  : 67.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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 (0.40), residues: 464
  helix:  0.27 (0.72), residues: 49
  sheet: -0.83 (0.42), residues: 170
  loop : -1.48 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 113 
 PHE   0.012   0.002   PHE L 101 
 TYR   0.022   0.002   TYR H 109 
 ARG   0.010   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03067 (  104)
  hydrogen bonds       : angle       6.03458 (  270)
  covalent geometry    : bond        0.00441 ( 3693)
  covalent geometry    : angle       0.88521 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.8920 (tpp) cc_final: 0.8332 (mmp)
REVERT: L   80 MET cc_start: 0.8800 (tmm) cc_final: 0.7936 (tmm)
REVERT: L   91 GLN cc_start: 0.7814 (tp40) cc_final: 0.7389 (tp40)
REVERT: H    6 GLN cc_start: 0.8169 (tp40) cc_final: 0.7633 (tp40)
REVERT: H    7 LEU cc_start: 0.8643 (tp) cc_final: 0.8293 (tp)
REVERT: H   42 GLN cc_start: 0.9004 (tt0) cc_final: 0.8465 (tp40)
REVERT: H   85 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8144 (tm-30)
REVERT: H  103 PHE cc_start: 0.9124 (m-80) cc_final: 0.8584 (m-10)
REVERT: H  111 ASP cc_start: 0.9182 (t0) cc_final: 0.8033 (p0)
REVERT: A   37 GLN cc_start: 0.9335 (tm-30) cc_final: 0.8788 (tm-30)
REVERT: A   46 LYS cc_start: 0.8374 (mppt) cc_final: 0.7989 (mppt)
REVERT: A   86 ARG cc_start: 0.8108 (ptt90) cc_final: 0.7319 (ptt90)
REVERT: A   98 GLN cc_start: 0.8931 (pt0) cc_final: 0.7721 (tp40)
REVERT: A  123 ASP cc_start: 0.8820 (t0) cc_final: 0.7953 (t0)
REVERT: A  129 ASN cc_start: 0.8196 (m110) cc_final: 0.7541 (m110)
REVERT: B   10 ASN cc_start: 0.8593 (m-40) cc_final: 0.8368 (t0)
REVERT: B   11 ILE cc_start: 0.8337 (mm) cc_final: 0.8074 (mm)
REVERT: B   14 ASP cc_start: 0.8821 (p0) cc_final: 0.8500 (p0)
REVERT: B   34 SER cc_start: 0.7691 (t) cc_final: 0.7034 (p)
REVERT: B   37 GLN cc_start: 0.8619 (tt0) cc_final: 0.7728 (pt0)
REVERT: B   54 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8506 (mm-40)
REVERT: B   59 ARG cc_start: 0.9128 (ttp-110) cc_final: 0.8452 (mtm180)
REVERT: B   60 LYS cc_start: 0.8975 (ptpp) cc_final: 0.8589 (ptpp)
REVERT: B   86 ARG cc_start: 0.8178 (ptt90) cc_final: 0.7437 (ptt90)
REVERT: B   87 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7989 (mm-40)
  outliers start: 23
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2015
  time to fit residues: 36.5478
Evaluate side-chains
  159 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   90 LYS
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.093017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.073349 restraints weight = 9398.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.076437 restraints weight = 4712.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.078494 restraints weight = 3009.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3693  Z= 0.216
  Angle     :  0.914  10.443   5025  Z= 0.458
  Chirality :  0.049   0.212    583
  Planarity :  0.005   0.079    645
  Dihedral  :  5.703  51.900    515
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 11.21 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 28.22 %
    Favored  : 66.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.57 (0.40), residues: 464
  helix:  0.21 (0.72), residues: 49
  sheet: -0.67 (0.44), residues: 164
  loop : -1.55 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 113 
 PHE   0.011   0.002   PHE L 101 
 TYR   0.023   0.002   TYR H 109 
 ARG   0.010   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  104)
  hydrogen bonds       : angle       6.17153 (  270)
  covalent geometry    : bond        0.00508 ( 3693)
  covalent geometry    : angle       0.91362 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.8885 (tpp) cc_final: 0.8325 (mmp)
REVERT: L   80 MET cc_start: 0.8831 (tmm) cc_final: 0.8009 (tmm)
REVERT: L   91 GLN cc_start: 0.7815 (tp40) cc_final: 0.7436 (tp40)
REVERT: H    6 GLN cc_start: 0.8283 (tp40) cc_final: 0.7684 (tp40)
REVERT: H    7 LEU cc_start: 0.8717 (tp) cc_final: 0.8388 (tp)
REVERT: H   85 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8038 (tm-30)
REVERT: H  103 PHE cc_start: 0.9106 (m-80) cc_final: 0.8624 (m-10)
REVERT: H  107 TYR cc_start: 0.8144 (p90) cc_final: 0.7916 (p90)
REVERT: A   69 GLN cc_start: 0.6981 (pp30) cc_final: 0.6125 (pp30)
REVERT: A   86 ARG cc_start: 0.8088 (ptt90) cc_final: 0.7291 (ptt90)
REVERT: A   98 GLN cc_start: 0.8943 (pt0) cc_final: 0.7751 (tp40)
REVERT: A  116 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8904 (mm)
REVERT: A  123 ASP cc_start: 0.8779 (t0) cc_final: 0.8170 (t0)
REVERT: A  129 ASN cc_start: 0.8189 (m110) cc_final: 0.7703 (m-40)
REVERT: B   11 ILE cc_start: 0.8427 (mm) cc_final: 0.8173 (mm)
REVERT: B   14 ASP cc_start: 0.8813 (p0) cc_final: 0.8495 (p0)
REVERT: B   34 SER cc_start: 0.7704 (t) cc_final: 0.7077 (p)
REVERT: B   37 GLN cc_start: 0.8616 (tt0) cc_final: 0.7608 (pt0)
REVERT: B   54 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8676 (mm-40)
REVERT: B   60 LYS cc_start: 0.8973 (ptpp) cc_final: 0.8612 (ptpp)
REVERT: B   87 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8135 (mm-40)
REVERT: B  111 GLU cc_start: 0.9368 (pt0) cc_final: 0.8921 (pp20)
  outliers start: 22
  outliers final: 19
  residues processed: 153
  average time/residue: 0.1921
  time to fit residues: 34.3741
Evaluate side-chains
  156 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   48 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   90 LYS
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.093789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.074182 restraints weight = 9749.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.077396 restraints weight = 5015.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.079617 restraints weight = 3237.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3693  Z= 0.164
  Angle     :  0.934  10.433   5025  Z= 0.464
  Chirality :  0.050   0.213    583
  Planarity :  0.005   0.072    645
  Dihedral  :  5.472  50.197    515
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.78 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 28.96 %
    Favored  : 66.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.59 (0.40), residues: 464
  helix:  0.14 (0.71), residues: 49
  sheet: -0.58 (0.45), residues: 157
  loop : -1.62 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  50 
 PHE   0.010   0.001   PHE L 101 
 TYR   0.020   0.002   TYR H  83 
 ARG   0.012   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02842 (  104)
  hydrogen bonds       : angle       6.08745 (  270)
  covalent geometry    : bond        0.00395 ( 3693)
  covalent geometry    : angle       0.93405 ( 5025)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.8924 (tpp) cc_final: 0.8258 (mmp)
REVERT: L   80 MET cc_start: 0.8839 (tmm) cc_final: 0.7947 (tmm)
REVERT: L   91 GLN cc_start: 0.7993 (tp40) cc_final: 0.7620 (tp40)
REVERT: H    6 GLN cc_start: 0.8039 (tp40) cc_final: 0.7835 (tp40)
REVERT: H   42 GLN cc_start: 0.8991 (tt0) cc_final: 0.8496 (tp40)
REVERT: H   85 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8121 (tm-30)
REVERT: A   37 GLN cc_start: 0.9378 (tm-30) cc_final: 0.9043 (tm-30)
REVERT: A   86 ARG cc_start: 0.8068 (ptt90) cc_final: 0.7251 (ptt90)
REVERT: A   98 GLN cc_start: 0.8905 (pt0) cc_final: 0.7451 (tp40)
REVERT: A  123 ASP cc_start: 0.8815 (t0) cc_final: 0.7927 (t0)
REVERT: A  129 ASN cc_start: 0.8152 (m110) cc_final: 0.7491 (m110)
REVERT: B   11 ILE cc_start: 0.8750 (mm) cc_final: 0.8536 (mm)
REVERT: B   14 ASP cc_start: 0.8822 (p0) cc_final: 0.8571 (p0)
REVERT: B   34 SER cc_start: 0.7702 (t) cc_final: 0.7077 (p)
REVERT: B   37 GLN cc_start: 0.8257 (tt0) cc_final: 0.7304 (pt0)
REVERT: B   54 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8564 (mm-40)
REVERT: B   59 ARG cc_start: 0.9134 (ttp-110) cc_final: 0.8865 (ttp-110)
REVERT: B   60 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8742 (ptpp)
REVERT: B   86 ARG cc_start: 0.8094 (ptt90) cc_final: 0.7335 (ptt90)
REVERT: B   87 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7972 (mm-40)
REVERT: B  111 GLU cc_start: 0.9190 (pt0) cc_final: 0.8808 (pp20)
REVERT: B  116 LEU cc_start: 0.8990 (mm) cc_final: 0.8757 (mm)
  outliers start: 19
  outliers final: 15
  residues processed: 154
  average time/residue: 0.2025
  time to fit residues: 36.6336
Evaluate side-chains
  157 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   48 LEU
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0470
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:   20.0000
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    2.0086

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

Flipped N/Q/H residues before XYZ refinement:
B  10 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.092570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.073056 restraints weight = 9651.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076138 restraints weight = 5022.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.078249 restraints weight = 3284.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3693  Z= 0.178
  Angle     :  0.939  11.491   5025  Z= 0.469
  Chirality :  0.049   0.196    583
  Planarity :  0.006   0.074    645
  Dihedral  :  5.498  50.240    515
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.78 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 30.94 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -1.51 (0.40), residues: 464
  helix:  0.25 (0.72), residues: 49
  sheet: -0.54 (0.45), residues: 157
  loop : -1.57 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  50 
 PHE   0.009   0.001   PHE L 101 
 TYR   0.021   0.002   TYR H 109 
 ARG   0.012   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  104)
  hydrogen bonds       : angle       6.00352 (  270)
  covalent geometry    : bond        0.00430 ( 3693)
  covalent geometry    : angle       0.93938 ( 5025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1708.18 seconds
wall clock time: 30 minutes 14.13 seconds (1814.13 seconds total)