Starting phenix.real_space_refine
on Fri Aug 22 13:58:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5t_37303/08_2025/8w5t_37303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5t_37303/08_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_37303/08_2025/8w5t_37303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5t_37303/08_2025/8w5t_37303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5t_37303/08_2025/8w5t_37303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5t_37303/08_2025/8w5t_37303.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.21, per 1000 atoms: 0.33
  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: 0.25
  Conformation dependent library (CDL) restraints added in 124.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.13
  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: 0.45

  Time building geometry restraints manager: 0.36 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:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.560
-------------------------------------------------------------------------------
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 : 12.76
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (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
 ARG   0.010   0.001   ARG L  79 
 TYR   0.015   0.001   TYR H 107 
 PHE   0.009   0.001   PHE H  32 
 TRP   0.021   0.002   TRP L  37 

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

*********************** 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  : 0.182 
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: 0.0868
  time to fit residues: 17.3271
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  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
L  55 ASN
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.097000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 19)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.077954 restraints weight = 9501.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.080991 restraints weight = 4829.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.083122 restraints weight = 3110.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.084584 restraints weight = 2283.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.085660 restraints weight = 1840.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3693  Z= 0.145
  Angle     :  0.817   8.097   5025  Z= 0.408
  Chirality :  0.049   0.156    583
  Planarity :  0.006   0.074    645
  Dihedral  :  5.191  50.526    515
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.34 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.33 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.40), residues: 464
  helix:  0.44 (0.73), residues: 48
  sheet: -0.70 (0.41), residues: 173
  loop : -1.61 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  47 
 TYR   0.024   0.002   TYR H 109 
 PHE   0.006   0.001   PHE A 107 
 TRP   0.014   0.001   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3693)
  covalent geometry    : angle       0.81719 ( 5025)
  hydrogen bonds       : bond        0.03622 (  104)
  hydrogen bonds       : angle       6.84570 (  270)

*********************** 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
  163 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   35 MET cc_start: 0.5925 (tpt) cc_final: 0.5689 (tpt)
REVERT: L   80 MET cc_start: 0.8772 (tmm) cc_final: 0.8530 (tmm)
REVERT: H    6 GLN cc_start: 0.8451 (tp40) cc_final: 0.7948 (tp40)
REVERT: H    7 LEU cc_start: 0.8768 (tp) cc_final: 0.8228 (tp)
REVERT: H   21 LEU cc_start: 0.7732 (pt) cc_final: 0.7440 (pt)
REVERT: H   22 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8092 (ttmm)
REVERT: H   85 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8290 (tp-100)
REVERT: H   92 GLU cc_start: 0.9273 (tp30) cc_final: 0.9071 (tp30)
REVERT: H   96 MET cc_start: 0.7881 (ppp) cc_final: 0.7476 (ppp)
REVERT: H  111 ASP cc_start: 0.8949 (t0) cc_final: 0.8519 (t70)
REVERT: A   37 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8982 (tm-30)
REVERT: A   46 LYS cc_start: 0.8487 (mppt) cc_final: 0.8209 (mppt)
REVERT: A  104 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7934 (mt-10)
REVERT: A  111 GLU cc_start: 0.9302 (tt0) cc_final: 0.9002 (tt0)
REVERT: A  116 LEU cc_start: 0.9390 (mm) cc_final: 0.9068 (mm)
REVERT: A  123 ASP cc_start: 0.9006 (t0) cc_final: 0.8398 (t0)
REVERT: B   14 ASP cc_start: 0.8850 (p0) cc_final: 0.8230 (p0)
REVERT: B   34 SER cc_start: 0.8249 (t) cc_final: 0.7851 (p)
REVERT: B   59 ARG cc_start: 0.9022 (ttp-110) cc_final: 0.8693 (ttp-110)
REVERT: B   60 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8545 (ptpp)
REVERT: B   86 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.7410 (ptt90)
REVERT: B  123 ASP cc_start: 0.8082 (t0) cc_final: 0.7649 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 155
  average time/residue: 0.0851
  time to fit residues: 15.3488
Evaluate side-chains
  143 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain H residue   68 LYS
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 31 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.095624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.076188 restraints weight = 9335.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.079249 restraints weight = 4724.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.081408 restraints weight = 3032.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.082919 restraints weight = 2231.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.083973 restraints weight = 1796.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2641

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= 0.152
  Angle     :  0.788  10.047   5025  Z= 0.397
  Chirality :  0.046   0.156    583
  Planarity :  0.005   0.074    645
  Dihedral  :  5.196  50.094    515
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.34 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.29 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.40), residues: 464
  helix:  0.42 (0.73), residues: 48
  sheet: -0.85 (0.41), residues: 173
  loop : -1.43 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  79 
 TYR   0.023   0.002   TYR H 109 
 PHE   0.006   0.001   PHE A  96 
 TRP   0.014   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3693)
  covalent geometry    : angle       0.78848 ( 5025)
  hydrogen bonds       : bond        0.03181 (  104)
  hydrogen bonds       : angle       6.22856 (  270)

*********************** 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: 14
    poor density    : 148
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   35 MET cc_start: 0.6524 (tpt) cc_final: 0.6303 (tpt)
REVERT: L   80 MET cc_start: 0.8743 (tmm) cc_final: 0.8393 (tmm)
REVERT: L   91 GLN cc_start: 0.7549 (tt0) cc_final: 0.7329 (tp40)
REVERT: L   96 TYR cc_start: 0.8030 (p90) cc_final: 0.7638 (p90)
REVERT: H    6 GLN cc_start: 0.8285 (tp40) cc_final: 0.7936 (tp40)
REVERT: H    7 LEU cc_start: 0.8680 (tp) cc_final: 0.8351 (tp)
REVERT: H   85 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8285 (tm-30)
REVERT: H   96 MET cc_start: 0.7518 (ppp) cc_final: 0.7260 (ppp)
REVERT: H  111 ASP cc_start: 0.9021 (t0) cc_final: 0.7776 (p0)
REVERT: A   14 ASP cc_start: 0.8360 (p0) cc_final: 0.8083 (p0)
REVERT: A   37 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: A   46 LYS cc_start: 0.8422 (mppt) cc_final: 0.8166 (mppt)
REVERT: A   98 GLN cc_start: 0.8966 (pt0) cc_final: 0.7681 (tp40)
REVERT: A  116 LEU cc_start: 0.9202 (mm) cc_final: 0.8969 (mm)
REVERT: A  123 ASP cc_start: 0.8925 (t0) cc_final: 0.8027 (t0)
REVERT: A  129 ASN cc_start: 0.8086 (m110) cc_final: 0.7460 (m110)
REVERT: B   14 ASP cc_start: 0.8675 (p0) cc_final: 0.8217 (p0)
REVERT: B   34 SER cc_start: 0.7987 (t) cc_final: 0.7547 (p)
REVERT: B   60 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8540 (ptpp)
REVERT: B  102 ASP cc_start: 0.8717 (p0) cc_final: 0.8513 (p0)
REVERT: B  123 ASP cc_start: 0.7981 (t0) cc_final: 0.7624 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 155
  average time/residue: 0.0872
  time to fit residues: 15.6635
Evaluate side-chains
  144 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 136
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  102 THR
Chi-restraints excluded: chain H residue  109 TYR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    0.1980
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0980
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.097437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.077712 restraints weight = 9522.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.080862 restraints weight = 4812.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.083123 restraints weight = 3098.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.084603 restraints weight = 2280.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.085782 restraints weight = 1845.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3693  Z= 0.136
  Angle     :  0.790   8.236   5025  Z= 0.393
  Chirality :  0.046   0.159    583
  Planarity :  0.005   0.074    645
  Dihedral  :  5.063  48.683    515
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  1.29 %
    Allowed  :  9.27 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.03 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.40), residues: 464
  helix:  0.44 (0.71), residues: 48
  sheet: -0.89 (0.40), residues: 180
  loop : -1.45 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 109 
 TYR   0.022   0.002   TYR H 109 
 PHE   0.009   0.001   PHE A 107 
 TRP   0.011   0.001   TRP H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3693)
  covalent geometry    : angle       0.79015 ( 5025)
  hydrogen bonds       : bond        0.02886 (  104)
  hydrogen bonds       : angle       6.12783 (  270)

*********************** 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
  159 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   35 MET cc_start: 0.6610 (tpt) cc_final: 0.6375 (tpt)
REVERT: L   80 MET cc_start: 0.8779 (tmm) cc_final: 0.8428 (tmm)
REVERT: L   96 TYR cc_start: 0.7969 (p90) cc_final: 0.7588 (p90)
REVERT: H    6 GLN cc_start: 0.8127 (tp40) cc_final: 0.7793 (tp40)
REVERT: H    7 LEU cc_start: 0.8566 (tp) cc_final: 0.8262 (tp)
REVERT: H   22 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7980 (ttmm)
REVERT: H   42 GLN cc_start: 0.8708 (tt0) cc_final: 0.8195 (tp40)
REVERT: H   49 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7454 (mt-10)
REVERT: H   85 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8050 (tm-30)
REVERT: H  111 ASP cc_start: 0.8959 (t0) cc_final: 0.7723 (p0)
REVERT: A   14 ASP cc_start: 0.8244 (p0) cc_final: 0.7875 (p0)
REVERT: A   46 LYS cc_start: 0.8220 (mppt) cc_final: 0.7921 (mppt)
REVERT: A   98 GLN cc_start: 0.8949 (pt0) cc_final: 0.7701 (tp40)
REVERT: A  104 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7877 (pt0)
REVERT: A  123 ASP cc_start: 0.8851 (t0) cc_final: 0.7978 (t0)
REVERT: A  129 ASN cc_start: 0.7926 (m110) cc_final: 0.7291 (m110)
REVERT: B   14 ASP cc_start: 0.8659 (p0) cc_final: 0.8152 (p0)
REVERT: B   34 SER cc_start: 0.7920 (t) cc_final: 0.7504 (p)
REVERT: B   54 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8676 (mm-40)
REVERT: B   59 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8350 (mtm180)
REVERT: B   60 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8516 (ptpp)
REVERT: B   86 ARG cc_start: 0.8437 (ptt90) cc_final: 0.7849 (ptt90)
REVERT: B  102 ASP cc_start: 0.8617 (p0) cc_final: 0.8404 (p0)
REVERT: B  111 GLU cc_start: 0.9169 (pt0) cc_final: 0.8884 (pp20)
REVERT: B  123 ASP cc_start: 0.7996 (t0) cc_final: 0.7658 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 154
  average time/residue: 0.0876
  time to fit residues: 15.6628
Evaluate side-chains
  143 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 H residue   68 LYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0070
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    2.8006

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.094902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.075208 restraints weight = 9310.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.078203 restraints weight = 4710.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.080332 restraints weight = 3041.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.081731 restraints weight = 2256.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.082788 restraints weight = 1841.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3225

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= 0.188
  Angle     :  0.803  10.632   5025  Z= 0.407
  Chirality :  0.046   0.162    583
  Planarity :  0.005   0.074    645
  Dihedral  :  5.255  50.357    515
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 10.78 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 23.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.41), residues: 464
  helix:  0.58 (0.73), residues: 48
  sheet: -0.90 (0.41), residues: 178
  loop : -1.32 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 109 
 TYR   0.024   0.002   TYR H 109 
 PHE   0.011   0.002   PHE L 101 
 TRP   0.018   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3693)
  covalent geometry    : angle       0.80299 ( 5025)
  hydrogen bonds       : bond        0.03088 (  104)
  hydrogen bonds       : angle       6.00306 (  270)

*********************** 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
  163 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   35 MET cc_start: 0.6914 (tpt) cc_final: 0.6707 (tpt)
REVERT: L   80 MET cc_start: 0.8738 (tmm) cc_final: 0.7978 (tmm)
REVERT: L   91 GLN cc_start: 0.7464 (tp40) cc_final: 0.7009 (tp40)
REVERT: H    6 GLN cc_start: 0.8249 (tp40) cc_final: 0.7782 (tp40)
REVERT: H    7 LEU cc_start: 0.8725 (tp) cc_final: 0.8347 (tp)
REVERT: H   42 GLN cc_start: 0.8729 (tt0) cc_final: 0.8268 (tp40)
REVERT: H   49 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7703 (mt-10)
REVERT: H   85 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8110 (tm-30)
REVERT: H   98 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7359 (m-10)
REVERT: H  111 ASP cc_start: 0.9159 (t0) cc_final: 0.8919 (t70)
REVERT: A   14 ASP cc_start: 0.8197 (p0) cc_final: 0.7949 (p0)
REVERT: A   46 LYS cc_start: 0.8367 (mppt) cc_final: 0.8038 (mppt)
REVERT: A   86 ARG cc_start: 0.8220 (ptt90) cc_final: 0.7334 (ptt90)
REVERT: A   98 GLN cc_start: 0.8963 (pt0) cc_final: 0.7734 (tp40)
REVERT: A  123 ASP cc_start: 0.8710 (t0) cc_final: 0.7831 (t0)
REVERT: A  129 ASN cc_start: 0.8079 (m110) cc_final: 0.7433 (m110)
REVERT: B   10 ASN cc_start: 0.8648 (m-40) cc_final: 0.8399 (t0)
REVERT: B   14 ASP cc_start: 0.8636 (p0) cc_final: 0.8140 (p0)
REVERT: B   34 SER cc_start: 0.8081 (t) cc_final: 0.7628 (p)
REVERT: B   37 GLN cc_start: 0.8579 (tt0) cc_final: 0.7683 (pt0)
REVERT: B   54 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8478 (mm-40)
REVERT: B   59 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8398 (mtm180)
REVERT: B   60 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8582 (ptpp)
REVERT: B   86 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8152 (ptt90)
REVERT: B   99 TYR cc_start: 0.9358 (m-80) cc_final: 0.9132 (m-80)
REVERT: B  102 ASP cc_start: 0.8777 (p0) cc_final: 0.8557 (p0)
REVERT: B  111 GLU cc_start: 0.9208 (pt0) cc_final: 0.8840 (pp20)
REVERT: B  123 ASP cc_start: 0.8074 (t0) cc_final: 0.7746 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 154
  average time/residue: 0.0852
  time to fit residues: 15.3843
Evaluate side-chains
  148 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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 L residue  107 LEU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   79 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   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0370
   chunk 38 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.7460

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.096627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.076223 restraints weight = 9499.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.079460 restraints weight = 4839.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.081782 restraints weight = 3119.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.083310 restraints weight = 2299.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.084486 restraints weight = 1865.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3486

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= 0.150
  Angle     :  0.861  14.574   5025  Z= 0.425
  Chirality :  0.047   0.157    583
  Planarity :  0.005   0.073    645
  Dihedral  :  5.099  48.496    515
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  1.29 %
    Allowed  :  9.48 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.49 %
    Favored  : 69.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.40), residues: 464
  helix:  0.82 (0.72), residues: 48
  sheet: -0.80 (0.41), residues: 180
  loop : -1.39 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  79 
 TYR   0.022   0.002   TYR H 109 
 PHE   0.007   0.001   PHE H 110 
 TRP   0.012   0.002   TRP H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3693)
  covalent geometry    : angle       0.86115 ( 5025)
  hydrogen bonds       : bond        0.02669 (  104)
  hydrogen bonds       : angle       5.95742 (  270)

*********************** 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
  160 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   35 MET cc_start: 0.6732 (tpt) cc_final: 0.6485 (tpt)
REVERT: L   80 MET cc_start: 0.8861 (tmm) cc_final: 0.8145 (tmm)
REVERT: L   91 GLN cc_start: 0.6980 (tp40) cc_final: 0.6744 (tp40)
REVERT: L   96 TYR cc_start: 0.7988 (p90) cc_final: 0.7661 (p90)
REVERT: H    6 GLN cc_start: 0.7986 (tp40) cc_final: 0.7537 (tp40)
REVERT: H    7 LEU cc_start: 0.8525 (tp) cc_final: 0.8192 (tp)
REVERT: H   42 GLN cc_start: 0.8611 (tt0) cc_final: 0.8265 (tp40)
REVERT: H   49 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7452 (mt-10)
REVERT: H   85 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8100 (tm-30)
REVERT: H  111 ASP cc_start: 0.8964 (t0) cc_final: 0.7696 (p0)
REVERT: A   14 ASP cc_start: 0.8423 (p0) cc_final: 0.7988 (p0)
REVERT: A   46 LYS cc_start: 0.8234 (mppt) cc_final: 0.7908 (mppt)
REVERT: A   86 ARG cc_start: 0.8093 (ptt90) cc_final: 0.7286 (ptt90)
REVERT: A   98 GLN cc_start: 0.8979 (pt0) cc_final: 0.7772 (tp40)
REVERT: A  123 ASP cc_start: 0.8620 (t0) cc_final: 0.8090 (t0)
REVERT: A  129 ASN cc_start: 0.7809 (m110) cc_final: 0.7403 (m110)
REVERT: B   11 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8285 (mm)
REVERT: B   14 ASP cc_start: 0.8586 (p0) cc_final: 0.8037 (p0)
REVERT: B   34 SER cc_start: 0.7828 (t) cc_final: 0.7338 (p)
REVERT: B   37 GLN cc_start: 0.8434 (tt0) cc_final: 0.7719 (pt0)
REVERT: B   54 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8251 (mm-40)
REVERT: B   59 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8322 (mtm180)
REVERT: B   60 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8500 (ptpp)
REVERT: B   86 ARG cc_start: 0.8392 (ptt90) cc_final: 0.8048 (ptt90)
REVERT: B   87 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7778 (mm-40)
REVERT: B   99 TYR cc_start: 0.9322 (m-80) cc_final: 0.9066 (m-80)
REVERT: B  102 ASP cc_start: 0.8583 (p0) cc_final: 0.8321 (p0)
REVERT: B  111 GLU cc_start: 0.9117 (pt0) cc_final: 0.8799 (pp20)
REVERT: B  116 LEU cc_start: 0.8966 (mm) cc_final: 0.8745 (mm)
REVERT: B  123 ASP cc_start: 0.7962 (t0) cc_final: 0.7653 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 154
  average time/residue: 0.0818
  time to fit residues: 14.7467
Evaluate side-chains
  149 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   98 TYR
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 B residue   11 ILE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0570
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 40 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.3102

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.095760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.075515 restraints weight = 9862.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.078826 restraints weight = 4994.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.081121 restraints weight = 3199.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.082713 restraints weight = 2357.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.083851 restraints weight = 1898.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3693  Z= 0.151
  Angle     :  0.839   9.823   5025  Z= 0.421
  Chirality :  0.046   0.184    583
  Planarity :  0.005   0.074    645
  Dihedral  :  5.105  48.200    515
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  1.29 %
    Allowed  :  9.91 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 27.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.41), residues: 464
  helix:  0.91 (0.73), residues: 48
  sheet: -0.71 (0.42), residues: 180
  loop : -1.34 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  79 
 TYR   0.022   0.002   TYR H 109 
 PHE   0.006   0.001   PHE L 101 
 TRP   0.011   0.001   TRP H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3693)
  covalent geometry    : angle       0.83904 ( 5025)
  hydrogen bonds       : bond        0.02670 (  104)
  hydrogen bonds       : angle       5.85405 (  270)

*********************** 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
  163 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   80 MET cc_start: 0.8792 (tmm) cc_final: 0.8023 (tmm)
REVERT: L   89 TYR cc_start: 0.8334 (m-10) cc_final: 0.8092 (m-10)
REVERT: H    6 GLN cc_start: 0.7966 (tp40) cc_final: 0.7619 (tp-100)
REVERT: H   49 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: H   85 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8090 (tm-30)
REVERT: H  111 ASP cc_start: 0.9024 (t0) cc_final: 0.8003 (p0)
REVERT: A   14 ASP cc_start: 0.8392 (p0) cc_final: 0.8093 (p0)
REVERT: A   46 LYS cc_start: 0.8224 (mppt) cc_final: 0.7931 (mppt)
REVERT: A   86 ARG cc_start: 0.8104 (ptt90) cc_final: 0.7301 (ptt90)
REVERT: A   98 GLN cc_start: 0.8983 (pt0) cc_final: 0.7779 (tp40)
REVERT: A  104 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7740 (pt0)
REVERT: A  111 GLU cc_start: 0.9326 (tt0) cc_final: 0.9053 (tt0)
REVERT: A  123 ASP cc_start: 0.8607 (t0) cc_final: 0.8070 (t0)
REVERT: A  129 ASN cc_start: 0.7821 (m110) cc_final: 0.7410 (m110)
REVERT: B   11 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8240 (mm)
REVERT: B   14 ASP cc_start: 0.8595 (p0) cc_final: 0.7994 (p0)
REVERT: B   34 SER cc_start: 0.7606 (t) cc_final: 0.6948 (p)
REVERT: B   37 GLN cc_start: 0.8495 (tt0) cc_final: 0.7727 (pt0)
REVERT: B   54 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8314 (mm-40)
REVERT: B   59 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8350 (mtm180)
REVERT: B   60 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8552 (ptpp)
REVERT: B   86 ARG cc_start: 0.8465 (ptt90) cc_final: 0.7677 (ptt90)
REVERT: B   87 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7686 (mm-40)
REVERT: B   99 TYR cc_start: 0.9330 (m-80) cc_final: 0.9076 (m-80)
REVERT: B  102 ASP cc_start: 0.8546 (p0) cc_final: 0.8274 (p0)
REVERT: B  111 GLU cc_start: 0.9160 (pt0) cc_final: 0.8839 (pp20)
REVERT: B  123 ASP cc_start: 0.7983 (t0) cc_final: 0.7706 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 156
  average time/residue: 0.0957
  time to fit residues: 17.3379
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain H residue   54 ILE
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   22 ASN
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:   30.0000
   chunk 14 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  10 ASN
B  22 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.071495 restraints weight = 9689.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.074429 restraints weight = 4871.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.076448 restraints weight = 3169.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.077847 restraints weight = 2369.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.078698 restraints weight = 1936.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   3693  Z= 0.291
  Angle     :  0.933   9.920   5025  Z= 0.472
  Chirality :  0.050   0.197    583
  Planarity :  0.006   0.081    645
  Dihedral  :  5.926  51.710    515
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 20.12
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 12.07 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 26.24 %
    Favored  : 68.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.41 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.57 (0.41), residues: 464
  helix:  0.53 (0.75), residues: 48
  sheet: -1.00 (0.41), residues: 178
  loop : -1.34 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  79 
 TYR   0.025   0.002   TYR H 109 
 PHE   0.027   0.003   PHE H  71 
 TRP   0.026   0.003   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 3693)
  covalent geometry    : angle       0.93288 ( 5025)
  hydrogen bonds       : bond        0.03725 (  104)
  hydrogen bonds       : angle       6.30997 (  270)

*********************** 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
  154 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.090 
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: 0.8811 (mmm) cc_final: 0.8522 (mmp)
REVERT: L   80 MET cc_start: 0.8757 (tmm) cc_final: 0.7909 (tmm)
REVERT: H    6 GLN cc_start: 0.8487 (tp40) cc_final: 0.8262 (tp40)
REVERT: H   42 GLN cc_start: 0.8974 (tt0) cc_final: 0.8512 (tp40)
REVERT: H   49 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7520 (mt-10)
REVERT: H   85 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8050 (tm-30)
REVERT: A    2 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5371 (mmtt)
REVERT: A   14 ASP cc_start: 0.8152 (p0) cc_final: 0.7760 (p0)
REVERT: A   46 LYS cc_start: 0.8406 (mppt) cc_final: 0.7836 (mppt)
REVERT: A   86 ARG cc_start: 0.8249 (ptt90) cc_final: 0.7388 (ptt90)
REVERT: A   98 GLN cc_start: 0.9136 (pt0) cc_final: 0.7843 (tp40)
REVERT: A  123 ASP cc_start: 0.8802 (t0) cc_final: 0.8146 (t0)
REVERT: A  129 ASN cc_start: 0.8188 (m110) cc_final: 0.7667 (m-40)
REVERT: B   14 ASP cc_start: 0.8689 (p0) cc_final: 0.8025 (p0)
REVERT: B   34 SER cc_start: 0.7950 (t) cc_final: 0.7296 (p)
REVERT: B   37 GLN cc_start: 0.8775 (tt0) cc_final: 0.7745 (pt0)
REVERT: B   54 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8393 (mm-40)
REVERT: B   59 ARG cc_start: 0.9134 (mtm-85) cc_final: 0.8854 (mtm-85)
REVERT: B   60 LYS cc_start: 0.8997 (ptpp) cc_final: 0.8617 (ptpp)
REVERT: B   86 ARG cc_start: 0.8520 (ptt90) cc_final: 0.7943 (ptt90)
REVERT: B   87 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8056 (mm-40)
REVERT: B  102 ASP cc_start: 0.8891 (p0) cc_final: 0.8572 (p0)
REVERT: B  123 ASP cc_start: 0.8091 (t0) cc_final: 0.7794 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 146
  average time/residue: 0.0731
  time to fit residues: 12.4938
Evaluate side-chains
  144 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   37 TRP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   79 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    2 LYS
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0870
   chunk 25 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1162

-------------------------------------------------------------------------------
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 = 0.3521 r_free = 0.3521 target = 0.093827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.073911 restraints weight = 9606.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.077069 restraints weight = 4953.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.079262 restraints weight = 3212.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.080751 restraints weight = 2387.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.081743 restraints weight = 1940.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3693  Z= 0.164
  Angle     :  0.925  10.352   5025  Z= 0.460
  Chirality :  0.050   0.215    583
  Planarity :  0.005   0.072    645
  Dihedral  :  5.405  49.889    515
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 11.21 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 28.22 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.41), residues: 464
  helix:  0.58 (0.72), residues: 48
  sheet: -0.71 (0.42), residues: 175
  loop : -1.51 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 109 
 TYR   0.020   0.002   TYR H 109 
 PHE   0.018   0.002   PHE H  71 
 TRP   0.013   0.002   TRP H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3693)
  covalent geometry    : angle       0.92473 ( 5025)
  hydrogen bonds       : bond        0.02904 (  104)
  hydrogen bonds       : angle       6.11036 (  270)

*********************** 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
  158 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.8610 (mmm) cc_final: 0.8313 (mmp)
REVERT: L   80 MET cc_start: 0.8795 (tmm) cc_final: 0.7939 (tmm)
REVERT: H    6 GLN cc_start: 0.8114 (tp40) cc_final: 0.7856 (tp40)
REVERT: H   42 GLN cc_start: 0.8934 (tt0) cc_final: 0.8486 (tp40)
REVERT: H   49 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: H   68 LYS cc_start: 0.9406 (ttmm) cc_final: 0.9187 (tptm)
REVERT: H   85 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8184 (tm-30)
REVERT: H  103 PHE cc_start: 0.9090 (m-80) cc_final: 0.8730 (m-10)
REVERT: A    2 LYS cc_start: 0.5663 (OUTLIER) cc_final: 0.5123 (mmtt)
REVERT: A   14 ASP cc_start: 0.8385 (p0) cc_final: 0.8004 (p0)
REVERT: A   37 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9044 (tm-30)
REVERT: A   86 ARG cc_start: 0.8083 (ptt90) cc_final: 0.7300 (ptt90)
REVERT: A   98 GLN cc_start: 0.8990 (pt0) cc_final: 0.7865 (tp40)
REVERT: A  111 GLU cc_start: 0.9219 (tt0) cc_final: 0.8915 (tt0)
REVERT: A  123 ASP cc_start: 0.8596 (t0) cc_final: 0.7687 (t0)
REVERT: A  129 ASN cc_start: 0.7976 (m110) cc_final: 0.7312 (m110)
REVERT: B   11 ILE cc_start: 0.8621 (mm) cc_final: 0.8355 (mm)
REVERT: B   14 ASP cc_start: 0.8559 (p0) cc_final: 0.7914 (p0)
REVERT: B   34 SER cc_start: 0.7736 (t) cc_final: 0.7089 (p)
REVERT: B   37 GLN cc_start: 0.8567 (tt0) cc_final: 0.7603 (pt0)
REVERT: B   54 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8401 (mm-40)
REVERT: B   59 ARG cc_start: 0.9035 (mtm-85) cc_final: 0.8337 (mtm180)
REVERT: B   60 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8589 (ptpp)
REVERT: B   86 ARG cc_start: 0.8437 (ptt90) cc_final: 0.7832 (ptt90)
REVERT: B   87 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7942 (mm-40)
REVERT: B   99 TYR cc_start: 0.9325 (m-80) cc_final: 0.9082 (m-80)
REVERT: B  102 ASP cc_start: 0.8580 (p0) cc_final: 0.8313 (p0)
REVERT: B  111 GLU cc_start: 0.9096 (pt0) cc_final: 0.8798 (pp20)
REVERT: B  123 ASP cc_start: 0.7969 (t0) cc_final: 0.7664 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 153
  average time/residue: 0.0884
  time to fit residues: 15.8831
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  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
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    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   56 SER
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 39 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.091483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.071302 restraints weight = 10024.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.074473 restraints weight = 5161.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.076655 restraints weight = 3360.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.078178 restraints weight = 2513.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.079174 restraints weight = 2046.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3693  Z= 0.189
  Angle     :  0.914  10.331   5025  Z= 0.456
  Chirality :  0.049   0.217    583
  Planarity :  0.005   0.074    645
  Dihedral  :  5.496  50.288    515
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 11.85 %
    Favored  : 87.07 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.96 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.41), residues: 464
  helix:  0.40 (0.71), residues: 48
  sheet: -0.86 (0.44), residues: 164
  loop : -1.34 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  79 
 TYR   0.023   0.002   TYR H 109 
 PHE   0.019   0.002   PHE H  71 
 TRP   0.015   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 3693)
  covalent geometry    : angle       0.91358 ( 5025)
  hydrogen bonds       : bond        0.03091 (  104)
  hydrogen bonds       : angle       6.04303 (  270)

********************** 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
  151 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   41 MET cc_start: 0.8612 (mmm) cc_final: 0.8289 (mmp)
REVERT: L   80 MET cc_start: 0.8819 (tmm) cc_final: 0.7992 (tmm)
REVERT: H    6 GLN cc_start: 0.8101 (tp40) cc_final: 0.7537 (tp40)
REVERT: H   42 GLN cc_start: 0.8865 (tt0) cc_final: 0.8393 (tp40)
REVERT: H   49 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7699 (mt-10)
REVERT: H   85 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8229 (tm-30)
REVERT: H  103 PHE cc_start: 0.9115 (m-80) cc_final: 0.8704 (m-10)
REVERT: A    2 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.5073 (mmtt)
REVERT: A   14 ASP cc_start: 0.8284 (p0) cc_final: 0.7904 (p0)
REVERT: A   46 LYS cc_start: 0.8322 (mppt) cc_final: 0.7855 (mppt)
REVERT: A   86 ARG cc_start: 0.8050 (ptt90) cc_final: 0.7599 (ptt90)
REVERT: A   98 GLN cc_start: 0.9153 (pt0) cc_final: 0.7857 (tp40)
REVERT: A  123 ASP cc_start: 0.8569 (t0) cc_final: 0.7756 (t0)
REVERT: A  129 ASN cc_start: 0.7971 (m110) cc_final: 0.7349 (m-40)
REVERT: B   10 ASN cc_start: 0.8870 (m-40) cc_final: 0.8667 (t0)
REVERT: B   11 ILE cc_start: 0.8604 (mm) cc_final: 0.8322 (mm)
REVERT: B   14 ASP cc_start: 0.8562 (p0) cc_final: 0.7984 (p0)
REVERT: B   34 SER cc_start: 0.7565 (t) cc_final: 0.6914 (p)
REVERT: B   37 GLN cc_start: 0.8614 (tt0) cc_final: 0.7611 (pt0)
REVERT: B   54 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8461 (mm-40)
REVERT: B   59 ARG cc_start: 0.9031 (mtm-85) cc_final: 0.8657 (ttp-110)
REVERT: B   60 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8619 (ptpp)
REVERT: B   86 ARG cc_start: 0.8382 (ptt90) cc_final: 0.7758 (ptt90)
REVERT: B   87 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7653 (mm-40)
REVERT: B   99 TYR cc_start: 0.9308 (m-80) cc_final: 0.9104 (m-80)
REVERT: B  111 GLU cc_start: 0.9110 (pt0) cc_final: 0.8772 (pp20)
REVERT: B  123 ASP cc_start: 0.7908 (t0) cc_final: 0.7614 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 146
  average time/residue: 0.0958
  time to fit residues: 16.3018
Evaluate side-chains
  147 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   37 TRP
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  120 LEU
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   56 SER
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 2 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0000
   chunk 29 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.092718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.073111 restraints weight = 9495.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.076039 restraints weight = 4911.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.078070 restraints weight = 3222.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.079490 restraints weight = 2425.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.080479 restraints weight = 1982.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3693  Z= 0.212
  Angle     :  0.931   9.902   5025  Z= 0.465
  Chirality :  0.050   0.207    583
  Planarity :  0.006   0.079    645
  Dihedral  :  5.626  51.024    515
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 12.07 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 29.46 %
    Favored  : 67.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.40), residues: 464
  helix:  0.37 (0.71), residues: 48
  sheet: -0.97 (0.42), residues: 170
  loop : -1.33 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  79 
 TYR   0.022   0.002   TYR H 109 
 PHE   0.014   0.002   PHE H  71 
 TRP   0.017   0.002   TRP H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 3693)
  covalent geometry    : angle       0.93124 ( 5025)
  hydrogen bonds       : bond        0.03330 (  104)
  hydrogen bonds       : angle       6.09383 (  270)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 824.20 seconds
wall clock time: 14 minutes 55.65 seconds (895.65 seconds total)