Starting phenix.real_space_refine
on Fri Oct 10 10:38:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xa4_38194/10_2025/8xa4_38194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xa4_38194/10_2025/8xa4_38194.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xa4_38194/10_2025/8xa4_38194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xa4_38194/10_2025/8xa4_38194.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xa4_38194/10_2025/8xa4_38194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xa4_38194/10_2025/8xa4_38194.map"
  }
  resolution = 3.08
  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=   0.001 sd=   0.037
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      12      5.16       5
     C    1906      2.51       5
     N     509      2.21       5
     O     616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3043
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 631
          Classifications: {'peptide': 82}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 648
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 948
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 6, 'TRANS': 117}
    Chain: "D"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
  Time building chain proxies: 0.94, per 1000 atoms: 0.31
  Number of scatterers: 3043
  At special positions: 0
  Unit cell: (59.976, 79.135, 78.302, 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      12     16.00
     O     616      8.00
     N     509      7.00
     C    1906      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 100 " - pdb=" SG  CYS B 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 105.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  726

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 10 sheets defined
      17.2% alpha, 33.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 129
    Processing helix  chain 'A' and resid 135 through 141
      removed outlier: 3.702A  pdb=" N   VAL A 139 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   THR A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 149
      removed outlier: 4.165A  pdb=" N   TYR A 147 " --> pdb=" O   TRP A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 174
      removed outlier: 3.751A  pdb=" N   GLN A 173 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 129
    Processing helix  chain 'B' and resid 144 through 149
    Processing helix  chain 'C' and resid 62 through 67
      removed outlier: 4.450A  pdb=" N   SER C  67 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 92
      removed outlier: 3.573A  pdb=" N   THR C  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 32
      No H-bonds generated for 'chain 'D' and resid 30 through 32'
    Processing helix  chain 'D' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 117
      removed outlier: 7.108A  pdb=" N   ASP A 115 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   TYR A 178 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A 117 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 104
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 117
      removed outlier: 6.933A  pdb=" N   ASP B 115 " --> pdb=" O   TYR B 178 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TYR B 178 " --> pdb=" O   ASP B 115 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS B 117 " --> pdb=" O   ARG B 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA6, first strand: chain 'C' and resid 59 through 60
      removed outlier: 5.074A  pdb=" N   TRP C  49 " --> pdb=" O   ARG C  40 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ARG C  40 " --> pdb=" O   TRP C  49 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   CYS C  97 " --> pdb=" O   TRP C 115 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   TRP C 115 " --> pdb=" O   CYS C  97 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ARG C  99 " --> pdb=" O   ASP C 113 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASP C 113 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60
      removed outlier: 5.074A  pdb=" N   TRP C  49 " --> pdb=" O   ARG C  40 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ARG C  40 " --> pdb=" O   TRP C  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 5
    Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12
      removed outlier: 5.802A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 106 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   TYR D  50 " --> pdb=" O   LEU D  34 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   TRP D  36 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 5.802A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 106 " (cutoff:3.500A)

    113 hydrogen bonds defined for protein.
    267 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: 0.30

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 986
        1.34 -     1.46: 785
        1.46 -     1.58: 1328
        1.58 -     1.70: 0
        1.70 -     1.81: 12
  Bond restraints: 3111
  Sorted by residual:
  bond pdb=" N   SER A  99 "
       pdb=" CA  SER A  99 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.28e+00
  bond pdb=" N   SER B  99 "
       pdb=" CA  SER B  99 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   GLU D   1 "
       pdb=" CA  GLU D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   GLN C   1 "
       pdb=" CA  GLN C   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.66e+00
  bond pdb=" CA  ILE D  59 "
       pdb=" CB  ILE D  59 "
    ideal  model  delta    sigma   weight residual
    1.537  1.524  0.013 1.29e-02 6.01e+03 1.08e+00
  ... (remaining 3106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 3979
        0.95 -     1.91: 192
        1.91 -     2.86: 38
        2.86 -     3.82: 18
        3.82 -     4.77: 3
  Bond angle restraints: 4230
  Sorted by residual:
  angle pdb=" N   SER D  94 "
        pdb=" CA  SER D  94 "
        pdb=" C   SER D  94 "
      ideal   model   delta    sigma   weight residual
     113.56  110.30    3.26 1.39e+00 5.18e-01 5.51e+00
  angle pdb=" CA  TYR B 105 "
        pdb=" CB  TYR B 105 "
        pdb=" CG  TYR B 105 "
      ideal   model   delta    sigma   weight residual
     113.90  117.11   -3.21 1.80e+00 3.09e-01 3.18e+00
  angle pdb=" N   GLY C  51 "
        pdb=" CA  GLY C  51 "
        pdb=" C   GLY C  51 "
      ideal   model   delta    sigma   weight residual
     110.75  113.29   -2.54 1.46e+00 4.69e-01 3.03e+00
  angle pdb=" CA  VAL B 139 "
        pdb=" CB  VAL B 139 "
        pdb=" CG1 VAL B 139 "
      ideal   model   delta    sigma   weight residual
     110.40  113.34   -2.94 1.70e+00 3.46e-01 2.99e+00
  angle pdb=" C   GLN C  79 "
        pdb=" N   PHE C  80 "
        pdb=" CA  PHE C  80 "
      ideal   model   delta    sigma   weight residual
     122.94  120.39    2.55 1.50e+00 4.44e-01 2.89e+00
  ... (remaining 4225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 1598
       17.98 -    35.96: 184
       35.96 -    53.94: 41
       53.94 -    71.91: 18
       71.91 -    89.89: 7
  Dihedral angle restraints: 1848
    sinusoidal: 707
      harmonic: 1141
  Sorted by residual:
  dihedral pdb=" CB  CYS B 126 "
           pdb=" SG  CYS B 126 "
           pdb=" SG  CYS B 180 "
           pdb=" CB  CYS B 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.19   80.19     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  97 "
           pdb=" CB  CYS C  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.14   47.86     1      1.00e+01 1.00e-02 3.16e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  89 "
           pdb=" CB  CYS D  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.72   32.28     1      1.00e+01 1.00e-02 1.48e+01
  ... (remaining 1845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 260
       0.028 -    0.056: 150
       0.056 -    0.083: 30
       0.083 -    0.111: 20
       0.111 -    0.139: 7
  Chirality restraints: 467
  Sorted by residual:
  chirality pdb=" CA  ILE C  39 "
            pdb=" N   ILE C  39 "
            pdb=" C   ILE C  39 "
            pdb=" CB  ILE C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE D  76 "
            pdb=" N   ILE D  76 "
            pdb=" C   ILE D  76 "
            pdb=" CB  ILE D  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE D  49 "
            pdb=" N   ILE D  49 "
            pdb=" C   ILE D  49 "
            pdb=" CB  ILE D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  ... (remaining 464 not shown)

  Planarity restraints: 542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  44 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO D  45 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO D  45 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  45 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  13 "   -0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO C  14 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C  14 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  14 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  46 "    0.099 9.50e-02 1.11e+02   4.44e-02 1.22e+00
        pdb=" NE  ARG D  46 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  46 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  46 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  46 "    0.004 2.00e-02 2.50e+03
  ... (remaining 539 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1300
        2.91 -     3.41: 2786
        3.41 -     3.90: 4663
        3.90 -     4.40: 5415
        4.40 -     4.90: 9330
  Nonbonded interactions: 23494
  Sorted by model distance:
  nonbonded pdb=" O   THR A 141 "
            pdb=" OG1 THR A 141 "
     model   vdw
     2.411 3.040
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OE1 GLN D  90 "
     model   vdw
     2.485 3.040
  nonbonded pdb=" OE1 GLU B 174 "
            pdb=" O   ASP D  93 "
     model   vdw
     2.516 3.040
  nonbonded pdb=" O   VAL B 139 "
            pdb=" CG1 VAL B 139 "
     model   vdw
     2.528 3.460
  nonbonded pdb=" O   ARG C 101 "
            pdb=" O   TYR C 109 "
     model   vdw
     2.531 3.040
  ... (remaining 23489 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'
  selection = (chain 'B' and (resid 99 through 164 or (resid 165 through 168 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 169 through 180))
}

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 individual isotropic
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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.960
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3117  Z= 0.149
  Angle     :  0.529   4.774   4242  Z= 0.288
  Chirality :  0.039   0.139    467
  Planarity :  0.004   0.044    542
  Dihedral  : 17.082  89.892   1104
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 25.74 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.64 (0.43), residues: 387
  helix: -0.18 (0.88), residues: 44
  sheet:  1.28 (0.61), residues: 78
  loop :  0.36 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  18 
 TYR   0.010   0.001   TYR C  96 
 PHE   0.016   0.002   PHE C  80 
 TRP   0.009   0.001   TRP B 143 
 HIS   0.001   0.000   HIS D  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3111)
  covalent geometry    : angle       0.52877 ( 4230)
  SS BOND              : bond        0.00204 (    6)
  SS BOND              : angle       0.57766 (   12)
  hydrogen bonds       : bond        0.16397 (   97)
  hydrogen bonds       : angle       7.18209 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  170 ASP cc_start: 0.8384 (t70) cc_final: 0.7915 (t0)
REVERT: B  117 LYS cc_start: 0.8915 (mttp) cc_final: 0.8709 (mttm)
REVERT: D   37 TYR cc_start: 0.8800 (m-80) cc_final: 0.8557 (m-80)
  outliers start: 4
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0787
  time to fit residues: 11.7377
Evaluate side-chains
  103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
C  32 ASN
C  33 ASN
D  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.097173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.075142 restraints weight = 5732.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 3.44
r_work: 0.2846 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3117  Z= 0.162
  Angle     :  0.635   7.027   4242  Z= 0.326
  Chirality :  0.042   0.139    467
  Planarity :  0.004   0.029    542
  Dihedral  :  4.231  13.956    431
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 23.96 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.78 (0.43), residues: 387
  helix: -0.14 (0.76), residues: 50
  sheet:  1.36 (0.61), residues: 78
  loop :  0.50 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 176 
 TYR   0.014   0.002   TYR B 105 
 PHE   0.014   0.002   PHE C  80 
 TRP   0.015   0.001   TRP B 143 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3111)
  covalent geometry    : angle       0.63403 ( 4230)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.83199 (   12)
  hydrogen bonds       : bond        0.03845 (   97)
  hydrogen bonds       : angle       5.20703 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 ASP cc_start: 0.8720 (t70) cc_final: 0.8421 (t0)
REVERT: C   48 GLU cc_start: 0.8586 (tt0) cc_final: 0.8367 (tt0)
REVERT: C   72 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8552 (p)
REVERT: C   91 ASP cc_start: 0.8999 (m-30) cc_final: 0.8492 (m-30)
REVERT: D   71 ASP cc_start: 0.8279 (t0) cc_final: 0.8019 (m-30)
REVERT: D   93 ASP cc_start: 0.7941 (t0) cc_final: 0.7669 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 114
  average time/residue: 0.0737
  time to fit residues: 9.9231
Evaluate side-chains
  107 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    0.0980
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 30 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 157 ASN
C  32 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.095645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.073365 restraints weight = 5733.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.43
r_work: 0.2813 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3117  Z= 0.154
  Angle     :  0.599   7.850   4242  Z= 0.311
  Chirality :  0.041   0.139    467
  Planarity :  0.004   0.027    542
  Dihedral  :  4.162  13.525    431
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 22.78 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.75 (0.43), residues: 387
  helix: -0.22 (0.74), residues: 50
  sheet:  1.45 (0.62), residues: 78
  loop :  0.45 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  55 
 TYR   0.013   0.002   TYR B 105 
 PHE   0.015   0.001   PHE C  80 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.001   0.000   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3111)
  covalent geometry    : angle       0.59825 ( 4230)
  SS BOND              : bond        0.00175 (    6)
  SS BOND              : angle       0.71324 (   12)
  hydrogen bonds       : bond        0.03645 (   97)
  hydrogen bonds       : angle       5.20280 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  170 ASP cc_start: 0.8706 (t70) cc_final: 0.8374 (t0)
REVERT: C   16 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8132 (mm-30)
REVERT: C   55 TYR cc_start: 0.8971 (p90) cc_final: 0.8708 (p90)
REVERT: C   91 ASP cc_start: 0.8988 (m-30) cc_final: 0.8469 (m-30)
REVERT: D   70 THR cc_start: 0.8993 (p) cc_final: 0.8526 (p)
REVERT: D   71 ASP cc_start: 0.8227 (t0) cc_final: 0.7952 (m-30)
REVERT: D   93 ASP cc_start: 0.8067 (t0) cc_final: 0.7817 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0651
  time to fit residues: 8.7234
Evaluate side-chains
  115 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 157 ASN
C  32 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.095053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.073285 restraints weight = 5736.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 3.37
r_work: 0.2815 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3117  Z= 0.145
  Angle     :  0.601   7.882   4242  Z= 0.309
  Chirality :  0.040   0.136    467
  Planarity :  0.004   0.026    542
  Dihedral  :  4.164  14.658    431
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 21.01 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.52 (0.42), residues: 387
  helix: -0.56 (0.68), residues: 56
  sheet:  1.30 (0.61), residues: 78
  loop :  0.35 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  18 
 TYR   0.011   0.001   TYR D  33 
 PHE   0.016   0.002   PHE C  80 
 TRP   0.009   0.001   TRP B 143 
 HIS   0.001   0.000   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3111)
  covalent geometry    : angle       0.59583 ( 4230)
  SS BOND              : bond        0.00120 (    6)
  SS BOND              : angle       1.57909 (   12)
  hydrogen bonds       : bond        0.03519 (   97)
  hydrogen bonds       : angle       5.21600 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  170 ASP cc_start: 0.8707 (t70) cc_final: 0.8380 (t0)
REVERT: B  106 GLN cc_start: 0.8830 (pt0) cc_final: 0.8569 (pt0)
REVERT: C   16 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8198 (mm-30)
REVERT: C   72 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8641 (p)
REVERT: C   91 ASP cc_start: 0.9021 (m-30) cc_final: 0.8537 (m-30)
REVERT: D   70 THR cc_start: 0.8996 (p) cc_final: 0.8537 (p)
REVERT: D   71 ASP cc_start: 0.8152 (t0) cc_final: 0.7858 (m-30)
REVERT: D   93 ASP cc_start: 0.8100 (t0) cc_final: 0.7873 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0689
  time to fit residues: 9.3091
Evaluate side-chains
  111 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
C  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.094550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.072480 restraints weight = 5783.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 3.41
r_work: 0.2811 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3117  Z= 0.140
  Angle     :  0.596   9.712   4242  Z= 0.303
  Chirality :  0.040   0.179    467
  Planarity :  0.004   0.026    542
  Dihedral  :  4.121  13.457    431
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 21.01 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.45 (0.42), residues: 387
  helix: -0.68 (0.68), residues: 56
  sheet:  1.19 (0.61), residues: 78
  loop :  0.35 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  18 
 TYR   0.010   0.001   TYR D  33 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.008   0.001   TRP B 143 
 HIS   0.001   0.000   HIS C 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3111)
  covalent geometry    : angle       0.59490 ( 4230)
  SS BOND              : bond        0.00144 (    6)
  SS BOND              : angle       0.79076 (   12)
  hydrogen bonds       : bond        0.03425 (   97)
  hydrogen bonds       : angle       5.17700 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  170 ASP cc_start: 0.8714 (t70) cc_final: 0.8394 (t0)
REVERT: B  106 GLN cc_start: 0.8808 (pt0) cc_final: 0.8583 (pt0)
REVERT: B  173 GLN cc_start: 0.8166 (pm20) cc_final: 0.7783 (pm20)
REVERT: B  174 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: C   16 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: C   72 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8657 (p)
REVERT: C   91 ASP cc_start: 0.8997 (m-30) cc_final: 0.8549 (m-30)
REVERT: D   70 THR cc_start: 0.9000 (p) cc_final: 0.8575 (p)
REVERT: D   71 ASP cc_start: 0.8151 (t0) cc_final: 0.7862 (m-30)
REVERT: D   93 ASP cc_start: 0.8044 (t0) cc_final: 0.7260 (t70)
  outliers start: 19
  outliers final: 15
  residues processed: 114
  average time/residue: 0.0594
  time to fit residues: 8.1681
Evaluate side-chains
  118 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0370
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 157 ASN
C  32 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.094088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.072400 restraints weight = 5719.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 3.38
r_work: 0.2809 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3117  Z= 0.131
  Angle     :  0.586   9.717   4242  Z= 0.300
  Chirality :  0.040   0.176    467
  Planarity :  0.004   0.026    542
  Dihedral  :  4.078  14.757    431
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 21.30 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.47 (0.43), residues: 387
  helix: -0.68 (0.69), residues: 56
  sheet:  1.18 (0.61), residues: 78
  loop :  0.37 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  18 
 TYR   0.015   0.001   TYR D  33 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.007   0.001   TRP B 143 
 HIS   0.001   0.000   HIS C 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3111)
  covalent geometry    : angle       0.58609 ( 4230)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       0.54791 (   12)
  hydrogen bonds       : bond        0.03352 (   97)
  hydrogen bonds       : angle       5.13373 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 ASP cc_start: 0.8712 (t70) cc_final: 0.8402 (t0)
REVERT: B  106 GLN cc_start: 0.8837 (pt0) cc_final: 0.8620 (pt0)
REVERT: B  174 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8064 (mm-30)
REVERT: C   16 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: C   72 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8681 (p)
REVERT: C   91 ASP cc_start: 0.8982 (m-30) cc_final: 0.8547 (m-30)
REVERT: D   28 ARG cc_start: 0.8875 (mtp-110) cc_final: 0.8240 (mtp-110)
REVERT: D   37 TYR cc_start: 0.9242 (m-80) cc_final: 0.8777 (m-80)
REVERT: D   70 THR cc_start: 0.9016 (p) cc_final: 0.8599 (p)
REVERT: D   71 ASP cc_start: 0.8164 (t0) cc_final: 0.7874 (m-30)
REVERT: D   93 ASP cc_start: 0.8005 (t0) cc_final: 0.7477 (t70)
  outliers start: 20
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0621
  time to fit residues: 8.5985
Evaluate side-chains
  120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0370
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9062

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

Flipped N/Q/H residues before XYZ refinement:
C  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.092994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.071426 restraints weight = 5747.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 3.37
r_work: 0.2803 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3117  Z= 0.151
  Angle     :  0.594   9.127   4242  Z= 0.307
  Chirality :  0.040   0.153    467
  Planarity :  0.004   0.027    542
  Dihedral  :  4.079  13.946    431
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 21.60 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.56 (0.43), residues: 387
  helix: -0.47 (0.72), residues: 50
  sheet:  1.13 (0.61), residues: 78
  loop :  0.41 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  18 
 TYR   0.018   0.001   TYR D  33 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.007   0.001   TRP C  36 
 HIS   0.001   0.000   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3111)
  covalent geometry    : angle       0.59395 ( 4230)
  SS BOND              : bond        0.00156 (    6)
  SS BOND              : angle       0.57420 (   12)
  hydrogen bonds       : bond        0.03390 (   97)
  hydrogen bonds       : angle       5.12369 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 ASP cc_start: 0.8695 (t70) cc_final: 0.8383 (t0)
REVERT: B  106 GLN cc_start: 0.8840 (pt0) cc_final: 0.8624 (pt0)
REVERT: B  174 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8157 (mm-30)
REVERT: C   16 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: C   72 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8705 (p)
REVERT: C   91 ASP cc_start: 0.8977 (m-30) cc_final: 0.8536 (m-30)
REVERT: D   28 ARG cc_start: 0.8906 (mtp-110) cc_final: 0.8259 (mtp-110)
REVERT: D   70 THR cc_start: 0.9026 (p) cc_final: 0.8609 (p)
REVERT: D   71 ASP cc_start: 0.8191 (t0) cc_final: 0.7910 (m-30)
REVERT: D   93 ASP cc_start: 0.8045 (t0) cc_final: 0.7537 (t70)
  outliers start: 23
  outliers final: 20
  residues processed: 116
  average time/residue: 0.0629
  time to fit residues: 8.8428
Evaluate side-chains
  121 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
C  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.093457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.071619 restraints weight = 5834.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 3.40
r_work: 0.2800 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3117  Z= 0.141
  Angle     :  0.600   8.984   4242  Z= 0.312
  Chirality :  0.040   0.155    467
  Planarity :  0.004   0.029    542
  Dihedral  :  4.087  14.974    431
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 22.78 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.57 (0.43), residues: 387
  helix: -0.46 (0.73), residues: 50
  sheet:  1.12 (0.61), residues: 78
  loop :  0.42 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  18 
 TYR   0.019   0.001   TYR D  33 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.008   0.001   TRP C  36 
 HIS   0.001   0.000   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3111)
  covalent geometry    : angle       0.59968 ( 4230)
  SS BOND              : bond        0.00149 (    6)
  SS BOND              : angle       0.65292 (   12)
  hydrogen bonds       : bond        0.03325 (   97)
  hydrogen bonds       : angle       5.11593 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  170 ASP cc_start: 0.8695 (t70) cc_final: 0.8385 (t0)
REVERT: B  174 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8148 (mm-30)
REVERT: C   16 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8105 (mm-30)
REVERT: D   28 ARG cc_start: 0.8892 (mtp-110) cc_final: 0.8250 (mtp-110)
REVERT: D   70 THR cc_start: 0.9068 (p) cc_final: 0.8672 (p)
REVERT: D   71 ASP cc_start: 0.8193 (t0) cc_final: 0.7918 (m-30)
REVERT: D   93 ASP cc_start: 0.8042 (t0) cc_final: 0.7541 (t70)
  outliers start: 20
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0675
  time to fit residues: 9.1879
Evaluate side-chains
  118 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   53 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    0.0030
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0370
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.5668

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

Flipped N/Q/H residues before XYZ refinement:
C  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.094130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.072156 restraints weight = 5892.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 3.44
r_work: 0.2811 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3117  Z= 0.130
  Angle     :  0.637  14.403   4242  Z= 0.321
  Chirality :  0.040   0.165    467
  Planarity :  0.004   0.032    542
  Dihedral  :  4.107  14.079    431
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 23.67 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.53 (0.43), residues: 387
  helix: -0.50 (0.73), residues: 50
  sheet:  1.05 (0.61), residues: 78
  loop :  0.42 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  18 
 TYR   0.018   0.001   TYR D  33 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.006   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3111)
  covalent geometry    : angle       0.63660 ( 4230)
  SS BOND              : bond        0.00179 (    6)
  SS BOND              : angle       0.75572 (   12)
  hydrogen bonds       : bond        0.03248 (   97)
  hydrogen bonds       : angle       5.11436 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 ASP cc_start: 0.8690 (t70) cc_final: 0.8395 (t0)
REVERT: B  174 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: C   16 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8108 (mm-30)
REVERT: C   91 ASP cc_start: 0.8954 (m-30) cc_final: 0.8563 (m-30)
REVERT: D   28 ARG cc_start: 0.8913 (mtp-110) cc_final: 0.8276 (mtp-110)
REVERT: D   70 THR cc_start: 0.9082 (p) cc_final: 0.8683 (p)
REVERT: D   71 ASP cc_start: 0.8213 (t0) cc_final: 0.7933 (m-30)
REVERT: D   93 ASP cc_start: 0.7984 (t0) cc_final: 0.7342 (t70)
  outliers start: 17
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0676
  time to fit residues: 9.3336
Evaluate side-chains
  118 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   53 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
C  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.093699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.071529 restraints weight = 5716.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 3.40
r_work: 0.2811 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3117  Z= 0.137
  Angle     :  0.642  14.091   4242  Z= 0.325
  Chirality :  0.040   0.172    467
  Planarity :  0.004   0.033    542
  Dihedral  :  4.140  14.803    431
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 23.37 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.51 (0.43), residues: 387
  helix: -0.53 (0.72), residues: 50
  sheet:  0.96 (0.61), residues: 78
  loop :  0.44 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  18 
 TYR   0.022   0.001   TYR D  33 
 PHE   0.016   0.002   PHE C  80 
 TRP   0.009   0.001   TRP B 143 
 HIS   0.001   0.000   HIS C 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3111)
  covalent geometry    : angle       0.64153 ( 4230)
  SS BOND              : bond        0.00139 (    6)
  SS BOND              : angle       0.89762 (   12)
  hydrogen bonds       : bond        0.03278 (   97)
  hydrogen bonds       : angle       5.09121 (  267)

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 ASP cc_start: 0.8690 (t70) cc_final: 0.8390 (t0)
REVERT: B  174 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7999 (mm-30)
REVERT: C   16 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8107 (mm-30)
REVERT: C   79 GLN cc_start: 0.8241 (mt0) cc_final: 0.7985 (mm-40)
REVERT: C   91 ASP cc_start: 0.8944 (m-30) cc_final: 0.8582 (m-30)
REVERT: D   28 ARG cc_start: 0.8912 (mtp-110) cc_final: 0.8274 (mtp-110)
REVERT: D   70 THR cc_start: 0.9092 (p) cc_final: 0.8711 (p)
REVERT: D   71 ASP cc_start: 0.8211 (t0) cc_final: 0.7943 (m-30)
REVERT: D   93 ASP cc_start: 0.7988 (t0) cc_final: 0.7407 (t70)
  outliers start: 15
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0675
  time to fit residues: 8.8977
Evaluate side-chains
  116 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain C residue   32 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   53 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0970
   chunk 35 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
C  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.093969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.071727 restraints weight = 5749.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.41
r_work: 0.2821 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.4282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3117  Z= 0.132
  Angle     :  0.637  13.400   4242  Z= 0.323
  Chirality :  0.040   0.172    467
  Planarity :  0.004   0.038    542
  Dihedral  :  4.153  14.344    431
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.67 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.51 (0.43), residues: 387
  helix: -0.50 (0.72), residues: 50
  sheet:  0.89 (0.61), residues: 78
  loop :  0.46 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  18 
 TYR   0.021   0.001   TYR D  33 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.012   0.001   TRP B 143 
 HIS   0.001   0.000   HIS C 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3111)
  covalent geometry    : angle       0.63570 ( 4230)
  SS BOND              : bond        0.00125 (    6)
  SS BOND              : angle       1.01589 (   12)
  hydrogen bonds       : bond        0.03243 (   97)
  hydrogen bonds       : angle       5.11047 (  267)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 971.38 seconds
wall clock time: 17 minutes 19.38 seconds (1039.38 seconds total)