Starting phenix.real_space_refine
on Tue Aug  4 16:00:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w03_65490/08_2026/9w03_65490_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w03_65490/08_2026/9w03_65490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w03_65490/08_2026/9w03_65490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w03_65490/08_2026/9w03_65490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w03_65490/08_2026/9w03_65490_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w03_65490/08_2026/9w03_65490_neut.cif"
  }
  resolution = 3.3
  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=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     P      36      5.49       5
     S      24      5.16       5
     C    2736      2.51       5
     N     855      2.21       5
     O     945      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4596
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1972
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 8, 'TRANS': 237}
    Chain: "B"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1850
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 774
          Classifications: {'DNA': 1, 'RNA': 36}
          Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 21, 'rna3p': 15}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 1.43, per 1000 atoms: 0.31
  Number of scatterers: 4596
  At special positions: 0
  Unit cell: (67.425, 65.25, 109.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      36     15.00
     O     945      8.00
     N     855      7.00
     C    2736      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: 0.40
  Conformation dependent library (CDL) restraints added in 133.6 milliseconds
  

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  896

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      71.2% alpha, 2.5% beta
      4 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 98
      removed outlier: 3.672A  pdb=" N   LYS A  87 " --> pdb=" O   LYS A  83 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 133
      removed outlier: 4.048A  pdb=" N   LEU A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
    Processing helix  chain 'A' and resid 150 through 160
    Processing helix  chain 'A' and resid 162 through 166
    Processing helix  chain 'A' and resid 170 through 177
      removed outlier: 3.619A  pdb=" N   ALA A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 190
      removed outlier: 4.106A  pdb=" N   GLY A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 212
      removed outlier: 3.644A  pdb=" N   LYS A 211 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 3.606A  pdb=" N   TYR A 221 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 242
      No H-bonds generated for 'chain 'A' and resid 240 through 242'
    Processing helix  chain 'A' and resid 253 through 281
      removed outlier: 3.877A  pdb=" N   ARG A 257 " --> pdb=" O   LYS A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'B' and resid 67 through 97
    Processing helix  chain 'B' and resid 104 through 134
      removed outlier: 3.717A  pdb=" N   PHE B 109 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 152 through 157
      removed outlier: 3.662A  pdb=" N   LEU B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 166
    Processing helix  chain 'B' and resid 170 through 177
      removed outlier: 3.551A  pdb=" N   ALA B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 185
    Processing helix  chain 'B' and resid 195 through 210
      removed outlier: 3.513A  pdb=" N   MET B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 230
      removed outlier: 4.258A  pdb=" N   VAL B 220 " --> pdb=" O   PRO B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 282
      removed outlier: 3.543A  pdb=" N   ARG B 257 " --> pdb=" O   LYS B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
    Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 239
    Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 238

    242 hydrogen bonds defined for protein.
    696 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1286
        1.33 -     1.45: 945
        1.45 -     1.57: 2418
        1.57 -     1.69: 72
        1.69 -     1.81: 44
  Bond restraints: 4765
  Sorted by residual:
  bond pdb=" P     G C  36 "
       pdb=" O5'   G C  36 "
    ideal  model  delta    sigma   weight residual
    1.593  1.612 -0.019 1.00e-02 1.00e+04 3.76e+00
  bond pdb=" P     A C  37 "
       pdb=" O5'   A C  37 "
    ideal  model  delta    sigma   weight residual
    1.593  1.612 -0.019 1.00e-02 1.00e+04 3.76e+00
  bond pdb=" P     A C  37 "
       pdb=" OP2   A C  37 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.00e+00
  bond pdb=" N   ARG A  64 "
       pdb=" CA  ARG A  64 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" N   ASP B  65 "
       pdb=" CA  ASP B  65 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  ... (remaining 4760 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 6164
        1.24 -     2.48: 348
        2.48 -     3.72: 74
        3.72 -     4.96: 16
        4.96 -     6.20: 5
  Bond angle restraints: 6607
  Sorted by residual:
  angle pdb=" O5'   U C  11 "
        pdb=" C5'   U C  11 "
        pdb=" C4'   U C  11 "
      ideal   model   delta    sigma   weight residual
     109.40  112.83   -3.43 8.00e-01 1.56e+00 1.83e+01
  angle pdb=" O5'   G C  10 "
        pdb=" C5'   G C  10 "
        pdb=" C4'   G C  10 "
      ideal   model   delta    sigma   weight residual
     109.40  112.65   -3.25 8.00e-01 1.56e+00 1.65e+01
  angle pdb=" O5'   C C  18 "
        pdb=" C5'   C C  18 "
        pdb=" C4'   C C  18 "
      ideal   model   delta    sigma   weight residual
     109.40  112.48   -3.08 8.00e-01 1.56e+00 1.48e+01
  angle pdb=" O5'   U C   3 "
        pdb=" C5'   U C   3 "
        pdb=" C4'   U C   3 "
      ideal   model   delta    sigma   weight residual
     109.40  112.27   -2.87 8.00e-01 1.56e+00 1.28e+01
  angle pdb=" C1'   U C  12 "
        pdb=" N1    U C  12 "
        pdb=" C2    U C  12 "
      ideal   model   delta    sigma   weight residual
     117.70  121.89   -4.19 1.20e+00 6.94e-01 1.22e+01
  ... (remaining 6602 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.34: 2747
       35.34 -    70.68: 143
       70.68 -   106.01: 18
      106.01 -   141.35: 5
      141.35 -   176.69: 1
  Dihedral angle restraints: 2914
    sinusoidal: 1531
      harmonic: 1383
  Sorted by residual:
  dihedral pdb=" O4'   U C  12 "
           pdb=" C1'   U C  12 "
           pdb=" N1    U C  12 "
           pdb=" C2    U C  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   75.93  124.07     1      1.50e+01 4.44e-03 6.66e+01
  dihedral pdb=" O4'   A C  29 "
           pdb=" C1'   A C  29 "
           pdb=" N9    A C  29 "
           pdb=" C4    A C  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  136.23  -68.23     1      1.70e+01 3.46e-03 2.09e+01
  dihedral pdb=" C4'   G C  10 "
           pdb=" C3'   G C  10 "
           pdb=" O3'   G C  10 "
           pdb=" P     U C  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   66.69 -176.69     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 2911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 720
       0.103 -    0.205: 23
       0.205 -    0.308: 0
       0.308 -    0.410: 0
       0.410 -    0.513: 2
  Chirality restraints: 745
  Sorted by residual:
  chirality pdb=" P     A C  37 "
            pdb=" OP1   A C  37 "
            pdb=" OP2   A C  37 "
            pdb=" O5'   A C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.85   -0.51 2.00e-01 2.50e+01 6.57e+00
  chirality pdb=" P     G C  36 "
            pdb=" OP1   G C  36 "
            pdb=" OP2   G C  36 "
            pdb=" O5'   G C  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.91   -0.50 2.00e-01 2.50e+01 6.30e+00
  chirality pdb=" C1'   G C   2 "
            pdb=" O4'   G C   2 "
            pdb=" C2'   G C   2 "
            pdb=" N9    G C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.31    0.16 2.00e-01 2.50e+01 6.54e-01
  ... (remaining 742 not shown)

  Planarity restraints: 710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 146 "   -0.041 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO B 147 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 221 "    0.014 2.00e-02 2.50e+03   1.30e-02 3.40e+00
        pdb=" CG  TYR B 221 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 221 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 221 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 221 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 221 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 221 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 221 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C   2 "   -0.024 2.00e-02 2.50e+03   1.04e-02 3.23e+00
        pdb=" N9    G C   2 "    0.025 2.00e-02 2.50e+03
        pdb=" C8    G C   2 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G C   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C   2 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G C   2 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G C   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C   2 "    0.002 2.00e-02 2.50e+03
        pdb=" N2    G C   2 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C   2 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G C   2 "    0.001 2.00e-02 2.50e+03
  ... (remaining 707 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 24
        2.42 -     3.04: 3056
        3.04 -     3.66: 7128
        3.66 -     4.28: 10214
        4.28 -     4.90: 16406
  Nonbonded interactions: 36828
  Sorted by model distance:
  nonbonded pdb=" O2'   A C  17 "
            pdb=" OP1   C C  18 "
     model   vdw
     1.800 3.040
  nonbonded pdb=" OD1 ASP A  77 "
            pdb=" OG1 THR B 106 "
     model   vdw
     2.006 3.040
  nonbonded pdb=" O   TRP A 249 "
            pdb=" OG1 THR A 252 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" OG1 THR A 106 "
            pdb=" OD2 ASP B  77 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" NH1 ARG B  78 "
            pdb=" OD1 ASP B 125 "
     model   vdw
     2.131 3.120
  ... (remaining 36823 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 65 through 187 or resid 194 through 287 or resid 297 throu \ 
gh 309))
  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 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:             1.670
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.610
  Find NCS groups from input model:        0.060
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
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   0.036   4765  Z= 0.221
  Angle     :  0.688   6.198   6607  Z= 0.476
  Chirality :  0.049   0.513    745
  Planarity :  0.005   0.061    710
  Dihedral  : 20.401 176.688   2018
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.98 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.21 %
    Favored  : 83.79 %
  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 are not related in a simple way.
  whole:  1.30 (0.40), residues: 468
  helix:  1.99 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.04 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 278 
 TYR   0.031   0.002   TYR B 221 
 PHE   0.005   0.001   PHE A 109 
 TRP   0.024   0.002   TRP B 249 
 HIS   0.005   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.22 ( 4765)
  covalent geometry    : angle       0.68777 /  0.48 ( 6607)
  hydrogen bonds       : bond        0.16122 / 10.85 (  251)
  hydrogen bonds       : angle       5.53019 /  4.04 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7888 (t80) cc_final: 0.7118 (t80)
REVERT: A  209 MET cc_start: 0.7298 (mtm) cc_final: 0.6992 (mtm)
REVERT: A  278 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7784 (mtp85)
REVERT: B  117 SER cc_start: 0.8319 (m) cc_final: 0.8043 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0974
  time to fit residues: 12.0375
Evaluate side-chains
  103 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.169984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.147943 restraints weight = 6964.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 2.64
r_work: 0.3883 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4765  Z= 0.177
  Angle     :  0.703   7.267   6607  Z= 0.374
  Chirality :  0.047   0.335    745
  Planarity :  0.005   0.040    710
  Dihedral  : 21.452 167.284   1060
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.56 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.71 %
    Favored  : 82.04 %
  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 are not related in a simple way.
  whole:  1.20 (0.40), residues: 468
  helix:  1.87 (0.29), residues: 292
  sheet:  None (None), residues: 0
  loop : -1.08 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 278 
 TYR   0.022   0.002   TYR B 221 
 PHE   0.007   0.002   PHE A 109 
 TRP   0.011   0.002   TRP B  67 
 HIS   0.003   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.18 ( 4765)
  covalent geometry    : angle       0.70310 /  0.37 ( 6607)
  hydrogen bonds       : bond        0.06658 /  4.73 (  251)
  hydrogen bonds       : angle       4.80555 /  3.40 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7929 (t80) cc_final: 0.7206 (t80)
REVERT: A  108 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6665 (tm-30)
REVERT: A  278 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7237 (mtp85)
REVERT: B   86 MET cc_start: 0.6503 (tmm) cc_final: 0.6245 (tmm)
REVERT: B  137 ASP cc_start: 0.7496 (t0) cc_final: 0.7258 (t0)
REVERT: B  305 ARG cc_start: 0.6668 (mtt180) cc_final: 0.6427 (mtt180)
  outliers start: 13
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1014
  time to fit residues: 13.4946
Evaluate side-chains
  114 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  308 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.7980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.170224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.148034 restraints weight = 6917.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.62
r_work: 0.3878 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4765  Z= 0.171
  Angle     :  0.651   7.181   6607  Z= 0.351
  Chirality :  0.046   0.311    745
  Planarity :  0.004   0.041    710
  Dihedral  : 21.309 167.342   1060
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.27 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.46 %
    Favored  : 79.80 %
  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 are not related in a simple way.
  whole:  1.28 (0.40), residues: 468
  helix:  1.88 (0.29), residues: 296
  sheet:  None (None), residues: 0
  loop : -1.02 (0.53), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.017   0.002   TYR B 221 
 PHE   0.008   0.001   PHE A 109 
 TRP   0.012   0.002   TRP B  67 
 HIS   0.005   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.17 ( 4765)
  covalent geometry    : angle       0.65063 /  0.35 ( 6607)
  hydrogen bonds       : bond        0.06316 /  4.53 (  251)
  hydrogen bonds       : angle       4.61514 /  3.24 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7953 (t80) cc_final: 0.7316 (t80)
REVERT: A  278 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7020 (mtp85)
REVERT: B   76 ASP cc_start: 0.8003 (t0) cc_final: 0.7693 (t0)
REVERT: B   86 MET cc_start: 0.6477 (tmm) cc_final: 0.6243 (tmm)
REVERT: B  137 ASP cc_start: 0.7392 (t0) cc_final: 0.7135 (t0)
REVERT: B  266 MET cc_start: 0.7327 (mtp) cc_final: 0.7101 (mtp)
  outliers start: 15
  outliers final: 9
  residues processed: 115
  average time/residue: 0.0947
  time to fit residues: 13.2841
Evaluate side-chains
  110 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  309 TRP
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  219 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0370
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 GLN
A 223 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.171086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.149052 restraints weight = 6933.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.64
r_work: 0.3896 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4765  Z= 0.146
  Angle     :  0.620   6.788   6607  Z= 0.335
  Chirality :  0.045   0.302    745
  Planarity :  0.004   0.041    710
  Dihedral  : 21.253 166.855   1060
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.20 %
    Favored  : 79.05 %
  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 are not related in a simple way.
  whole:  1.45 (0.41), residues: 468
  helix:  2.00 (0.29), residues: 296
  sheet:  None (None), residues: 0
  loop : -0.91 (0.53), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 305 
 TYR   0.014   0.002   TYR A 221 
 PHE   0.006   0.001   PHE A 109 
 TRP   0.010   0.001   TRP B 309 
 HIS   0.003   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.15 ( 4765)
  covalent geometry    : angle       0.62040 /  0.34 ( 6607)
  hydrogen bonds       : bond        0.05936 /  4.30 (  251)
  hydrogen bonds       : angle       4.44159 /  3.10 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.6011 (tmm) cc_final: 0.5805 (tmm)
REVERT: A   95 TYR cc_start: 0.7957 (t80) cc_final: 0.7254 (t80)
REVERT: A  279 GLU cc_start: 0.7983 (tp30) cc_final: 0.7609 (tp30)
REVERT: B   76 ASP cc_start: 0.8004 (t0) cc_final: 0.7694 (t0)
REVERT: B   86 MET cc_start: 0.6426 (tmm) cc_final: 0.6218 (tmm)
REVERT: B  137 ASP cc_start: 0.7449 (t0) cc_final: 0.7170 (t0)
REVERT: B  305 ARG cc_start: 0.6651 (mtt180) cc_final: 0.6374 (mtt180)
  outliers start: 7
  outliers final: 5
  residues processed: 109
  average time/residue: 0.0918
  time to fit residues: 12.2314
Evaluate side-chains
  109 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.170747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.148749 restraints weight = 6903.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 2.56
r_work: 0.3889 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4765  Z= 0.137
  Angle     :  0.614   9.634   6607  Z= 0.328
  Chirality :  0.043   0.298    745
  Planarity :  0.004   0.040    710
  Dihedral  : 21.216 167.213   1060
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.70 %
    Favored  : 77.06 %
  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 are not related in a simple way.
  whole:  1.58 (0.40), residues: 468
  helix:  2.11 (0.29), residues: 298
  sheet:  None (None), residues: 0
  loop : -0.91 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 199 
 TYR   0.013   0.001   TYR A 221 
 PHE   0.003   0.001   PHE A 275 
 TRP   0.012   0.001   TRP B  67 
 HIS   0.003   0.001   HIS B 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 ( 4765)
  covalent geometry    : angle       0.61424 /  0.33 ( 6607)
  hydrogen bonds       : bond        0.05674 /  4.12 (  251)
  hydrogen bonds       : angle       4.27308 /  2.96 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5894 (tmm) cc_final: 0.5622 (tmm)
REVERT: A   95 TYR cc_start: 0.7951 (t80) cc_final: 0.7357 (t80)
REVERT: A  279 GLU cc_start: 0.7986 (tp30) cc_final: 0.7588 (tp30)
REVERT: B   76 ASP cc_start: 0.7952 (t0) cc_final: 0.7657 (t0)
REVERT: B  104 GLN cc_start: 0.7786 (mp10) cc_final: 0.7516 (mp10)
REVERT: B  137 ASP cc_start: 0.7325 (t0) cc_final: 0.7036 (t0)
REVERT: B  266 MET cc_start: 0.7322 (mtp) cc_final: 0.7108 (mtp)
  outliers start: 13
  outliers final: 9
  residues processed: 113
  average time/residue: 0.0933
  time to fit residues: 12.8732
Evaluate side-chains
  117 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 GLN
B  90 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.169777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.147761 restraints weight = 7027.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 2.60
r_work: 0.3869 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4765  Z= 0.153
  Angle     :  0.601   6.813   6607  Z= 0.324
  Chirality :  0.044   0.303    745
  Planarity :  0.004   0.041    710
  Dihedral  : 21.232 167.682   1060
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.70 %
    Favored  : 77.56 %
  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 are not related in a simple way.
  whole:  1.62 (0.40), residues: 468
  helix:  2.12 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.89 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 278 
 TYR   0.014   0.002   TYR A 221 
 PHE   0.009   0.001   PHE A 109 
 TRP   0.011   0.001   TRP B 309 
 HIS   0.004   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.15 ( 4765)
  covalent geometry    : angle       0.60097 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05655 /  4.12 (  251)
  hydrogen bonds       : angle       4.31151 /  2.98 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5924 (tmm) cc_final: 0.5637 (tmm)
REVERT: A   95 TYR cc_start: 0.7987 (t80) cc_final: 0.7402 (t80)
REVERT: A  222 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6949 (mt-10)
REVERT: A  278 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7765 (mtp85)
REVERT: A  279 GLU cc_start: 0.8031 (tp30) cc_final: 0.7665 (tp30)
REVERT: B   76 ASP cc_start: 0.7949 (t0) cc_final: 0.7669 (t0)
REVERT: B   86 MET cc_start: 0.6498 (tmm) cc_final: 0.6227 (tmm)
REVERT: B  137 ASP cc_start: 0.7324 (t0) cc_final: 0.7068 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0966
  time to fit residues: 13.3915
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.169802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.148045 restraints weight = 6851.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 2.60
r_work: 0.3890 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4765  Z= 0.151
  Angle     :  0.608   6.707   6607  Z= 0.327
  Chirality :  0.044   0.308    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.260 167.628   1060
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.20 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.40), residues: 468
  helix:  2.13 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.89 (0.53), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 278 
 TYR   0.014   0.001   TYR A 221 
 PHE   0.006   0.001   PHE B 269 
 TRP   0.012   0.001   TRP B 309 
 HIS   0.004   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 ( 4765)
  covalent geometry    : angle       0.60846 /  0.33 ( 6607)
  hydrogen bonds       : bond        0.05596 /  4.09 (  251)
  hydrogen bonds       : angle       4.30322 /  2.97 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5885 (tmm) cc_final: 0.5540 (tmm)
REVERT: A   95 TYR cc_start: 0.8036 (t80) cc_final: 0.7425 (t80)
REVERT: A  115 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7724 (t0)
REVERT: A  222 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6923 (mt-10)
REVERT: A  278 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7782 (mtp85)
REVERT: A  279 GLU cc_start: 0.8021 (tp30) cc_final: 0.7636 (tp30)
REVERT: A  285 THR cc_start: 0.7890 (p) cc_final: 0.7620 (p)
REVERT: B   76 ASP cc_start: 0.8027 (t0) cc_final: 0.7725 (t0)
REVERT: B  104 GLN cc_start: 0.7818 (mp10) cc_final: 0.7602 (mp10)
REVERT: B  137 ASP cc_start: 0.7401 (t0) cc_final: 0.7164 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 118
  average time/residue: 0.0746
  time to fit residues: 10.5896
Evaluate side-chains
  122 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   chunk 27 optimal weight:    0.0970
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4156

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.171107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.149545 restraints weight = 6992.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 2.59
r_work: 0.3892 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4765  Z= 0.129
  Angle     :  0.600   6.947   6607  Z= 0.323
  Chirality :  0.043   0.310    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.239 167.340   1060
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.45 %
    Favored  : 77.06 %
  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 are not related in a simple way.
  whole:  1.67 (0.41), residues: 468
  helix:  2.15 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.85 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 278 
 TYR   0.013   0.001   TYR A 221 
 PHE   0.004   0.001   PHE A 275 
 TRP   0.041   0.002   TRP B 309 
 HIS   0.003   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.13 ( 4765)
  covalent geometry    : angle       0.60006 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05425 /  3.97 (  251)
  hydrogen bonds       : angle       4.19691 /  2.90 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5869 (tmm) cc_final: 0.5538 (tmm)
REVERT: A   95 TYR cc_start: 0.7971 (t80) cc_final: 0.7361 (t80)
REVERT: A  115 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7647 (t0)
REVERT: A  222 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6960 (mt-10)
REVERT: A  279 GLU cc_start: 0.7944 (tp30) cc_final: 0.7576 (tp30)
REVERT: A  285 THR cc_start: 0.7880 (p) cc_final: 0.7613 (p)
REVERT: B  104 GLN cc_start: 0.7834 (mp10) cc_final: 0.7526 (mp10)
REVERT: B  126 ARG cc_start: 0.7304 (mtt90) cc_final: 0.6729 (mtm110)
REVERT: B  137 ASP cc_start: 0.7295 (t0) cc_final: 0.7052 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1025
  time to fit residues: 14.4059
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0970
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.171568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.150096 restraints weight = 6882.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.56
r_work: 0.3912 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4765  Z= 0.129
  Angle     :  0.598   7.405   6607  Z= 0.324
  Chirality :  0.042   0.314    745
  Planarity :  0.004   0.043    710
  Dihedral  : 21.219 167.403   1060
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.06 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.20 %
    Favored  : 77.06 %
  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 are not related in a simple way.
  whole:  1.72 (0.41), residues: 468
  helix:  2.19 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.82 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 278 
 TYR   0.016   0.001   TYR A 221 
 PHE   0.034   0.003   PHE A 109 
 TRP   0.011   0.001   TRP B  67 
 HIS   0.003   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.13 ( 4765)
  covalent geometry    : angle       0.59750 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05287 /  3.86 (  251)
  hydrogen bonds       : angle       4.19950 /  2.91 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5881 (tmm) cc_final: 0.5542 (tmm)
REVERT: A   95 TYR cc_start: 0.7977 (t80) cc_final: 0.7335 (t80)
REVERT: A  115 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7615 (t0)
REVERT: A  222 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6926 (mt-10)
REVERT: A  279 GLU cc_start: 0.7910 (tp30) cc_final: 0.7530 (tp30)
REVERT: B   76 ASP cc_start: 0.7992 (t0) cc_final: 0.7682 (t0)
REVERT: B   86 MET cc_start: 0.6410 (tmm) cc_final: 0.6153 (tmm)
REVERT: B  104 GLN cc_start: 0.8003 (mp10) cc_final: 0.7679 (mp10)
REVERT: B  126 ARG cc_start: 0.7310 (mtt90) cc_final: 0.6680 (mtm110)
REVERT: B  137 ASP cc_start: 0.7336 (t0) cc_final: 0.7104 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 113
  average time/residue: 0.1029
  time to fit residues: 13.9625
Evaluate side-chains
  112 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 GLN
** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.169972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.148306 restraints weight = 6910.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 2.57
r_work: 0.3879 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4765  Z= 0.170
  Angle     :  0.632   8.308   6607  Z= 0.340
  Chirality :  0.044   0.318    745
  Planarity :  0.004   0.043    710
  Dihedral  : 21.269 168.061   1060
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.45 %
    Favored  : 76.06 %
  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 are not related in a simple way.
  whole:  1.43 (0.40), residues: 468
  helix:  1.92 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.84 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 278 
 TYR   0.018   0.002   TYR A 221 
 PHE   0.009   0.002   PHE B 269 
 TRP   0.010   0.002   TRP B 307 
 HIS   0.004   0.001   HIS B 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.17 ( 4765)
  covalent geometry    : angle       0.63218 /  0.34 ( 6607)
  hydrogen bonds       : bond        0.05545 /  4.01 (  251)
  hydrogen bonds       : angle       4.34630 /  3.02 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5904 (tmm) cc_final: 0.5570 (tmm)
REVERT: A   95 TYR cc_start: 0.8053 (t80) cc_final: 0.7460 (t80)
REVERT: A  115 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7604 (t0)
REVERT: A  222 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6956 (mt-10)
REVERT: A  278 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7505 (mtp85)
REVERT: A  279 GLU cc_start: 0.8022 (tp30) cc_final: 0.7643 (tp30)
REVERT: B   76 ASP cc_start: 0.7942 (t0) cc_final: 0.7660 (t0)
REVERT: B   86 MET cc_start: 0.6518 (tmm) cc_final: 0.6256 (tmm)
REVERT: B  137 ASP cc_start: 0.7309 (t0) cc_final: 0.7085 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1005
  time to fit residues: 13.2078
Evaluate side-chains
  114 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.171024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.149423 restraints weight = 6929.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.4058 rms_B_bonded: 2.57
r_work: 0.3890 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4765  Z= 0.146
  Angle     :  0.608   7.826   6607  Z= 0.328
  Chirality :  0.043   0.319    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.268 167.372   1060
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.45 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.40), residues: 468
  helix:  1.97 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.81 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 278 
 TYR   0.017   0.001   TYR A 221 
 PHE   0.029   0.003   PHE A 109 
 TRP   0.008   0.001   TRP B 309 
 HIS   0.003   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.15 ( 4765)
  covalent geometry    : angle       0.60810 /  0.33 ( 6607)
  hydrogen bonds       : bond        0.05377 /  3.92 (  251)
  hydrogen bonds       : angle       4.25151 /  2.95 (  706)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1178.84 seconds
wall clock time: 20 minutes 59.17 seconds (1259.17 seconds total)