Starting phenix.real_space_refine
on Thu Jul  2 00:30:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w03_65490/07_2026/9w03_65490_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w03_65490/07_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_65490/07_2026/9w03_65490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w03_65490/07_2026/9w03_65490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w03_65490/07_2026/9w03_65490_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w03_65490/07_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-dev-6108/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: 1.02, per 1000 atoms: 0.22
  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: 0.42
  Conformation dependent library (CDL) restraints added in 84.0 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: 0.43
  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: 0.57

  Time building geometry restraints manager: 0.54 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     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
  bond pdb=" P     A C  37 "
       pdb=" OP1   A C  37 "
    ideal  model  delta    sigma   weight residual
    1.480  1.513 -0.033 2.00e-02 2.50e+03 2.69e+00
  ... (remaining 4760 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 6264
        1.24 -     2.48: 261
        2.48 -     3.72: 61
        3.72 -     4.96: 16
        4.96 -     6.20: 5
  Bond angle restraints: 6607
  Sorted by residual:
  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
  angle pdb=" C1'   G C  26 "
        pdb=" N9    G C  26 "
        pdb=" C4    G C  26 "
      ideal   model   delta    sigma   weight residual
     126.50  130.95   -4.45 1.30e+00 5.92e-01 1.17e+01
  angle pdb=" C1'   G C  26 "
        pdb=" N9    G C  26 "
        pdb=" C8    G C  26 "
      ideal   model   delta    sigma   weight residual
     127.00  122.76    4.24 1.30e+00 5.92e-01 1.06e+01
  angle pdb=" CA  GLN A  66 "
        pdb=" CB  GLN A  66 "
        pdb=" CG  GLN A  66 "
      ideal   model   delta    sigma   weight residual
     114.10  120.30   -6.20 2.00e+00 2.50e-01 9.60e+00
  angle pdb=" N9    G C  26 "
        pdb=" C4    G C  26 "
        pdb=" N3    G C  26 "
      ideal   model   delta    sigma   weight residual
     126.00  127.62   -1.62 6.00e-01 2.78e+00 7.28e+00
  ... (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: 727
       0.103 -    0.205: 16
       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=" CA  VAL B 146 "
            pdb=" N   VAL B 146 "
            pdb=" C   VAL B 146 "
            pdb=" CB  VAL B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.69e-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:             2.060
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.670
  Find NCS groups from input model:        0.050
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.140
-------------------------------------------------------------------------------
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= 0.213
  Angle     :  0.644   6.198   6607  Z= 0.409
  Chirality :  0.044   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        0.00364 /  0.21 ( 4765)
  covalent geometry    : angle       0.64366 /  0.41 ( 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  : 0.135 
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: 0.0792
  time to fit residues: 9.8543
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  : 0.086 
-------------------------------------------------------------------------------
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:    9.9990
   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 = 0.4286 r_free = 0.4286 target = 0.169683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.147368 restraints weight = 6961.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 2.67
r_work: 0.3882 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4765  Z= 0.174
  Angle     :  0.670   7.155   6607  Z= 0.366
  Chirality :  0.043   0.247    745
  Planarity :  0.005   0.037    710
  Dihedral  : 21.516 167.876   1060
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.56 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.71 %
    Favored  : 82.29 %
  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:  1.21 (0.40), residues: 468
  helix:  1.86 (0.29), residues: 292
  sheet:  None (None), residues: 0
  loop : -1.05 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 278 
 TYR   0.021   0.002   TYR B 221 
 PHE   0.007   0.001   PHE A 109 
 TRP   0.013   0.002   TRP B  67 
 HIS   0.003   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.17 ( 4765)
  covalent geometry    : angle       0.67017 /  0.37 ( 6607)
  hydrogen bonds       : bond        0.06550 /  4.64 (  251)
  hydrogen bonds       : angle       4.80094 /  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
  118 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7888 (t80) cc_final: 0.7179 (t80)
REVERT: A  108 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6665 (tm-30)
REVERT: A  205 MET cc_start: 0.8043 (ttm) cc_final: 0.7764 (ttm)
REVERT: B   86 MET cc_start: 0.6510 (tmm) cc_final: 0.6239 (tmm)
REVERT: B  117 SER cc_start: 0.8116 (m) cc_final: 0.7909 (p)
REVERT: B  137 ASP cc_start: 0.7500 (t0) cc_final: 0.7262 (t0)
REVERT: B  305 ARG cc_start: 0.6661 (mtt180) cc_final: 0.6419 (mtt180)
  outliers start: 12
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0795
  time to fit residues: 10.3507
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  : 0.138 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0270
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6038

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.170571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.148318 restraints weight = 6946.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.65
r_work: 0.3888 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4765  Z= 0.150
  Angle     :  0.611   6.885   6607  Z= 0.337
  Chirality :  0.042   0.249    745
  Planarity :  0.004   0.040    710
  Dihedral  : 21.328 167.209   1060
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.96 %
    Favored  : 80.80 %
  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:  1.45 (0.41), residues: 468
  helix:  2.00 (0.29), residues: 297
  sheet:  None (None), residues: 0
  loop : -0.94 (0.54), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.016   0.002   TYR B 221 
 PHE   0.004   0.001   PHE A 269 
 TRP   0.012   0.002   TRP B  67 
 HIS   0.004   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.15 ( 4765)
  covalent geometry    : angle       0.61079 /  0.34 ( 6607)
  hydrogen bonds       : bond        0.06057 /  4.35 (  251)
  hydrogen bonds       : angle       4.50178 /  3.16 (  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
  126 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7928 (t80) cc_final: 0.7174 (t80)
REVERT: A  278 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.6976 (mtp85)
REVERT: A  279 GLU cc_start: 0.7908 (tp30) cc_final: 0.7555 (tp30)
REVERT: B   76 ASP cc_start: 0.8050 (t0) cc_final: 0.7736 (t0)
REVERT: B   86 MET cc_start: 0.6451 (tmm) cc_final: 0.6229 (tmm)
REVERT: B  117 SER cc_start: 0.8107 (m) cc_final: 0.7901 (p)
REVERT: B  137 ASP cc_start: 0.7425 (t0) cc_final: 0.7171 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 119
  average time/residue: 0.0721
  time to fit residues: 10.4720
Evaluate side-chains
  116 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
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  205 MET
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  159 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:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0050
   chunk 10 optimal weight:    0.4980
   chunk 20 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.2752

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.172809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.150615 restraints weight = 6964.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 2.63
r_work: 0.3915 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4765  Z= 0.127
  Angle     :  0.578   6.183   6607  Z= 0.321
  Chirality :  0.041   0.253    745
  Planarity :  0.004   0.039    710
  Dihedral  : 21.237 166.615   1060
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.46 %
    Favored  : 80.55 %
  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:  1.75 (0.41), residues: 468
  helix:  2.23 (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   0.003   0.000   ARG B 199 
 TYR   0.010   0.001   TYR B 221 
 PHE   0.006   0.001   PHE A 109 
 TRP   0.010   0.001   TRP B  67 
 HIS   0.003   0.001   HIS B 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.13 ( 4765)
  covalent geometry    : angle       0.57827 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05525 /  4.01 (  251)
  hydrogen bonds       : angle       4.24500 /  2.97 (  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
  115 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7868 (t80) cc_final: 0.7185 (t80)
REVERT: A  205 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7719 (ttm)
REVERT: A  279 GLU cc_start: 0.7899 (tp30) cc_final: 0.7536 (tp30)
REVERT: A  305 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8175 (mtt90)
REVERT: B   86 MET cc_start: 0.6416 (tmm) cc_final: 0.6214 (tmm)
REVERT: B   91 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: B  117 SER cc_start: 0.7973 (m) cc_final: 0.7771 (p)
REVERT: B  126 ARG cc_start: 0.7370 (mtt90) cc_final: 0.6847 (mtm110)
REVERT: B  137 ASP cc_start: 0.7276 (t0) cc_final: 0.6989 (t0)
REVERT: B  305 ARG cc_start: 0.6537 (mtt180) cc_final: 0.6288 (mtt180)
  outliers start: 8
  outliers final: 5
  residues processed: 110
  average time/residue: 0.1046
  time to fit residues: 14.0034
Evaluate side-chains
  114 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 MET
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:    0.0030
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.171774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.149574 restraints weight = 6907.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 2.65
r_work: 0.3880 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4765  Z= 0.137
  Angle     :  0.590   9.412   6607  Z= 0.323
  Chirality :  0.041   0.258    745
  Planarity :  0.004   0.040    710
  Dihedral  : 21.208 167.605   1060
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.06 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.45 %
    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:  1.78 (0.41), residues: 468
  helix:  2.26 (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   0.009   0.000   ARG A 278 
 TYR   0.011   0.001   TYR A 221 
 PHE   0.004   0.001   PHE B 269 
 TRP   0.012   0.001   TRP B  67 
 HIS   0.003   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.14 ( 4765)
  covalent geometry    : angle       0.58973 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05436 /  3.93 (  251)
  hydrogen bonds       : angle       4.18899 /  2.90 (  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
  123 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5919 (tmm) cc_final: 0.5646 (tmm)
REVERT: A   95 TYR cc_start: 0.7987 (t80) cc_final: 0.7399 (t80)
REVERT: A  278 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7296 (mtp85)
REVERT: A  279 GLU cc_start: 0.7944 (tp30) cc_final: 0.7554 (tp30)
REVERT: B   76 ASP cc_start: 0.8004 (t0) cc_final: 0.7686 (t0)
REVERT: B  104 GLN cc_start: 0.7799 (mp10) cc_final: 0.7532 (mp10)
REVERT: B  117 SER cc_start: 0.8002 (m) cc_final: 0.7797 (p)
REVERT: B  126 ARG cc_start: 0.7363 (mtt90) cc_final: 0.6749 (mtm110)
REVERT: B  137 ASP cc_start: 0.7382 (t0) cc_final: 0.7102 (t0)
REVERT: B  266 MET cc_start: 0.7239 (mtp) cc_final: 0.7024 (mtp)
REVERT: B  305 ARG cc_start: 0.6758 (mtt180) cc_final: 0.6474 (mtt180)
  outliers start: 12
  outliers final: 6
  residues processed: 118
  average time/residue: 0.0945
  time to fit residues: 13.4802
Evaluate side-chains
  117 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   overall best weight:    0.5958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 223 GLN
B  90 ASN
** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.171606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.149070 restraints weight = 7002.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4058 rms_B_bonded: 2.69
r_work: 0.3884 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
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   0.033   4765  Z= 0.145
  Angle     :  0.581   7.156   6607  Z= 0.321
  Chirality :  0.041   0.259    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.208 167.577   1060
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.95 %
    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:  1.79 (0.41), residues: 468
  helix:  2.25 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.80 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 278 
 TYR   0.015   0.002   TYR A 221 
 PHE   0.005   0.001   PHE A 275 
 TRP   0.012   0.001   TRP A 274 
 HIS   0.003   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.15 ( 4765)
  covalent geometry    : angle       0.58091 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05434 /  3.95 (  251)
  hydrogen bonds       : angle       4.23720 /  2.93 (  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
  118 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5932 (tmm) cc_final: 0.5617 (tmm)
REVERT: A   95 TYR cc_start: 0.7954 (t80) cc_final: 0.7340 (t80)
REVERT: A  279 GLU cc_start: 0.7988 (tp30) cc_final: 0.7601 (tp30)
REVERT: B   76 ASP cc_start: 0.7954 (t0) cc_final: 0.7647 (t0)
REVERT: B  126 ARG cc_start: 0.7374 (mtt90) cc_final: 0.6797 (mtm110)
REVERT: B  137 ASP cc_start: 0.7328 (t0) cc_final: 0.7031 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 114
  average time/residue: 0.1025
  time to fit residues: 13.9860
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  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.0030
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0970
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.4325 r_free = 0.4325 target = 0.172412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.150754 restraints weight = 6843.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.57
r_work: 0.3909 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4765  Z= 0.125
  Angle     :  0.580   6.744   6607  Z= 0.319
  Chirality :  0.040   0.259    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.196 167.349   1060
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.06 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.95 %
    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:  1.87 (0.41), residues: 468
  helix:  2.31 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.77 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 278 
 TYR   0.013   0.001   TYR A 221 
 PHE   0.011   0.001   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        0.00249 /  0.12 ( 4765)
  covalent geometry    : angle       0.57970 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05190 /  3.80 (  251)
  hydrogen bonds       : angle       4.15007 /  2.88 (  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
  117 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5950 (tmm) cc_final: 0.5624 (tmm)
REVERT: A   95 TYR cc_start: 0.7936 (t80) cc_final: 0.7260 (t80)
REVERT: A  278 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7398 (mtp85)
REVERT: A  279 GLU cc_start: 0.7901 (tp30) cc_final: 0.7521 (tp30)
REVERT: B   76 ASP cc_start: 0.7921 (t0) cc_final: 0.7638 (t0)
REVERT: B  137 ASP cc_start: 0.7239 (t0) cc_final: 0.6959 (t0)
REVERT: B  305 ARG cc_start: 0.6617 (mtt180) cc_final: 0.6398 (mtt180)
  outliers start: 9
  outliers final: 8
  residues processed: 112
  average time/residue: 0.0977
  time to fit residues: 13.0837
Evaluate side-chains
  116 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  256 HIS
Chi-restraints excluded: chain A residue  303 GLN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0020
   overall best weight:    0.4988

-------------------------------------------------------------------------------
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 = 0.4321 r_free = 0.4321 target = 0.172062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.150032 restraints weight = 7011.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.61
r_work: 0.3901 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4765  Z= 0.136
  Angle     :  0.581   7.552   6607  Z= 0.319
  Chirality :  0.040   0.261    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.197 167.752   1060
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.95 %
    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:  1.82 (0.41), residues: 468
  helix:  2.27 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.79 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 278 
 TYR   0.014   0.001   TYR A 221 
 PHE   0.008   0.002   PHE A 275 
 TRP   0.013   0.001   TRP B 309 
 HIS   0.003   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.14 ( 4765)
  covalent geometry    : angle       0.58082 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05191 /  3.79 (  251)
  hydrogen bonds       : angle       4.17919 /  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
  117 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5969 (tmm) cc_final: 0.5645 (tmm)
REVERT: A   95 TYR cc_start: 0.7947 (t80) cc_final: 0.7323 (t80)
REVERT: A  222 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6930 (mt-10)
REVERT: A  279 GLU cc_start: 0.7979 (tp30) cc_final: 0.7593 (tp30)
REVERT: B   76 ASP cc_start: 0.7981 (t0) cc_final: 0.7687 (t0)
REVERT: B  137 ASP cc_start: 0.7298 (t0) cc_final: 0.7019 (t0)
REVERT: B  305 ARG cc_start: 0.6677 (mtt180) cc_final: 0.6364 (mtt180)
  outliers start: 12
  outliers final: 9
  residues processed: 111
  average time/residue: 0.0889
  time to fit residues: 12.0946
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=1.50
-------------------------------------------------------------------------------
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:    0.3980
   chunk 40 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4320 r_free = 0.4320 target = 0.172119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.150311 restraints weight = 6855.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.61
r_work: 0.3905 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4765  Z= 0.135
  Angle     :  0.583   7.464   6607  Z= 0.320
  Chirality :  0.040   0.262    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.203 167.777   1060
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.27 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.70 %
    Favored  : 76.31 %
  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:  1.81 (0.41), residues: 468
  helix:  2.26 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.78 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 278 
 TYR   0.014   0.001   TYR A 221 
 PHE   0.040   0.003   PHE A 109 
 TRP   0.013   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 ( 4765)
  covalent geometry    : angle       0.58281 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05110 /  3.73 (  251)
  hydrogen bonds       : angle       4.15200 /  2.87 (  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: 12
    poor density    : 107
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5941 (tmm) cc_final: 0.5588 (tmm)
REVERT: A   95 TYR cc_start: 0.7942 (t80) cc_final: 0.7382 (t80)
REVERT: A  222 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6919 (mt-10)
REVERT: A  278 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7357 (mtp85)
REVERT: A  279 GLU cc_start: 0.7969 (tp30) cc_final: 0.7585 (tp30)
REVERT: B   76 ASP cc_start: 0.7953 (t0) cc_final: 0.7665 (t0)
REVERT: B  126 ARG cc_start: 0.7373 (mtt90) cc_final: 0.6977 (mtm110)
REVERT: B  137 ASP cc_start: 0.7238 (t0) cc_final: 0.6981 (t0)
REVERT: B  219 THR cc_start: 0.7659 (m) cc_final: 0.7370 (p)
REVERT: B  305 ARG cc_start: 0.6687 (mtt180) cc_final: 0.6372 (mtt180)
  outliers start: 12
  outliers final: 10
  residues processed: 112
  average time/residue: 0.0887
  time to fit residues: 11.8621
Evaluate side-chains
  117 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  303 GLN
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 48 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0020
   overall best weight:    0.6388

-------------------------------------------------------------------------------
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 = 0.4314 r_free = 0.4314 target = 0.171353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.149558 restraints weight = 6920.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 2.56
r_work: 0.3898 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
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      :  0.003   0.040   4765  Z= 0.150
  Angle     :  0.589   7.029   6607  Z= 0.325
  Chirality :  0.041   0.263    745
  Planarity :  0.004   0.041    710
  Dihedral  : 21.239 168.026   1060
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.91 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.45 %
    Favored  : 76.56 %
  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:  1.75 (0.41), residues: 468
  helix:  2.20 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.78 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 278 
 TYR   0.017   0.002   TYR A 221 
 PHE   0.011   0.002   PHE A 275 
 TRP   0.014   0.002   TRP A 274 
 HIS   0.003   0.001   HIS B 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.15 ( 4765)
  covalent geometry    : angle       0.58900 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05200 /  3.79 (  251)
  hydrogen bonds       : angle       4.18521 /  2.90 (  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
  117 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5946 (tmm) cc_final: 0.5617 (tmm)
REVERT: A   95 TYR cc_start: 0.7978 (t80) cc_final: 0.7344 (t80)
REVERT: A  199 ARG cc_start: 0.7675 (ttm170) cc_final: 0.7169 (ttp-170)
REVERT: A  222 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6908 (mt-10)
REVERT: A  278 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7516 (mtp85)
REVERT: A  279 GLU cc_start: 0.7967 (tp30) cc_final: 0.7597 (tp30)
REVERT: B   76 ASP cc_start: 0.7899 (t0) cc_final: 0.7624 (t0)
REVERT: B  126 ARG cc_start: 0.7375 (mtt90) cc_final: 0.6738 (mtm110)
REVERT: B  137 ASP cc_start: 0.7227 (t0) cc_final: 0.6965 (t0)
REVERT: B  305 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6491 (mtt180)
  outliers start: 12
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0835
  time to fit residues: 11.2296
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  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4312 r_free = 0.4312 target = 0.171212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.149405 restraints weight = 6934.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.58
r_work: 0.3894 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4765  Z= 0.152
  Angle     :  0.581   6.957   6607  Z= 0.321
  Chirality :  0.041   0.263    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.264 167.865   1060
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.20 %
    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:  1.72 (0.41), residues: 468
  helix:  2.18 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.80 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 278 
 TYR   0.018   0.002   TYR A 221 
 PHE   0.013   0.002   PHE A 275 
 TRP   0.014   0.002   TRP B 309 
 HIS   0.004   0.001   HIS B 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.15 ( 4765)
  covalent geometry    : angle       0.58124 /  0.32 ( 6607)
  hydrogen bonds       : bond        0.05193 /  3.78 (  251)
  hydrogen bonds       : angle       4.20735 /  2.91 (  706)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1117.65 seconds
wall clock time: 19 minutes 56.35 seconds (1196.35 seconds total)