Starting phenix.real_space_refine
on Tue Feb  3 15:47:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xzs_72370/02_2026/9xzs_72370_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xzs_72370/02_2026/9xzs_72370.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xzs_72370/02_2026/9xzs_72370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xzs_72370/02_2026/9xzs_72370.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xzs_72370/02_2026/9xzs_72370_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xzs_72370/02_2026/9xzs_72370_neut.cif"
  }
  resolution = 3.89
  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=  -0.000 sd=   0.002
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      71      5.49       5
     S      14      5.16       5
     C    2578      2.51       5
     N     791      2.21       5
     O    1059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4513
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1513
          Classifications: {'RNA': 71}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 12, 'rna3p': 58}
    Chain: "B"
      Number of atoms: 1421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1421
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 5, 'TRANS': 165}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1551
          Classifications: {'peptide': 188}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 180}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'AN6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.22, per 1000 atoms: 0.27
  Number of scatterers: 4513
  At special positions: 0
  Unit cell: (65.096, 76.632, 117.832, 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      14     16.00
     P      71     15.00
     O    1059      8.00
     N     791      7.00
     C    2578      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 290.2 milliseconds
  

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  690

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 3 sheets defined
      38.9% alpha, 2.8% beta
      19 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'B' and resid 108 through 127
      removed outlier: 3.901A  pdb=" N   ILE B 112 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 152
      removed outlier: 4.033A  pdb=" N   ARG B 147 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 160
      removed outlier: 3.533A  pdb=" N   ASN B 159 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TRP B 160 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 156 through 160'
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 216 through 225
    Processing helix  chain 'B' and resid 253 through 262
    Processing helix  chain 'C' and resid 108 through 129
    Processing helix  chain 'C' and resid 143 through 151
    Processing helix  chain 'C' and resid 152 through 155
      removed outlier: 3.540A  pdb=" N   THR C 155 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 152 through 155'
    Processing helix  chain 'C' and resid 169 through 173
      removed outlier: 3.504A  pdb=" N   MET C 172 " --> pdb=" O   ASP C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 225
    Processing helix  chain 'C' and resid 247 through 262
    Processing helix  chain 'C' and resid 265 through 272
    Processing sheet with id=AA1, first strand: chain 'B' and resid 184 through 185
      removed outlier: 6.769A  pdb=" N   VAL B 184 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 136 through 137
      removed outlier: 4.310A  pdb=" N   VAL C 137 " --> pdb=" O   LYS C 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 182 through 185
      removed outlier: 6.607A  pdb=" N   LYS C 182 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   ILE C 204 " --> pdb=" O   LYS C 182 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL C 184 " --> pdb=" O   ILE C 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    83 hydrogen bonds defined for protein.
    231 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      100 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 0.43

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 610
        1.31 -     1.43: 1659
        1.43 -     1.56: 2309
        1.56 -     1.68: 147
        1.68 -     1.81: 25
  Bond restraints: 4750
  Sorted by residual:
  bond pdb=" C4'   G A   9 "
       pdb=" C3'   G A   9 "
    ideal  model  delta    sigma   weight residual
    1.527  1.269  0.258 1.50e-02 4.44e+03 2.96e+02
  bond pdb=" C4'   G A   9 "
       pdb=" O4'   G A   9 "
    ideal  model  delta    sigma   weight residual
    1.454  1.697 -0.243 1.50e-02 4.44e+03 2.62e+02
  bond pdb=" C2' AN6 A 101 "
       pdb=" C3' AN6 A 101 "
    ideal  model  delta    sigma   weight residual
    1.532  1.278  0.254 2.00e-02 2.50e+03 1.61e+02
  bond pdb=" C6  AN6 A 101 "
       pdb=" N6  AN6 A 101 "
    ideal  model  delta    sigma   weight residual
    1.334  1.516 -0.182 2.00e-02 2.50e+03 8.29e+01
  bond pdb=" C2    G A   9 "
       pdb=" N3    G A   9 "
    ideal  model  delta    sigma   weight residual
    1.323  1.478 -0.155 2.00e-02 2.50e+03 6.04e+01
  ... (remaining 4745 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.89: 6743
        9.89 -    19.77: 9
       19.77 -    29.66: 1
       29.66 -    39.55: 0
       39.55 -    49.43: 1
  Bond angle restraints: 6754
  Sorted by residual:
  angle pdb=" C3'   G A   9 "
        pdb=" O3'   G A   9 "
        pdb=" P     G A  10 "
      ideal   model   delta    sigma   weight residual
     120.20  169.63  -49.43 1.50e+00 4.44e-01 1.09e+03
  angle pdb=" O3'   A A   8 "
        pdb=" P     G A   9 "
        pdb=" O5'   G A   9 "
      ideal   model   delta    sigma   weight residual
     104.00   85.22   18.78 1.50e+00 4.44e-01 1.57e+02
  angle pdb=" O3'   A A   8 "
        pdb=" P     G A   9 "
        pdb=" OP1   G A   9 "
      ideal   model   delta    sigma   weight residual
     108.00   84.79   23.21 3.00e+00 1.11e-01 5.98e+01
  angle pdb=" O3'   G A   9 "
        pdb=" P     G A  10 "
        pdb=" O5'   G A  10 "
      ideal   model   delta    sigma   weight residual
     104.00  115.52  -11.52 1.50e+00 4.44e-01 5.90e+01
  angle pdb=" C5    G A   9 "
        pdb=" C6    G A   9 "
        pdb=" O6    G A   9 "
      ideal   model   delta    sigma   weight residual
     128.60  114.35   14.25 3.00e+00 1.11e-01 2.25e+01
  ... (remaining 6749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.87: 2699
       31.87 -    63.74: 249
       63.74 -    95.62: 38
       95.62 -   127.49: 1
      127.49 -   159.36: 1
  Dihedral angle restraints: 2988
    sinusoidal: 1927
      harmonic: 1061
  Sorted by residual:
  dihedral pdb=" C4'   G A   9 "
           pdb=" C3'   G A   9 "
           pdb=" O3'   G A   9 "
           pdb=" P     G A  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     250.00   90.64  159.36     1      3.50e+01 8.16e-04 1.52e+01
  dihedral pdb=" C4'   U A  11 "
           pdb=" O4'   U A  11 "
           pdb=" C1'   U A  11 "
           pdb=" C2'   U A  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -21.00    1.79  -22.79     1      8.00e+00 1.56e-02 1.17e+01
  dihedral pdb=" C3'   U A  11 "
           pdb=" C4'   U A  11 "
           pdb=" O4'   U A  11 "
           pdb=" C1'   U A  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00  -24.16   22.16     1      8.00e+00 1.56e-02 1.11e+01
  ... (remaining 2985 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.470: 800
       0.470 -    0.940: 0
       0.940 -    1.409: 0
       1.409 -    1.879: 0
       1.879 -    2.349: 1
  Chirality restraints: 801
  Sorted by residual:
  chirality pdb=" P     G A   9 "
            pdb=" OP1   G A   9 "
            pdb=" OP2   G A   9 "
            pdb=" O5'   G A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -0.06    2.35 2.00e-01 2.50e+01 1.38e+02
  chirality pdb=" C3' AN6 A 101 "
            pdb=" C2' AN6 A 101 "
            pdb=" C4' AN6 A 101 "
            pdb=" O3' AN6 A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.41   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CA' AN6 A 101 "
            pdb=" C'  AN6 A 101 "
            pdb=" CB' AN6 A 101 "
            pdb=" N'  AN6 A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.62   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 798 not shown)

  Planarity restraints: 599
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  66 "   -0.036 2.00e-02 2.50e+03   2.38e-02 1.28e+01
        pdb=" N1    U A  66 "    0.056 2.00e-02 2.50e+03
        pdb=" C2    U A  66 "   -0.021 2.00e-02 2.50e+03
        pdb=" O2    U A  66 "    0.011 2.00e-02 2.50e+03
        pdb=" N3    U A  66 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U A  66 "   -0.005 2.00e-02 2.50e+03
        pdb=" O4    U A  66 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    U A  66 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U A  66 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  63 "    0.016 2.00e-02 2.50e+03   1.18e-02 4.17e+00
        pdb=" N9    G A  63 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8    G A  63 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G A  63 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    G A  63 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    G A  63 "    0.005 2.00e-02 2.50e+03
        pdb=" O6    G A  63 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A  63 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    G A  63 "   -0.004 2.00e-02 2.50e+03
        pdb=" N2    G A  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    G A  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G A  63 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  62 "   -0.015 2.00e-02 2.50e+03   1.12e-02 3.78e+00
        pdb=" N9    G A  62 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    G A  62 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G A  62 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G A  62 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    G A  62 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G A  62 "    0.001 2.00e-02 2.50e+03
        pdb=" N1    G A  62 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G A  62 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G A  62 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    G A  62 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    G A  62 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 596 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 409
        2.74 -     3.28: 4792
        3.28 -     3.82: 8459
        3.82 -     4.36: 9730
        4.36 -     4.90: 13985
  Nonbonded interactions: 37375
  Sorted by model distance:
  nonbonded pdb=" N2    G A  10 "
            pdb=" O2    C A  45 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" CE  LYS B 211 "
            pdb=" N1  AN6 A 101 "
     model   vdw
     2.247 3.520
  nonbonded pdb=" OG1 THR B 248 "
            pdb=" O'  AN6 A 101 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O6    G A   9 "
            pdb=" O3' AN6 A 101 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O4    U A  52 "
            pdb=" N7    A A  56 "
     model   vdw
     2.366 2.496
  ... (remaining 37370 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 'B'
  selection = (chain 'C' and resid 94 through 264)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.070
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.200
  Find NCS groups from input model:        0.030
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5273
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      :  0.010   0.258   4751  Z= 0.587
  Angle     :  1.124  49.434   6754  Z= 0.613
  Chirality :  0.095   2.349    801
  Planarity :  0.004   0.024    599
  Dihedral  : 21.247 159.358   2298
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 11.27 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.27 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 (0.47), residues: 355
  helix:  1.24 (0.51), residues: 115
  sheet: -2.99 (1.22), residues: 20
  loop : -2.09 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 202 
 TYR   0.011   0.002   TYR B 123 
 PHE   0.019   0.002   PHE B 163 
 TRP   0.012   0.003   TRP B 160 
 HIS   0.004   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.01040 ( 4750)
  covalent geometry    : angle       1.12414 ( 6754)
  hydrogen bonds       : bond        0.11359 (  135)
  hydrogen bonds       : angle       6.33293 (  331)
  Misc. bond           : bond        0.02968 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.159 
Fit side-chains
REVERT: B  107 MET cc_start: 0.2810 (mpp) cc_final: 0.2551 (mpp)
REVERT: B  254 LEU cc_start: 0.8601 (mt) cc_final: 0.8385 (mt)
REVERT: C  107 MET cc_start: 0.1129 (OUTLIER) cc_final: 0.0799 (pp-130)
REVERT: C  146 GLN cc_start: 0.9481 (mp10) cc_final: 0.9275 (mp10)
REVERT: C  225 MET cc_start: 0.1190 (ptm) cc_final: 0.0472 (ppp)
  outliers start: 8
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0465
  time to fit residues: 3.0719
Evaluate side-chains
  30 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  249 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0040
   chunk 37 optimal weight:    0.0270
   overall best weight:    0.4050

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

Flipped N/Q/H residues before XYZ refinement:
B 154 ASN
B 162 HIS
B 223 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.135965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.115499 restraints weight = 35136.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.118156 restraints weight = 25405.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.119952 restraints weight = 20533.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.121172 restraints weight = 17580.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.121544 restraints weight = 15711.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5057
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4751  Z= 0.116
  Angle     :  0.643  10.925   6754  Z= 0.313
  Chirality :  0.039   0.245    801
  Planarity :  0.004   0.025    599
  Dihedral  : 21.065 127.702   1525
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  1.13 %
    Allowed  : 11.83 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.52 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -1.64 (0.45), residues: 355
  helix:  0.88 (0.50), residues: 117
  sheet: -3.12 (1.23), residues: 20
  loop : -2.14 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 202 
 TYR   0.013   0.002   TYR C 157 
 PHE   0.009   0.001   PHE C 259 
 TRP   0.007   0.001   TRP C 264 
 HIS   0.009   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4750)
  covalent geometry    : angle       0.64342 ( 6754)
  hydrogen bonds       : bond        0.03511 (  135)
  hydrogen bonds       : angle       4.97313 (  331)
  Misc. bond           : bond        0.00276 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B  107 MET cc_start: 0.2865 (mpp) cc_final: 0.2625 (mpp)
REVERT: B  254 LEU cc_start: 0.8682 (mt) cc_final: 0.8454 (mt)
REVERT: C  107 MET cc_start: 0.1202 (OUTLIER) cc_final: 0.0865 (pp-130)
REVERT: C  201 MET cc_start: 0.2832 (mmt) cc_final: 0.2563 (mmm)
REVERT: C  225 MET cc_start: 0.1168 (ptm) cc_final: 0.0489 (ppp)
  outliers start: 9
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0315
  time to fit residues: 1.6427
Evaluate side-chains
  33 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  235 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 ASN
C 253 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.125320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.104974 restraints weight = 35361.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.107189 restraints weight = 26276.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.108392 restraints weight = 21642.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.109721 restraints weight = 18993.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.110546 restraints weight = 17097.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.4461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5555
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4751  Z= 0.176
  Angle     :  0.695  10.336   6754  Z= 0.348
  Chirality :  0.039   0.206    801
  Planarity :  0.005   0.047    599
  Dihedral  : 21.567 126.172   1524
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 20.83
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.39 %
    Favored  : 86.20 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 20.61 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -1.76 (0.45), residues: 355
  helix:  0.47 (0.49), residues: 113
  sheet: -3.96 (1.70), residues: 10
  loop : -2.02 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 143 
 TYR   0.024   0.003   TYR B 185 
 PHE   0.017   0.002   PHE B 163 
 TRP   0.010   0.002   TRP C 160 
 HIS   0.009   0.002   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4750)
  covalent geometry    : angle       0.69538 ( 6754)
  hydrogen bonds       : bond        0.04302 (  135)
  hydrogen bonds       : angle       5.21445 (  331)
  Misc. bond           : bond        0.00292 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 27
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: B  185 TYR cc_start: 0.7903 (t80) cc_final: 0.7602 (t80)
REVERT: B  254 LEU cc_start: 0.9000 (mt) cc_final: 0.8568 (mt)
REVERT: C  163 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8078 (m-80)
REVERT: C  225 MET cc_start: 0.1617 (ptm) cc_final: 0.1007 (ppp)
  outliers start: 18
  outliers final: 11
  residues processed: 38
  average time/residue: 0.0449
  time to fit residues: 2.6044
Evaluate side-chains
  36 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  256 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0870
   chunk 21 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0670
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.0302

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

Flipped N/Q/H residues before XYZ refinement:
C 131 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.127602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.107632 restraints weight = 35238.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.109851 restraints weight = 26170.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.111419 restraints weight = 21439.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.112491 restraints weight = 18619.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.112831 restraints weight = 16769.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5440
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4751  Z= 0.121
  Angle     :  0.642   9.208   6754  Z= 0.316
  Chirality :  0.038   0.181    801
  Planarity :  0.004   0.032    599
  Dihedral  : 21.424 127.286   1521
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.96 %
    Favored  : 85.63 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.03 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -1.83 (0.44), residues: 355
  helix:  0.43 (0.49), residues: 117
  sheet: -3.84 (1.72), residues: 10
  loop : -2.13 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 127 
 TYR   0.014   0.002   TYR C 157 
 PHE   0.008   0.001   PHE B 163 
 TRP   0.006   0.001   TRP C 160 
 HIS   0.012   0.002   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4750)
  covalent geometry    : angle       0.64160 ( 6754)
  hydrogen bonds       : bond        0.03219 (  135)
  hydrogen bonds       : angle       4.81735 (  331)
  Misc. bond           : bond        0.00304 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 27
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: B  185 TYR cc_start: 0.7870 (t80) cc_final: 0.7513 (t80)
REVERT: B  254 LEU cc_start: 0.9018 (mt) cc_final: 0.8665 (mt)
REVERT: C  163 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8134 (m-80)
REVERT: C  225 MET cc_start: 0.1692 (ptm) cc_final: 0.0964 (ppp)
  outliers start: 15
  outliers final: 12
  residues processed: 36
  average time/residue: 0.0447
  time to fit residues: 2.4729
Evaluate side-chains
  40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  256 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    0.0980
   chunk 21 optimal weight:   20.0000
   chunk 34 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
C 161 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.127434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.107448 restraints weight = 35402.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.109749 restraints weight = 26076.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.111461 restraints weight = 21186.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.112572 restraints weight = 18241.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.113360 restraints weight = 16361.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5474
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4751  Z= 0.112
  Angle     :  0.621   8.266   6754  Z= 0.306
  Chirality :  0.037   0.155    801
  Planarity :  0.004   0.033    599
  Dihedral  : 21.386 128.617   1521
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.39 %
    Favored  : 86.20 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 22.12 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 (0.45), residues: 355
  helix:  0.60 (0.49), residues: 117
  sheet: -3.74 (1.77), residues: 10
  loop : -2.10 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 127 
 TYR   0.016   0.001   TYR C 157 
 PHE   0.008   0.001   PHE B 163 
 TRP   0.007   0.001   TRP C 160 
 HIS   0.006   0.001   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4750)
  covalent geometry    : angle       0.62140 ( 6754)
  hydrogen bonds       : bond        0.03069 (  135)
  hydrogen bonds       : angle       4.51135 (  331)
  Misc. bond           : bond        0.00253 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 26
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 LEU cc_start: 0.9074 (mt) cc_final: 0.8732 (mt)
REVERT: C  154 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.6176 (p0)
REVERT: C  163 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8320 (m-80)
REVERT: C  225 MET cc_start: 0.1730 (ptm) cc_final: 0.1000 (ppp)
  outliers start: 18
  outliers final: 14
  residues processed: 38
  average time/residue: 0.0525
  time to fit residues: 2.9165
Evaluate side-chains
  40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  160 TRP
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0050
   chunk 39 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 38 optimal weight:    0.0470
   chunk 35 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0970
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.4092

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

Flipped N/Q/H residues before XYZ refinement:
C 161 ASN
** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.129046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.109041 restraints weight = 36390.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.111561 restraints weight = 26427.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.113231 restraints weight = 21263.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.114378 restraints weight = 18236.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.115248 restraints weight = 16229.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.4537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5329
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4751  Z= 0.104
  Angle     :  0.616   8.386   6754  Z= 0.303
  Chirality :  0.037   0.156    801
  Planarity :  0.004   0.031    599
  Dihedral  : 21.344 129.112   1521
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.11 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 23.64 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 (0.45), residues: 355
  helix:  0.61 (0.49), residues: 117
  sheet: -3.73 (1.72), residues: 10
  loop : -1.95 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 127 
 TYR   0.016   0.001   TYR C 157 
 PHE   0.008   0.001   PHE C 148 
 TRP   0.009   0.001   TRP C 160 
 HIS   0.006   0.001   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 4750)
  covalent geometry    : angle       0.61595 ( 6754)
  hydrogen bonds       : bond        0.02943 (  135)
  hydrogen bonds       : angle       4.32812 (  331)
  Misc. bond           : bond        0.00261 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 28
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 LEU cc_start: 0.8989 (mt) cc_final: 0.8619 (mt)
REVERT: C  163 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8362 (m-80)
REVERT: C  225 MET cc_start: 0.1491 (ptm) cc_final: 0.0786 (ppp)
  outliers start: 17
  outliers final: 16
  residues processed: 38
  average time/residue: 0.0462
  time to fit residues: 2.6731
Evaluate side-chains
  42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 25
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  160 TRP
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  256 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** C 212 ASN ** 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 = 0.4721 r_free = 0.4721 target = 0.127382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.107283 restraints weight = 35551.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.109628 restraints weight = 26133.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.111260 restraints weight = 21210.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.112397 restraints weight = 18278.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.113193 restraints weight = 16410.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5467
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4751  Z= 0.110
  Angle     :  0.618   9.330   6754  Z= 0.303
  Chirality :  0.037   0.153    801
  Planarity :  0.004   0.034    599
  Dihedral  : 21.428 129.703   1521
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.39 %
    Favored  : 86.20 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 24.24 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -1.74 (0.45), residues: 355
  helix:  0.10 (0.47), residues: 128
  sheet: -3.82 (1.72), residues: 10
  loop : -1.90 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 143 
 TYR   0.015   0.001   TYR C 157 
 PHE   0.011   0.001   PHE B 163 
 TRP   0.007   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4750)
  covalent geometry    : angle       0.61768 ( 6754)
  hydrogen bonds       : bond        0.02991 (  135)
  hydrogen bonds       : angle       4.38252 (  331)
  Misc. bond           : bond        0.00207 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 24
  time to evaluate  : 0.149 
Fit side-chains
REVERT: B  254 LEU cc_start: 0.9063 (mt) cc_final: 0.8698 (mt)
REVERT: C  154 ASN cc_start: 0.6409 (OUTLIER) cc_final: 0.6129 (p0)
REVERT: C  163 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8401 (m-80)
REVERT: C  225 MET cc_start: 0.1648 (ptm) cc_final: 0.0961 (ppp)
  outliers start: 18
  outliers final: 14
  residues processed: 37
  average time/residue: 0.0465
  time to fit residues: 2.6043
Evaluate side-chains
  39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 23
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  160 TRP
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  256 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0170
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.6022

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.124414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.104671 restraints weight = 36832.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.106644 restraints weight = 26375.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.108384 restraints weight = 21388.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.109239 restraints weight = 18394.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.110223 restraints weight = 16614.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.4482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5580
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4751  Z= 0.127
  Angle     :  0.638   9.975   6754  Z= 0.316
  Chirality :  0.038   0.148    801
  Planarity :  0.004   0.034    599
  Dihedral  : 21.508 129.441   1521
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.11 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 24.24 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 (0.45), residues: 355
  helix:  0.22 (0.48), residues: 122
  sheet: -3.92 (1.72), residues: 10
  loop : -1.97 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 143 
 TYR   0.015   0.002   TYR C 157 
 PHE   0.013   0.001   PHE B 163 
 TRP   0.009   0.002   TRP C 160 
 HIS   0.004   0.001   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4750)
  covalent geometry    : angle       0.63752 ( 6754)
  hydrogen bonds       : bond        0.03166 (  135)
  hydrogen bonds       : angle       4.45327 (  331)
  Misc. bond           : bond        0.00179 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 24
  time to evaluate  : 0.153 
Fit side-chains
REVERT: B  185 TYR cc_start: 0.7396 (t80) cc_final: 0.7179 (t80)
REVERT: B  254 LEU cc_start: 0.9112 (mt) cc_final: 0.8739 (mt)
REVERT: C  154 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.6532 (p0)
REVERT: C  163 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8434 (m-80)
REVERT: C  225 MET cc_start: 0.1893 (ptm) cc_final: 0.1204 (ppp)
  outliers start: 19
  outliers final: 14
  residues processed: 38
  average time/residue: 0.0457
  time to fit residues: 2.6542
Evaluate side-chains
  40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  160 TRP
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  256 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0670
   chunk 40 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    2.1722

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** 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 = 0.4655 r_free = 0.4655 target = 0.121536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.101671 restraints weight = 36744.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.103768 restraints weight = 26383.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.105552 restraints weight = 21211.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.106653 restraints weight = 18255.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.107435 restraints weight = 16354.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.4438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5640
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4751  Z= 0.153
  Angle     :  0.661   9.857   6754  Z= 0.330
  Chirality :  0.039   0.142    801
  Planarity :  0.005   0.038    599
  Dihedral  : 21.585 128.624   1521
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 13.24 %
    Favored  : 85.35 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 25.15 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -1.99 (0.44), residues: 355
  helix:  0.09 (0.47), residues: 122
  sheet: -3.93 (1.72), residues: 10
  loop : -2.14 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 127 
 TYR   0.016   0.002   TYR C 123 
 PHE   0.015   0.002   PHE B 163 
 TRP   0.009   0.002   TRP C 160 
 HIS   0.011   0.002   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4750)
  covalent geometry    : angle       0.66120 ( 6754)
  hydrogen bonds       : bond        0.03681 (  135)
  hydrogen bonds       : angle       4.60107 (  331)
  Misc. bond           : bond        0.00173 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 23
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: B  185 TYR cc_start: 0.7650 (t80) cc_final: 0.7311 (t80)
REVERT: B  254 LEU cc_start: 0.9130 (mt) cc_final: 0.8749 (mt)
REVERT: C  154 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6611 (p0)
REVERT: C  163 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (m-80)
REVERT: C  225 MET cc_start: 0.1883 (ptm) cc_final: 0.1262 (ppp)
  outliers start: 16
  outliers final: 13
  residues processed: 34
  average time/residue: 0.0527
  time to fit residues: 2.6421
Evaluate side-chains
  38 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  163 PHE
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  257 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:   10.9990
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 131 HIS
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 ASN
** C 212 ASN ** 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 = 0.4604 r_free = 0.4604 target = 0.116397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.096884 restraints weight = 37285.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.098882 restraints weight = 27123.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.100576 restraints weight = 21953.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.101613 restraints weight = 18845.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.102196 restraints weight = 16896.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5702
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4751  Z= 0.163
  Angle     :  0.708  10.713   6754  Z= 0.359
  Chirality :  0.042   0.149    801
  Planarity :  0.005   0.050    599
  Dihedral  : 21.897 120.959   1521
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 13.80 %
    Favored  : 84.79 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 24.85 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -2.31 (0.43), residues: 355
  helix: -0.18 (0.47), residues: 120
  sheet: -4.93 (1.17), residues: 10
  loop : -2.27 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 143 
 TYR   0.018   0.002   TYR C 157 
 PHE   0.014   0.003   PHE B 132 
 TRP   0.011   0.002   TRP C 160 
 HIS   0.005   0.001   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4750)
  covalent geometry    : angle       0.70761 ( 6754)
  hydrogen bonds       : bond        0.03793 (  135)
  hydrogen bonds       : angle       4.82540 (  331)
  Misc. bond           : bond        0.00041 (    1)

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 LEU cc_start: 0.9027 (mt) cc_final: 0.8632 (mt)
REVERT: C  225 MET cc_start: 0.2134 (ptm) cc_final: 0.1627 (ppp)
  outliers start: 16
  outliers final: 13
  residues processed: 35
  average time/residue: 0.0513
  time to fit residues: 2.6392
Evaluate side-chains
  36 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 23
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  131 HIS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  235 ASP
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  257 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 41 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0020
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
B 131 HIS
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 159 ASN
** C 212 ASN ** 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 = 0.4675 r_free = 0.4675 target = 0.121948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.102242 restraints weight = 37448.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.104681 restraints weight = 26441.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.106413 restraints weight = 21016.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.107588 restraints weight = 17836.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.108212 restraints weight = 15803.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5516
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4751  Z= 0.113
  Angle     :  0.649   9.954   6754  Z= 0.329
  Chirality :  0.039   0.156    801
  Planarity :  0.004   0.043    599
  Dihedral  : 21.408 109.894   1521
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  : 12.39 %
    Favored  : 86.20 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 26.36 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -2.00 (0.44), residues: 355
  helix:  0.03 (0.48), residues: 120
  sheet: -4.19 (1.53), residues: 10
  loop : -2.08 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 127 
 TYR   0.037   0.002   TYR B 185 
 PHE   0.031   0.002   PHE B 132 
 TRP   0.005   0.001   TRP C 160 
 HIS   0.008   0.002   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4750)
  covalent geometry    : angle       0.64866 ( 6754)
  hydrogen bonds       : bond        0.03252 (  135)
  hydrogen bonds       : angle       4.46413 (  331)
  Misc. bond           : bond        0.00066 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1441.17 seconds
wall clock time: 25 minutes 30.81 seconds (1530.81 seconds total)