Starting phenix.real_space_refine
on Fri Aug 22 16:17:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exa_28656/08_2025/8exa_28656.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exa_28656/08_2025/8exa_28656.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exa_28656/08_2025/8exa_28656.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exa_28656/08_2025/8exa_28656.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exa_28656/08_2025/8exa_28656.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exa_28656/08_2025/8exa_28656.cif"
  }
  resolution = 3.14
  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=   1.000
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     139      5.49       5
     S       2      5.16       5
     C    2984      2.51       5
     N    1029      2.21       5
     O    1385      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5539
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2610
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 9, 'TRANS': 331}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 161
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 101
    Chain: "B"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2163
          Classifications: {'RNA': 101}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 42}
          Link IDs: {'rna2p': 10, 'rna3p': 90}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 252
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1, ' DT:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 514
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
  Time building chain proxies: 1.38, per 1000 atoms: 0.25
  Number of scatterers: 5539
  At special positions: 0
  Unit cell: (81.4, 86.9, 97.9, 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       2     16.00
     P     139     15.00
     O    1385      8.00
     N    1029      7.00
     C    2984      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: 0.56
  Conformation dependent library (CDL) restraints added in 236.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 2 sheets defined
      53.7% alpha, 15.2% beta
      56 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 46
    Processing helix  chain 'A' and resid 51 through 65
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 75 through 96
      removed outlier: 3.714A  pdb=" N   LEU A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   THR A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 236 through 271
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 288 through 299
      removed outlier: 4.628A  pdb=" N   LEU A 293 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   SER A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 360 through 377
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121
      removed outlier: 7.383A  pdb=" N   ILE A 154 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   GLU A 174 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN A 156 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR A 167 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209
      removed outlier: 4.215A  pdb=" N   VAL A 200 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   PHE A 186 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   GLU A 278 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   VAL A 192 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   VAL A 321 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   THR A 277 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)

    169 hydrogen bonds defined for protein.
    489 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      141 hydrogen bonds
      238 hydrogen bond angles
      0 basepair planarities
      56 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 923
        1.33 -     1.45: 2154
        1.45 -     1.57: 2579
        1.57 -     1.69: 273
        1.69 -     1.80: 3
  Bond restraints: 5932
  Sorted by residual:
  bond pdb=" N   GLN A  80 "
       pdb=" CA  GLN A  80 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.23e-02 6.61e+03 3.44e+00
  bond pdb=" CB  TRP A 313 "
       pdb=" CG  TRP A 313 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 8.46e-01
  bond pdb=" C3'  DC C   3 "
       pdb=" O3'  DC C   3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.448 -0.026 3.00e-02 1.11e+03 7.34e-01
  bond pdb=" C4'  DT C   0 "
       pdb=" O4'  DT C   0 "
    ideal  model  delta    sigma   weight residual
    1.450  1.433  0.017 2.00e-02 2.50e+03 6.97e-01
  bond pdb=" CA  GLN A  80 "
       pdb=" C   GLN A  80 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.29e-02 6.01e+03 6.52e-01
  ... (remaining 5927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 8117
        0.99 -     1.97: 448
        1.97 -     2.96: 87
        2.96 -     3.94: 15
        3.94 -     4.93: 6
  Bond angle restraints: 8673
  Sorted by residual:
  angle pdb=" CA  TYR A 309 "
        pdb=" CB  TYR A 309 "
        pdb=" CG  TYR A 309 "
      ideal   model   delta    sigma   weight residual
     113.90  118.72   -4.82 1.80e+00 3.09e-01 7.18e+00
  angle pdb=" C2'   G B   3 "
        pdb=" C1'   G B   3 "
        pdb=" N9    G B   3 "
      ideal   model   delta    sigma   weight residual
     112.00  115.28   -3.28 1.50e+00 4.44e-01 4.79e+00
  angle pdb=" N   ILE A 275 "
        pdb=" CA  ILE A 275 "
        pdb=" C   ILE A 275 "
      ideal   model   delta    sigma   weight residual
     106.53  109.29   -2.76 1.41e+00 5.03e-01 3.83e+00
  angle pdb=" C2'   U B   9 "
        pdb=" C1'   U B   9 "
        pdb=" N1    U B   9 "
      ideal   model   delta    sigma   weight residual
     114.00  111.36    2.64 1.50e+00 4.44e-01 3.10e+00
  angle pdb=" C4'  DG C  -5 "
        pdb=" O4'  DG C  -5 "
        pdb=" C1'  DG C  -5 "
      ideal   model   delta    sigma   weight residual
     109.70  107.08    2.62 1.50e+00 4.44e-01 3.05e+00
  ... (remaining 8668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.56: 3069
       28.56 -    57.13: 370
       57.13 -    85.69: 148
       85.69 -   114.25: 1
      114.25 -   142.82: 1
  Dihedral angle restraints: 3589
    sinusoidal: 2600
      harmonic: 989
  Sorted by residual:
  dihedral pdb=" C4'  DC C   3 "
           pdb=" C3'  DC C   3 "
           pdb=" O3'  DC C   3 "
           pdb=" P    DA C   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.18  142.82     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" O4'   U B -89 "
           pdb=" C1'   U B -89 "
           pdb=" N1    U B -89 "
           pdb=" C2    U B -89 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -119.23  -40.77     1      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  LEU A 136 "
           pdb=" C   LEU A 136 "
           pdb=" N   PRO A 137 "
           pdb=" CA  PRO A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.05  -15.95     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 3586 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 769
       0.030 -    0.060: 213
       0.060 -    0.090: 47
       0.090 -    0.119: 26
       0.119 -    0.149: 7
  Chirality restraints: 1062
  Sorted by residual:
  chirality pdb=" CA  PHE A  35 "
            pdb=" N   PHE A  35 "
            pdb=" C   PHE A  35 "
            pdb=" CB  PHE A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.56e-01
  chirality pdb=" C1'   A B   2 "
            pdb=" O4'   A B   2 "
            pdb=" C2'   A B   2 "
            pdb=" N9    A B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.17e-01
  chirality pdb=" CA  PRO A 137 "
            pdb=" N   PRO A 137 "
            pdb=" C   PRO A 137 "
            pdb=" CB  PRO A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 1059 not shown)

  Planarity restraints: 596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   3 "   -0.031 2.00e-02 2.50e+03   1.28e-02 4.95e+00
        pdb=" N9    G B   3 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    G B   3 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    G B   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B   3 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G B   3 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G B   3 "    0.007 2.00e-02 2.50e+03
        pdb=" N2    G B   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G B   3 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B   3 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   9 "    0.026 2.00e-02 2.50e+03   1.39e-02 4.35e+00
        pdb=" N1    U B   9 "   -0.031 2.00e-02 2.50e+03
        pdb=" C2    U B   9 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    U B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    U B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" O4    U B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U B   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B   9 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   2 "   -0.023 2.00e-02 2.50e+03   1.03e-02 2.92e+00
        pdb=" N9    A B   2 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    A B   2 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   2 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A B   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A B   2 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   2 "    0.003 2.00e-02 2.50e+03
  ... (remaining 593 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 899
        2.76 -     3.29: 5072
        3.29 -     3.83: 11101
        3.83 -     4.36: 12729
        4.36 -     4.90: 18341
  Nonbonded interactions: 48142
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 117 "
            pdb=" OP1   U B   4 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O2    C B-107 "
            pdb=" N2    G B  -6 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" NH1 ARG A  39 "
            pdb=" OE1 GLU A  87 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" N2    G B-114 "
            pdb=" O4    U B -89 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NH1 ARG A 110 "
            pdb=" OP1   C B   5 "
     model   vdw
     2.319 3.120
  ... (remaining 48137 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.560
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.770
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  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:    8.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
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   0.029   5932  Z= 0.173
  Angle     :  0.538   4.927   8673  Z= 0.286
  Chirality :  0.033   0.149   1062
  Planarity :  0.003   0.023    596
  Dihedral  : 22.737 142.816   2953
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  8.50 %
    Favored  : 91.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.47), residues: 337
  helix:  1.86 (0.40), residues: 175
  sheet: -1.83 (0.63), residues: 65
  loop : -1.41 (0.60), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  39 
 TYR   0.024   0.002   TYR A 309 
 PHE   0.018   0.002   PHE A  35 
 TRP   0.006   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5932)
  covalent geometry    : angle       0.53846 ( 8673)
  hydrogen bonds       : bond        0.08927 (  310)
  hydrogen bonds       : angle       3.99413 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.9058 (mt) cc_final: 0.8835 (mt)
REVERT: A   95 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7187 (mtm110)
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0944
  time to fit residues: 5.6443
Evaluate side-chains
  39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
A 227 GLN
A 250 HIS
A 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.195014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.154707 restraints weight = 7522.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 1.70
r_work: 0.3774 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.0817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5932  Z= 0.172
  Angle     :  0.537   5.648   8673  Z= 0.282
  Chirality :  0.033   0.126   1062
  Planarity :  0.003   0.023    596
  Dihedral  : 23.870 142.500   2371
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  :  9.31 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.48), residues: 337
  helix:  2.43 (0.39), residues: 169
  sheet: -1.80 (0.65), residues: 66
  loop : -1.17 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 252 
 TYR   0.022   0.002   TYR A 309 
 PHE   0.024   0.002   PHE A  35 
 TRP   0.008   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5932)
  covalent geometry    : angle       0.53685 ( 8673)
  hydrogen bonds       : bond        0.05014 (  310)
  hydrogen bonds       : angle       3.37105 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8892 (mt) cc_final: 0.8673 (mt)
REVERT: A  143 LYS cc_start: 0.7169 (tttt) cc_final: 0.6419 (mtmt)
REVERT: A  214 TYR cc_start: 0.7304 (m-80) cc_final: 0.6927 (m-80)
REVERT: A  302 GLU cc_start: 0.7502 (tt0) cc_final: 0.7288 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0871
  time to fit residues: 5.4166
Evaluate side-chains
  44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0980
   chunk 19 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.189675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.149215 restraints weight = 7501.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 1.69
r_work: 0.3714 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   5932  Z= 0.295
  Angle     :  0.684   7.178   8673  Z= 0.353
  Chirality :  0.040   0.147   1062
  Planarity :  0.005   0.030    596
  Dihedral  : 23.959 143.259   2371
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 10.53 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.47), residues: 337
  helix:  1.50 (0.38), residues: 176
  sheet: -1.94 (0.66), residues: 71
  loop : -1.41 (0.63), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  95 
 TYR   0.027   0.003   TYR A 309 
 PHE   0.027   0.003   PHE A  35 
 TRP   0.008   0.002   TRP A 300 
 HIS   0.005   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 ( 5932)
  covalent geometry    : angle       0.68386 ( 8673)
  hydrogen bonds       : bond        0.06559 (  310)
  hydrogen bonds       : angle       3.75436 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.8356 (m-80) cc_final: 0.8135 (m-80)
REVERT: A   95 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7272 (mtm110)
REVERT: A  143 LYS cc_start: 0.7075 (tttt) cc_final: 0.6423 (mtmt)
REVERT: A  246 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7371 (tp)
REVERT: A  255 ASN cc_start: 0.7477 (m-40) cc_final: 0.7124 (m110)
  outliers start: 9
  outliers final: 6
  residues processed: 46
  average time/residue: 0.1115
  time to fit residues: 6.2577
Evaluate side-chains
  42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.197566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.158116 restraints weight = 7349.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 1.68
r_work: 0.3816 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5932  Z= 0.123
  Angle     :  0.491   4.784   8673  Z= 0.260
  Chirality :  0.031   0.141   1062
  Planarity :  0.003   0.027    596
  Dihedral  : 23.691 141.954   2371
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 12.55 %
    Favored  : 83.81 %
  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 aren not related in a simple way.
  whole:  0.73 (0.48), residues: 337
  helix:  2.24 (0.39), residues: 176
  sheet: -1.57 (0.69), residues: 66
  loop : -1.29 (0.61), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 119 
 TYR   0.021   0.002   TYR A 309 
 PHE   0.020   0.002   PHE A  35 
 TRP   0.006   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5932)
  covalent geometry    : angle       0.49057 ( 8673)
  hydrogen bonds       : bond        0.04595 (  310)
  hydrogen bonds       : angle       3.20019 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   40 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4813 (tp)
REVERT: A  143 LYS cc_start: 0.7263 (tttt) cc_final: 0.6492 (mtmt)
REVERT: A  255 ASN cc_start: 0.7108 (m-40) cc_final: 0.6835 (m-40)
  outliers start: 9
  outliers final: 4
  residues processed: 46
  average time/residue: 0.0943
  time to fit residues: 5.4712
Evaluate side-chains
  38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.191469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.151060 restraints weight = 7608.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 1.70
r_work: 0.3734 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   5932  Z= 0.256
  Angle     :  0.622   6.745   8673  Z= 0.323
  Chirality :  0.037   0.134   1062
  Planarity :  0.004   0.028    596
  Dihedral  : 23.787 142.859   2371
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 13.77 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.47), residues: 337
  helix:  1.78 (0.39), residues: 176
  sheet: -1.74 (0.68), residues: 66
  loop : -1.54 (0.61), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 248 
 TYR   0.025   0.003   TYR A 309 
 PHE   0.026   0.002   PHE A  35 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.005   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 5932)
  covalent geometry    : angle       0.62218 ( 8673)
  hydrogen bonds       : bond        0.06039 (  310)
  hydrogen bonds       : angle       3.54960 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ILE cc_start: 0.5321 (OUTLIER) cc_final: 0.5023 (tp)
REVERT: A  143 LYS cc_start: 0.7074 (tttt) cc_final: 0.6493 (mtmt)
REVERT: A  255 ASN cc_start: 0.7306 (m-40) cc_final: 0.6968 (m-40)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 0.1109
  time to fit residues: 6.3705
Evaluate side-chains
  44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  368 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.193924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.153893 restraints weight = 7454.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 1.68
r_work: 0.3766 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5932  Z= 0.177
  Angle     :  0.545   5.701   8673  Z= 0.286
  Chirality :  0.034   0.126   1062
  Planarity :  0.004   0.026    596
  Dihedral  : 23.726 142.908   2371
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 13.36 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.48), residues: 337
  helix:  1.97 (0.38), residues: 176
  sheet: -1.72 (0.67), residues: 66
  loop : -1.40 (0.61), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 248 
 TYR   0.022   0.002   TYR A 309 
 PHE   0.021   0.002   PHE A  35 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5932)
  covalent geometry    : angle       0.54529 ( 8673)
  hydrogen bonds       : bond        0.05220 (  310)
  hydrogen bonds       : angle       3.35653 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ILE cc_start: 0.5137 (OUTLIER) cc_final: 0.4874 (tp)
REVERT: A   95 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7150 (mtm110)
REVERT: A  143 LYS cc_start: 0.7273 (tttt) cc_final: 0.6538 (mtmt)
REVERT: A  250 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6800 (m90)
REVERT: A  255 ASN cc_start: 0.7240 (m-40) cc_final: 0.6970 (m-40)
  outliers start: 13
  outliers final: 6
  residues processed: 48
  average time/residue: 0.1215
  time to fit residues: 7.0213
Evaluate side-chains
  41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 32 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.197625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.157805 restraints weight = 7473.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 1.72
r_work: 0.3814 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5932  Z= 0.125
  Angle     :  0.487   5.229   8673  Z= 0.257
  Chirality :  0.030   0.123   1062
  Planarity :  0.003   0.026    596
  Dihedral  : 23.660 142.352   2371
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.38 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.48), residues: 337
  helix:  2.26 (0.39), residues: 176
  sheet: -1.64 (0.67), residues: 66
  loop : -1.29 (0.62), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 248 
 TYR   0.020   0.002   TYR A 309 
 PHE   0.018   0.002   PHE A  35 
 TRP   0.008   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5932)
  covalent geometry    : angle       0.48688 ( 8673)
  hydrogen bonds       : bond        0.04612 (  310)
  hydrogen bonds       : angle       3.16931 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ILE cc_start: 0.5069 (OUTLIER) cc_final: 0.4830 (tp)
REVERT: A   95 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7316 (mtm110)
REVERT: A  143 LYS cc_start: 0.7241 (tttt) cc_final: 0.6485 (mtmt)
REVERT: A  250 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6694 (m90)
REVERT: A  252 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7366 (mtp-110)
  outliers start: 9
  outliers final: 6
  residues processed: 44
  average time/residue: 0.1146
  time to fit residues: 6.0622
Evaluate side-chains
  43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 279 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.189273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.148765 restraints weight = 7545.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 1.74
r_work: 0.3706 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   5932  Z= 0.333
  Angle     :  0.722   7.780   8673  Z= 0.372
  Chirality :  0.042   0.144   1062
  Planarity :  0.005   0.031    596
  Dihedral  : 23.888 143.865   2371
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 15.38 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.46), residues: 337
  helix:  1.25 (0.38), residues: 176
  sheet: -2.23 (0.63), residues: 72
  loop : -1.51 (0.63), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 248 
 TYR   0.029   0.003   TYR A 309 
 PHE   0.022   0.003   PHE A  35 
 TRP   0.008   0.002   TRP A 300 
 HIS   0.005   0.002   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00718 ( 5932)
  covalent geometry    : angle       0.72205 ( 8673)
  hydrogen bonds       : bond        0.07059 (  310)
  hydrogen bonds       : angle       3.80158 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   35 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6914 (t80)
REVERT: A   40 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.5182 (tp)
REVERT: A  143 LYS cc_start: 0.7239 (tttt) cc_final: 0.6545 (mtmt)
REVERT: A  250 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6865 (m90)
  outliers start: 12
  outliers final: 5
  residues processed: 45
  average time/residue: 0.1099
  time to fit residues: 6.0271
Evaluate side-chains
  42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0980
   chunk 27 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0770
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.4938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.196949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.157644 restraints weight = 7424.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 1.66
r_work: 0.3830 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5932  Z= 0.124
  Angle     :  0.515   7.843   8673  Z= 0.268
  Chirality :  0.031   0.147   1062
  Planarity :  0.004   0.054    596
  Dihedral  : 23.683 142.757   2371
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.79 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.47), residues: 337
  helix:  1.95 (0.39), residues: 176
  sheet: -1.68 (0.67), residues: 66
  loop : -1.54 (0.60), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  95 
 TYR   0.020   0.002   TYR A 309 
 PHE   0.013   0.002   PHE A  35 
 TRP   0.008   0.001   TRP A 300 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5932)
  covalent geometry    : angle       0.51496 ( 8673)
  hydrogen bonds       : bond        0.04699 (  310)
  hydrogen bonds       : angle       3.29063 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6361 (t80)
REVERT: A  143 LYS cc_start: 0.7234 (tttt) cc_final: 0.6489 (mtmt)
REVERT: A  250 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6787 (m90)
REVERT: A  264 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7007 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0984
  time to fit residues: 5.1700
Evaluate side-chains
  41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 37 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.193188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.152991 restraints weight = 7566.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.72
r_work: 0.3757 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5932  Z= 0.225
  Angle     :  0.612   8.249   8673  Z= 0.319
  Chirality :  0.036   0.140   1062
  Planarity :  0.004   0.038    596
  Dihedral  : 23.726 143.522   2371
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 17.00 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.47), residues: 337
  helix:  1.58 (0.38), residues: 176
  sheet: -2.07 (0.65), residues: 72
  loop : -1.48 (0.63), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  95 
 TYR   0.024   0.003   TYR A 309 
 PHE   0.021   0.003   PHE A  35 
 TRP   0.008   0.002   TRP A 300 
 HIS   0.004   0.002   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 5932)
  covalent geometry    : angle       0.61180 ( 8673)
  hydrogen bonds       : bond        0.05744 (  310)
  hydrogen bonds       : angle       3.58291 (  727)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   35 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6548 (t80)
REVERT: A  143 LYS cc_start: 0.7257 (tttt) cc_final: 0.6501 (mtmt)
REVERT: A  250 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7214 (m-70)
  outliers start: 9
  outliers final: 5
  residues processed: 41
  average time/residue: 0.1019
  time to fit residues: 5.0916
Evaluate side-chains
  41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0270
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:   20.0000
   chunk 27 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.196750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.157207 restraints weight = 7472.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 1.69
r_work: 0.3824 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5932  Z= 0.130
  Angle     :  0.530   9.007   8673  Z= 0.275
  Chirality :  0.031   0.124   1062
  Planarity :  0.004   0.037    596
  Dihedral  : 23.648 142.532   2371
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.22 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.47), residues: 337
  helix:  1.86 (0.38), residues: 176
  sheet: -1.62 (0.68), residues: 67
  loop : -1.53 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  95 
 TYR   0.020   0.002   TYR A 309 
 PHE   0.015   0.002   PHE A  35 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5932)
  covalent geometry    : angle       0.53010 ( 8673)
  hydrogen bonds       : bond        0.04745 (  310)
  hydrogen bonds       : angle       3.34929 (  727)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1188.92 seconds
wall clock time: 21 minutes 3.17 seconds (1263.17 seconds total)