Starting phenix.real_space_refine
on Tue Feb 11 12:54:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exa_28656/02_2025/8exa_28656.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exa_28656/02_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_28656/02_2025/8exa_28656.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exa_28656/02_2025/8exa_28656.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exa_28656/02_2025/8exa_28656.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exa_28656/02_2025/8exa_28656.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5}
          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:plan2': 1, ' DC:plan': 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: 4.13, per 1000 atoms: 0.75
  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: 1.50
  Conformation dependent library (CDL) restraints added in 533.3 milliseconds
  

  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: 2.34
  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: 2.51

  Time building geometry restraints manager: 1.72 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:             0.350
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.310
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.770
-------------------------------------------------------------------------------
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= 0.219
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.006   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 
 PHE   0.018   0.002   PHE A  35 
 TYR   0.024   0.002   TYR A 309 
 ARG   0.002   0.000   ARG A  39 

*********************** 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  : 0.405 
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: 0.2277
  time to fit residues: 13.5805
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  : 0.407 
-------------------------------------------------------------------------------
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 39 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.196863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.157209 restraints weight = 7391.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.65
r_work: 0.3801 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.0977

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= 0.173
  Angle     :  0.499   5.111   8673  Z= 0.264
  Chirality :  0.031   0.126   1062
  Planarity :  0.003   0.020    596
  Dihedral  : 23.801 142.230   2371
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  9.31 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.48), residues: 337
  helix:  2.63 (0.40), residues: 169
  sheet: -1.68 (0.65), residues: 65
  loop : -1.12 (0.60), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 
 PHE   0.022   0.002   PHE A  35 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.003   0.000   ARG A 110 

*********************** 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
  50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8884 (mt) cc_final: 0.8643 (mt)
REVERT: A  143 LYS cc_start: 0.7274 (tttt) cc_final: 0.6482 (mtmt)
REVERT: A  255 ASN cc_start: 0.7357 (m110) cc_final: 0.6996 (m110)
REVERT: A  264 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7049 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.1965
  time to fit residues: 12.0611
Evaluate side-chains
  40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  264 LEU
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 18 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.4326 r_free = 0.4326 target = 0.193794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153551 restraints weight = 7413.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 1.65
r_work: 0.3764 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5932  Z= 0.263
  Angle     :  0.565   6.294   8673  Z= 0.294
  Chirality :  0.034   0.130   1062
  Planarity :  0.004   0.023    596
  Dihedral  : 23.820 142.652   2371
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 10.53 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.48), residues: 337
  helix:  2.38 (0.39), residues: 167
  sheet: -1.90 (0.64), residues: 71
  loop : -0.99 (0.62), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A 166 
 PHE   0.023   0.002   PHE A  35 
 TYR   0.023   0.002   TYR A 309 
 ARG   0.005   0.001   ARG A  95 

*********************** 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: 8
    poor density    : 40
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8921 (mt) cc_final: 0.8712 (mt)
REVERT: A  143 LYS cc_start: 0.7181 (tttt) cc_final: 0.6429 (mtmt)
REVERT: A  264 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.7001 (tt)
REVERT: A  302 GLU cc_start: 0.7443 (tt0) cc_final: 0.7235 (tt0)
  outliers start: 8
  outliers final: 5
  residues processed: 45
  average time/residue: 0.2311
  time to fit residues: 12.9279
Evaluate side-chains
  45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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  264 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 43 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 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 = 0.4326 r_free = 0.4326 target = 0.193887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153644 restraints weight = 7536.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 1.68
r_work: 0.3765 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.1132

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= 0.253
  Angle     :  0.557   6.080   8673  Z= 0.291
  Chirality :  0.034   0.127   1062
  Planarity :  0.004   0.027    596
  Dihedral  : 23.750 142.970   2371
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 11.34 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.48), residues: 337
  helix:  2.05 (0.39), residues: 174
  sheet: -1.70 (0.68), residues: 66
  loop : -1.08 (0.62), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A 262 
 PHE   0.022   0.002   PHE A  35 
 TYR   0.024   0.002   TYR A 309 
 ARG   0.005   0.001   ARG A  95 

*********************** 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  : 0.372 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8931 (mt) cc_final: 0.8705 (mt)
REVERT: A  143 LYS cc_start: 0.7084 (tttt) cc_final: 0.6481 (mtmt)
REVERT: A  255 ASN cc_start: 0.7229 (m110) cc_final: 0.6865 (m110)
  outliers start: 9
  outliers final: 6
  residues processed: 45
  average time/residue: 0.2277
  time to fit residues: 12.8495
Evaluate side-chains
  43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 5 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 13 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.197861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.158049 restraints weight = 7397.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.69
r_work: 0.3814 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.1415

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= 0.156
  Angle     :  0.492   7.863   8673  Z= 0.257
  Chirality :  0.031   0.123   1062
  Planarity :  0.003   0.028    596
  Dihedral  : 23.652 142.384   2371
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.55 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.49), residues: 337
  helix:  2.77 (0.39), residues: 167
  sheet: -1.61 (0.68), residues: 66
  loop : -0.95 (0.61), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 262 
 PHE   0.018   0.002   PHE A  35 
 TYR   0.020   0.002   TYR A 309 
 ARG   0.006   0.000   ARG A  95 

*********************** 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
  47 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.7260 (tttt) cc_final: 0.6499 (mtmt)
REVERT: A  252 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7498 (mtp-110)
  outliers start: 7
  outliers final: 5
  residues processed: 46
  average time/residue: 0.2792
  time to fit residues: 15.5834
Evaluate side-chains
  39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
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  275 ILE
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 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 = 0.4337 r_free = 0.4337 target = 0.194909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.154844 restraints weight = 7414.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 1.66
r_work: 0.3781 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5932  Z= 0.256
  Angle     :  0.559   6.156   8673  Z= 0.291
  Chirality :  0.034   0.139   1062
  Planarity :  0.004   0.031    596
  Dihedral  : 23.677 142.900   2371
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.96 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.48), residues: 337
  helix:  2.02 (0.39), residues: 174
  sheet: -1.74 (0.67), residues: 67
  loop : -0.95 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A 262 
 PHE   0.024   0.002   PHE A  35 
 TYR   0.024   0.002   TYR A 214 
 ARG   0.006   0.001   ARG A  95 

*********************** 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
  46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ILE cc_start: 0.5301 (OUTLIER) cc_final: 0.5009 (tp)
REVERT: A  143 LYS cc_start: 0.7062 (tttt) cc_final: 0.6470 (mtmt)
REVERT: A  255 ASN cc_start: 0.7157 (m110) cc_final: 0.6824 (m110)
  outliers start: 10
  outliers final: 6
  residues processed: 44
  average time/residue: 0.2585
  time to fit residues: 13.9006
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  : 0.399 
-------------------------------------------------------------------------------
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  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 17 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.197893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.158323 restraints weight = 7414.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 1.68
r_work: 0.3817 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.1546

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= 0.168
  Angle     :  0.502   6.336   8673  Z= 0.261
  Chirality :  0.031   0.141   1062
  Planarity :  0.004   0.035    596
  Dihedral  : 23.640 143.215   2371
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.96 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.48), residues: 337
  helix:  2.26 (0.39), residues: 174
  sheet: -1.59 (0.67), residues: 66
  loop : -0.88 (0.62), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.026   0.002   PHE A  35 
 TYR   0.020   0.002   TYR A 309 
 ARG   0.007   0.000   ARG A  95 

*********************** 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
  46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.7049 (tttt) cc_final: 0.6402 (mtmt)
REVERT: A  250 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6652 (m90)
  outliers start: 10
  outliers final: 5
  residues processed: 44
  average time/residue: 0.2716
  time to fit residues: 14.4662
Evaluate side-chains
  41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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  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 30 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4353 r_free = 0.4353 target = 0.196616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156932 restraints weight = 7457.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.66
r_work: 0.3803 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5932  Z= 0.209
  Angle     :  0.526   5.663   8673  Z= 0.274
  Chirality :  0.032   0.139   1062
  Planarity :  0.004   0.035    596
  Dihedral  : 23.631 143.003   2371
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 13.36 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.48), residues: 337
  helix:  2.14 (0.39), residues: 174
  sheet: -1.73 (0.66), residues: 67
  loop : -0.91 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.014   0.002   PHE A  94 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.007   0.001   ARG A  95 

*********************** 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
  46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6591 (t80)
REVERT: A   40 ILE cc_start: 0.5181 (OUTLIER) cc_final: 0.4943 (tp)
REVERT: A  143 LYS cc_start: 0.7086 (tttt) cc_final: 0.6465 (mtmt)
REVERT: A  250 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6768 (m90)
  outliers start: 9
  outliers final: 4
  residues processed: 44
  average time/residue: 0.2637
  time to fit residues: 14.2534
Evaluate side-chains
  45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.1980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0670
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
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 = 0.4414 r_free = 0.4414 target = 0.202592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.163306 restraints weight = 7483.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 1.74
r_work: 0.3879 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6542
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5932  Z= 0.134
  Angle     :  0.466   5.127   8673  Z= 0.245
  Chirality :  0.029   0.140   1062
  Planarity :  0.003   0.038    596
  Dihedral  : 23.596 141.812   2371
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.77 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.48), residues: 337
  helix:  2.81 (0.38), residues: 170
  sheet: -1.48 (0.67), residues: 66
  loop : -1.13 (0.59), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.010   0.001   PHE A  35 
 TYR   0.017   0.001   TYR A 309 
 ARG   0.007   0.000   ARG A  95 

*********************** 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
  42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6130 (t80)
REVERT: A   71 LEU cc_start: 0.7292 (mt) cc_final: 0.6882 (tt)
REVERT: A  143 LYS cc_start: 0.7144 (tttt) cc_final: 0.6435 (mtmt)
REVERT: A  250 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6697 (m90)
  outliers start: 8
  outliers final: 4
  residues processed: 41
  average time/residue: 0.2485
  time to fit residues: 12.7200
Evaluate side-chains
  37 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
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 14 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.200365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.160525 restraints weight = 7510.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.74
r_work: 0.3845 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5932  Z= 0.165
  Angle     :  0.482   5.106   8673  Z= 0.254
  Chirality :  0.030   0.137   1062
  Planarity :  0.003   0.035    596
  Dihedral  : 23.560 142.212   2371
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.98 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.48), residues: 337
  helix:  2.41 (0.38), residues: 177
  sheet: -1.55 (0.66), residues: 67
  loop : -1.07 (0.61), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.012   0.002   PHE A  35 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.008   0.000   ARG A  95 

********************** 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
  41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   35 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6382 (t80)
REVERT: A  143 LYS cc_start: 0.7171 (tttt) cc_final: 0.6404 (mtmt)
REVERT: A  250 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.7018 (m-70)
  outliers start: 6
  outliers final: 3
  residues processed: 39
  average time/residue: 0.2768
  time to fit residues: 13.2287
Evaluate side-chains
  39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.7760

-------------------------------------------------------------------------------
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 = 0.4388 r_free = 0.4388 target = 0.200156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.160424 restraints weight = 7556.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 1.74
r_work: 0.3840 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5932  Z= 0.167
  Angle     :  0.483   5.033   8673  Z= 0.254
  Chirality :  0.030   0.140   1062
  Planarity :  0.003   0.036    596
  Dihedral  : 23.568 142.159   2371
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.98 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.47), residues: 337
  helix:  2.34 (0.38), residues: 177
  sheet: -1.52 (0.66), residues: 67
  loop : -1.11 (0.61), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.013   0.002   PHE A  30 
 TYR   0.020   0.002   TYR A 309 
 ARG   0.008   0.000   ARG A  95 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2388.93 seconds
wall clock time: 43 minutes 16.71 seconds (2596.71 seconds total)