Starting phenix.real_space_refine
on Thu Sep 10 20:59:25 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dwj_27756/09_2026/8dwj_27756.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      14      5.49       5
     S      13      5.16       5
     C    1905      2.51       5
     N     525      2.21       5
     O     585      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3043
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "P"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 117
          Unusual residues: {'GTP': 1}
          Classifications: {'RNAv2': 4, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 3, None: 1}
            Not linked:
              pdbres="GTP P   1 "
              pdbres="  C P   2 "
    Chain: "T"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 144
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "A"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2781
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 24, 'TRANS': 314}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    556  SG  CYS A  37      35.483  27.676  19.865  1.00234.26           S
  ATOM    576  SG  CYS A  40      35.253  23.162  19.878  1.00251.45           S
  ATOM    775  SG  CYS A  65      36.508  25.850  23.034  1.00220.03           S
  ATOM    801  SG  CYS A  68      38.485  25.430  20.056  1.00211.90           S

  Time building chain proxies: 0.92, per 1000 atoms: 0.30
  Number of scatterers: 3043
  At special positions: 0
  Unit cell: (67.914, 67.914, 82.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      13     16.00
     P      14     15.00
     O     585      8.00
     N     525      7.00
     C    1905      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 100.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  40 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  37 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  65 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  68 "
      Number of angles added : 6


  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:  642

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 4 sheets defined
      38.9% alpha, 14.2% beta
      3 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 17
    Processing helix  chain 'A' and resid 74 through 82
    Processing helix  chain 'A' and resid 82 through 97
      removed outlier: 3.545A  pdb=" N   ARG A  94 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 146 through 152
      removed outlier: 4.212A  pdb=" N   LYS A 151 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
    Processing helix  chain 'A' and resid 221 through 225
    Processing helix  chain 'A' and resid 235 through 240
    Processing helix  chain 'A' and resid 274 through 287
      removed outlier: 3.522A  pdb=" N   ALA A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 297
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 314 through 324
      removed outlier: 3.512A  pdb=" N   ILE A 318 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 341
      removed outlier: 4.306A  pdb=" N   LYS A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220
    Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292

    116 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      3 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 0.43

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 801
        1.34 -     1.45: 621
        1.45 -     1.57: 1675
        1.57 -     1.69: 25
        1.69 -     1.81: 20
  Bond restraints: 3142
  Sorted by residual:
  bond pdb=" N   VAL A 232 "
       pdb=" CA  VAL A 232 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.21e-02 6.83e+03 8.34e+00
  bond pdb=" N   ILE A 308 "
       pdb=" CA  ILE A 308 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.21e-02 6.83e+03 8.01e+00
  bond pdb=" N   LYS A 300 "
       pdb=" CA  LYS A 300 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.14e-02 7.69e+03 7.83e+00
  bond pdb=" N   ILE A 103 "
       pdb=" CA  ILE A 103 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.26e-02 6.30e+03 7.56e+00
  bond pdb=" N   SER A 100 "
       pdb=" CA  SER A 100 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.21e-02 6.83e+03 7.40e+00
  ... (remaining 3137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 4110
        2.27 -     4.54: 152
        4.54 -     6.80: 20
        6.80 -     9.07: 9
        9.07 -    11.34: 6
  Bond angle restraints: 4297
  Sorted by residual:
  angle pdb=" N   ARG A  87 "
        pdb=" CA  ARG A  87 "
        pdb=" C   ARG A  87 "
      ideal   model   delta    sigma   weight residual
     110.97  105.46    5.51 1.09e+00 8.42e-01 2.55e+01
  angle pdb=" CA  LYS A 161 "
        pdb=" CB  LYS A 161 "
        pdb=" CG  LYS A 161 "
      ideal   model   delta    sigma   weight residual
     114.10  122.41   -8.31 2.00e+00 2.50e-01 1.73e+01
  angle pdb=" N3   DT T   1 "
        pdb=" C4   DT T   1 "
        pdb=" O4   DT T   1 "
      ideal   model   delta    sigma   weight residual
     119.90  122.24   -2.34 6.00e-01 2.78e+00 1.53e+01
  angle pdb=" O4'  DC T   5 "
        pdb=" C4'  DC T   5 "
        pdb=" C3'  DC T   5 "
      ideal   model   delta    sigma   weight residual
     106.00  103.71    2.29 6.00e-01 2.78e+00 1.45e+01
  angle pdb=" PB  GTP P   1 "
        pdb=" O3B GTP P   1 "
        pdb=" PG  GTP P   1 "
      ideal   model   delta    sigma   weight residual
     120.50  131.84  -11.34 3.00e+00 1.11e-01 1.43e+01
  ... (remaining 4292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 1652
       17.58 -    35.16: 166
       35.16 -    52.73: 43
       52.73 -    70.31: 13
       70.31 -    87.88: 5
  Dihedral angle restraints: 1879
    sinusoidal: 881
      harmonic: 998
  Sorted by residual:
  dihedral pdb=" O5'   C P   2 "
           pdb=" C5'   C P   2 "
           pdb=" C4'   C P   2 "
           pdb=" C3'   C P   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   33.03   26.97     3      6.40e+00 2.44e-02 2.19e+01
  dihedral pdb=" C5' GTP P   1 "
           pdb=" O5' GTP P   1 "
           pdb=" PA  GTP P   1 "
           pdb=" O3A GTP P   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  143.55  -74.28     1      2.00e+01 2.50e-03 1.75e+01
  dihedral pdb=" C8  GTP P   1 "
           pdb=" C1' GTP P   1 "
           pdb=" N9  GTP P   1 "
           pdb=" O4' GTP P   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   42.71   61.88     1      2.00e+01 2.50e-03 1.27e+01
  ... (remaining 1876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 307
       0.054 -    0.108: 94
       0.108 -    0.162: 38
       0.162 -    0.216: 8
       0.216 -    0.269: 4
  Chirality restraints: 451
  Sorted by residual:
  chirality pdb=" P     C P   2 "
            pdb=" OP1   C P   2 "
            pdb=" OP2   C P   2 "
            pdb=" O5'   C P   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.44   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" P     G P   4 "
            pdb=" OP1   G P   4 "
            pdb=" OP2   G P   4 "
            pdb=" O5'   G P   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" P     C P   3 "
            pdb=" OP1   C P   3 "
            pdb=" OP2   C P   3 "
            pdb=" O5'   C P   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 448 not shown)

  Planarity restraints: 506
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 145 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO A 146 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 203 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.58e+00
        pdb=" N   PRO A 204 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 314 "   -0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO A 315 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 503 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 364
        2.75 -     3.29: 2886
        3.29 -     3.83: 5595
        3.83 -     4.36: 6432
        4.36 -     4.90: 10310
  Nonbonded interactions: 25587
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A   8 "
            pdb=" OH  TYR A  89 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR A  55 "
            pdb=" OH  TYR A  66 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   LEU A 268 "
            pdb=" NE1 TRP A 294 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" NE2 GLN A 195 "
            pdb=" OG1 THR A 209 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" N   ASP A  84 "
            pdb=" OD1 ASP A  84 "
     model   vdw
     2.384 3.120
  ... (remaining 25582 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.360
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.290
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5735
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      :  0.008   0.182   3147  Z= 0.429
  Angle     :  1.191  22.256   4303  Z= 0.622
  Chirality :  0.065   0.269    451
  Planarity :  0.008   0.064    506
  Dihedral  : 15.705  87.883   1237
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 14.29 %
    Favored  : 85.38 %
  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 are not related in a simple way.
  whole: -2.71 (0.41), residues: 337
  helix: -2.26 (0.37), residues: 116
  sheet: -1.88 (0.68), residues: 51
  loop : -1.29 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.015   0.002   TYR A 321 
 PHE   0.010   0.002   PHE A 293 
 TRP   0.031   0.003   TRP A 266 
 HIS   0.002   0.001   HIS A  71 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00559 /  0.37 ( 3142)
  covalent geometry    : angle       1.06782 /  0.61 ( 4297)
  hydrogen bonds       : bond        0.18315 /  9.54 (  125)
  hydrogen bonds       : angle       9.02912 /  8.35 (  324)
  metal coordination   : bond        0.16030 /  8.02 (    4)
  metal coordination   : angle      14.13845 /  4.71 (    6)
  Misc. bond           : bond        0.05167 /  2.58 (    1)

*********************** 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
  98 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TRP cc_start: 0.4145 (m100) cc_final: 0.3609 (m100)
REVERT: A   54 TYR cc_start: 0.5763 (t80) cc_final: 0.5438 (t80)
REVERT: A   87 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5065 (mtt180)
REVERT: A   91 PHE cc_start: 0.6079 (t80) cc_final: 0.5870 (t80)
REVERT: A   95 LYS cc_start: 0.7872 (tttt) cc_final: 0.6654 (mmmt)
REVERT: A  137 ILE cc_start: 0.6298 (mm) cc_final: 0.6040 (tp)
REVERT: A  138 LYS cc_start: 0.7391 (mttt) cc_final: 0.7189 (tptm)
REVERT: A  158 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6956 (mm-30)
REVERT: A  176 SER cc_start: 0.4986 (m) cc_final: 0.4550 (p)
REVERT: A  177 GLU cc_start: 0.6150 (tt0) cc_final: 0.5704 (mp0)
REVERT: A  183 PRO cc_start: 0.5778 (Cg_exo) cc_final: 0.5374 (Cg_endo)
REVERT: A  197 ARG cc_start: 0.5058 (tpt170) cc_final: 0.4835 (tpt170)
REVERT: A  238 ASP cc_start: 0.6641 (m-30) cc_final: 0.6290 (t0)
REVERT: A  264 ARG cc_start: 0.6642 (ptt180) cc_final: 0.6248 (ptt180)
REVERT: A  267 VAL cc_start: 0.7865 (t) cc_final: 0.7536 (t)
REVERT: A  279 LYS cc_start: 0.8306 (tttt) cc_final: 0.7955 (mtpp)
REVERT: A  292 MET cc_start: 0.8457 (tmm) cc_final: 0.8070 (tpt)
REVERT: A  322 MET cc_start: 0.7560 (mmt) cc_final: 0.7044 (ptp)
REVERT: A  334 MET cc_start: 0.1538 (mmt) cc_final: 0.0138 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0864
  time to fit residues: 9.7480
Evaluate side-chains
  50 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0010
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    0.9190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 ASN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.133038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.116975 restraints weight = 12012.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.117089 restraints weight = 10179.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.117577 restraints weight = 8350.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.117610 restraints weight = 6712.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.118077 restraints weight = 6715.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5596
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3147  Z= 0.171
  Angle     :  0.785   7.397   4303  Z= 0.396
  Chirality :  0.050   0.188    451
  Planarity :  0.007   0.055    506
  Dihedral  : 13.484  79.789    505
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.60 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.42), residues: 337
  helix: -0.71 (0.45), residues: 110
  sheet: -2.46 (0.68), residues: 47
  loop : -0.97 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 264 
 TYR   0.015   0.002   TYR A 185 
 PHE   0.014   0.002   PHE A 260 
 TRP   0.015   0.002   TRP A 294 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.17 ( 3142)
  covalent geometry    : angle       0.77541 /  0.40 ( 4297)
  hydrogen bonds       : bond        0.04777 /  2.56 (  125)
  hydrogen bonds       : angle       7.05408 /  7.64 (  324)
  metal coordination   : bond        0.00803 /  0.40 (    4)
  metal coordination   : angle       3.30656 /  1.10 (    6)
  Misc. bond           : bond        0.00949 /  0.47 (    1)

*********************** 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
  59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7572 (tmt-80) cc_final: 0.5004 (mtt-85)
REVERT: A   95 LYS cc_start: 0.6637 (tttt) cc_final: 0.6197 (mmmt)
REVERT: A  127 LEU cc_start: 0.3843 (OUTLIER) cc_final: 0.3504 (mm)
REVERT: A  176 SER cc_start: 0.3502 (m) cc_final: 0.3219 (p)
REVERT: A  177 GLU cc_start: 0.6005 (tt0) cc_final: 0.4813 (mp0)
REVERT: A  334 MET cc_start: 0.2377 (mmt) cc_final: 0.2019 (ttp)
  outliers start: 8
  outliers final: 1
  residues processed: 56
  average time/residue: 0.0963
  time to fit residues: 6.1835
Evaluate side-chains
  38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 7 optimal weight:   40.0000
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    4.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  24 GLN
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.130321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.115199 restraints weight = 12215.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.114603 restraints weight = 12076.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.115206 restraints weight = 9701.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.115418 restraints weight = 8071.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.115526 restraints weight = 7391.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5689
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3147  Z= 0.219
  Angle     :  0.843   9.990   4303  Z= 0.422
  Chirality :  0.052   0.197    451
  Planarity :  0.007   0.051    506
  Dihedral  : 13.321  79.856    501
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.93 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.42), residues: 337
  helix: -0.29 (0.47), residues: 110
  sheet: -2.22 (0.68), residues: 52
  loop : -1.12 (0.42), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 126 
 TYR   0.022   0.002   TYR A 220 
 PHE   0.014   0.002   PHE A 260 
 TRP   0.013   0.002   TRP A 299 
 HIS   0.006   0.002   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00488 /  0.22 ( 3142)
  covalent geometry    : angle       0.83383 /  0.42 ( 4297)
  hydrogen bonds       : bond        0.04761 /  2.51 (  125)
  hydrogen bonds       : angle       6.92596 /  7.64 (  324)
  metal coordination   : bond        0.01269 /  0.63 (    4)
  metal coordination   : angle       3.48354 /  1.16 (    6)
  Misc. bond           : bond        0.00110 /  0.05 (    1)

*********************** 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
  46 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 VAL cc_start: 0.4748 (t) cc_final: 0.4491 (t)
REVERT: A   87 ARG cc_start: 0.7655 (tmt-80) cc_final: 0.5092 (mtt180)
REVERT: A   95 LYS cc_start: 0.7051 (tttt) cc_final: 0.6484 (mmmt)
REVERT: A  176 SER cc_start: 0.4900 (m) cc_final: 0.4490 (p)
REVERT: A  177 GLU cc_start: 0.5983 (tt0) cc_final: 0.4788 (mp0)
REVERT: A  238 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5907 (t0)
REVERT: A  334 MET cc_start: 0.2816 (OUTLIER) cc_final: 0.1294 (ttp)
  outliers start: 9
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0912
  time to fit residues: 4.4638
Evaluate side-chains
  37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0170
   chunk 12 optimal weight:    0.3980
   chunk 13 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    1.2620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.131568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.114334 restraints weight = 11938.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.115367 restraints weight = 8345.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.116119 restraints weight = 6613.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.116378 restraints weight = 5763.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.116378 restraints weight = 5414.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5691
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3147  Z= 0.132
  Angle     :  0.700  10.887   4303  Z= 0.348
  Chirality :  0.050   0.218    451
  Planarity :  0.006   0.053    506
  Dihedral  : 12.960  78.614    501
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.26 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.43), residues: 337
  helix:  0.22 (0.48), residues: 110
  sheet: -2.01 (0.62), residues: 62
  loop : -1.06 (0.44), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 264 
 TYR   0.024   0.002   TYR A 220 
 PHE   0.012   0.002   PHE A 194 
 TRP   0.023   0.002   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 ( 3142)
  covalent geometry    : angle       0.69679 /  0.35 ( 4297)
  hydrogen bonds       : bond        0.03880 /  2.07 (  125)
  hydrogen bonds       : angle       6.55633 /  7.46 (  324)
  metal coordination   : bond        0.00564 /  0.28 (    4)
  metal coordination   : angle       1.91241 /  0.64 (    6)
  Misc. bond           : bond        0.00046 /  0.02 (    1)

*********************** 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
  38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7620 (tmt-80) cc_final: 0.5045 (mtt180)
REVERT: A   95 LYS cc_start: 0.7006 (tttt) cc_final: 0.6315 (mmmt)
REVERT: A  177 GLU cc_start: 0.6180 (tt0) cc_final: 0.4913 (mp0)
REVERT: A  334 MET cc_start: 0.2804 (OUTLIER) cc_final: 0.1548 (ttp)
  outliers start: 6
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0956
  time to fit residues: 4.0376
Evaluate side-chains
  32 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  305 ASN
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.129642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.115207 restraints weight = 11692.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.115302 restraints weight = 10296.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.115634 restraints weight = 8091.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.115831 restraints weight = 7201.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.115989 restraints weight = 6327.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5668
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3147  Z= 0.183
  Angle     :  0.766   9.054   4303  Z= 0.385
  Chirality :  0.050   0.185    451
  Planarity :  0.006   0.053    506
  Dihedral  : 13.089  80.341    501
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 19.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.93 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.42), residues: 337
  helix:  0.15 (0.47), residues: 110
  sheet: -2.09 (0.61), residues: 62
  loop : -1.16 (0.44), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 280 
 TYR   0.023   0.002   TYR A 220 
 PHE   0.020   0.002   PHE A 241 
 TRP   0.042   0.003   TRP A 150 
 HIS   0.004   0.002   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.18 ( 3142)
  covalent geometry    : angle       0.76123 /  0.39 ( 4297)
  hydrogen bonds       : bond        0.04305 /  2.27 (  125)
  hydrogen bonds       : angle       6.59113 /  7.45 (  324)
  metal coordination   : bond        0.01171 /  0.59 (    4)
  metal coordination   : angle       2.50365 /  0.83 (    6)
  Misc. bond           : bond        0.00107 /  0.05 (    1)

*********************** 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
  37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7263 (tmt-80) cc_final: 0.4836 (mtt180)
REVERT: A   95 LYS cc_start: 0.7024 (tttt) cc_final: 0.6509 (mmmt)
REVERT: A  177 GLU cc_start: 0.5763 (tt0) cc_final: 0.4688 (mp0)
REVERT: A  334 MET cc_start: 0.2243 (OUTLIER) cc_final: 0.1115 (ttp)
  outliers start: 7
  outliers final: 5
  residues processed: 35
  average time/residue: 0.0743
  time to fit residues: 3.1703
Evaluate side-chains
  34 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  305 ASN
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  48 ASN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.130692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.113257 restraints weight = 11910.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.114326 restraints weight = 8285.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.114741 restraints weight = 6653.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.115343 restraints weight = 5915.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.115348 restraints weight = 5482.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5697
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3147  Z= 0.132
  Angle     :  0.724  11.660   4303  Z= 0.363
  Chirality :  0.048   0.181    451
  Planarity :  0.006   0.053    506
  Dihedral  : 12.974  80.389    501
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.26 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.43), residues: 337
  helix:  0.34 (0.48), residues: 110
  sheet: -1.90 (0.62), residues: 60
  loop : -1.31 (0.43), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 280 
 TYR   0.022   0.001   TYR A 220 
 PHE   0.013   0.002   PHE A 194 
 TRP   0.070   0.003   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 3142)
  covalent geometry    : angle       0.72101 /  0.36 ( 4297)
  hydrogen bonds       : bond        0.03871 /  2.04 (  125)
  hydrogen bonds       : angle       6.51566 /  7.39 (  324)
  metal coordination   : bond        0.00661 /  0.33 (    4)
  metal coordination   : angle       1.93737 /  0.65 (    6)
  Misc. bond           : bond        0.00081 /  0.04 (    1)

*********************** 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
  40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   48 ASN cc_start: 0.3908 (OUTLIER) cc_final: 0.3486 (t0)
REVERT: A   87 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.4798 (mtt180)
REVERT: A   95 LYS cc_start: 0.7051 (tttt) cc_final: 0.6444 (mmmt)
REVERT: A  177 GLU cc_start: 0.5981 (tt0) cc_final: 0.4869 (mp0)
REVERT: A  334 MET cc_start: 0.2850 (OUTLIER) cc_final: 0.1355 (ttp)
  outliers start: 9
  outliers final: 4
  residues processed: 37
  average time/residue: 0.0737
  time to fit residues: 3.2880
Evaluate side-chains
  35 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ASN
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  305 ASN
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0470
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    2.3484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.130371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.112691 restraints weight = 11807.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.113835 restraints weight = 8004.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.114306 restraints weight = 6406.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.114707 restraints weight = 5700.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.115120 restraints weight = 5389.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5715
moved from start:          0.4492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3147  Z= 0.139
  Angle     :  0.696   8.514   4303  Z= 0.352
  Chirality :  0.048   0.170    451
  Planarity :  0.006   0.052    506
  Dihedral  : 12.941  81.324    501
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.92 %
    Favored  : 73.09 %
  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 are not related in a simple way.
  whole: -1.35 (0.43), residues: 337
  helix:  0.45 (0.49), residues: 110
  sheet: -1.94 (0.61), residues: 60
  loop : -1.37 (0.44), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.020   0.001   TYR A 220 
 PHE   0.010   0.001   PHE A 260 
 TRP   0.066   0.003   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 ( 3142)
  covalent geometry    : angle       0.69217 /  0.35 ( 4297)
  hydrogen bonds       : bond        0.03841 /  2.01 (  125)
  hydrogen bonds       : angle       6.38548 /  7.36 (  324)
  metal coordination   : bond        0.00817 /  0.41 (    4)
  metal coordination   : angle       2.02045 /  0.67 (    6)
  Misc. bond           : bond        0.00089 /  0.04 (    1)

*********************** 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
  42 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.4812 (mtt180)
REVERT: A   95 LYS cc_start: 0.7146 (tttt) cc_final: 0.6482 (mmmt)
REVERT: A  177 GLU cc_start: 0.5967 (tt0) cc_final: 0.4824 (mp0)
REVERT: A  334 MET cc_start: 0.2915 (OUTLIER) cc_final: 0.1312 (ttp)
  outliers start: 9
  outliers final: 5
  residues processed: 39
  average time/residue: 0.0656
  time to fit residues: 3.1231
Evaluate side-chains
  35 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  305 ASN
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 26 optimal weight:    0.0050
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.6800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.130442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.114884 restraints weight = 12159.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.114664 restraints weight = 11013.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.115158 restraints weight = 8699.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.115271 restraints weight = 7505.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.115387 restraints weight = 6639.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5659
moved from start:          0.4657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3147  Z= 0.134
  Angle     :  0.744   9.506   4303  Z= 0.378
  Chirality :  0.048   0.196    451
  Planarity :  0.005   0.052    506
  Dihedral  : 12.883  81.722    501
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.58 %
    Favored  : 72.76 %
  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 are not related in a simple way.
  whole: -1.40 (0.43), residues: 337
  helix:  0.37 (0.49), residues: 110
  sheet: -1.92 (0.61), residues: 60
  loop : -1.40 (0.44), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 280 
 TYR   0.020   0.001   TYR A 220 
 PHE   0.012   0.002   PHE A 241 
 TRP   0.054   0.003   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 3142)
  covalent geometry    : angle       0.74097 /  0.38 ( 4297)
  hydrogen bonds       : bond        0.03795 /  1.98 (  125)
  hydrogen bonds       : angle       6.43290 /  7.32 (  324)
  metal coordination   : bond        0.00694 /  0.35 (    4)
  metal coordination   : angle       1.90264 /  0.63 (    6)
  Misc. bond           : bond        0.00079 /  0.04 (    1)

*********************** 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
  41 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.4827 (mtt180)
REVERT: A   95 LYS cc_start: 0.6835 (tttt) cc_final: 0.6388 (mmmt)
REVERT: A  177 GLU cc_start: 0.5648 (tt0) cc_final: 0.4640 (mp0)
REVERT: A  225 VAL cc_start: 0.7244 (m) cc_final: 0.6859 (p)
REVERT: A  334 MET cc_start: 0.2549 (OUTLIER) cc_final: 0.0947 (ttp)
  outliers start: 8
  outliers final: 5
  residues processed: 38
  average time/residue: 0.0806
  time to fit residues: 3.6164
Evaluate side-chains
  35 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  305 ASN
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0670
   chunk 5 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0470
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.8020

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  24 GLN
A 305 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.130753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.114875 restraints weight = 12161.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.115051 restraints weight = 9080.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.115529 restraints weight = 7147.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.115569 restraints weight = 6426.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.115711 restraints weight = 6043.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5659
moved from start:          0.4765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3147  Z= 0.125
  Angle     :  0.717   9.883   4303  Z= 0.363
  Chirality :  0.047   0.154    451
  Planarity :  0.005   0.053    506
  Dihedral  : 12.781  82.030    501
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.58 %
    Favored  : 72.76 %
  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 are not related in a simple way.
  whole: -1.32 (0.43), residues: 337
  helix:  0.49 (0.49), residues: 110
  sheet: -1.98 (0.60), residues: 62
  loop : -1.32 (0.44), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 309 
 TYR   0.020   0.001   TYR A 220 
 PHE   0.009   0.001   PHE A 260 
 TRP   0.069   0.003   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 3142)
  covalent geometry    : angle       0.71452 /  0.36 ( 4297)
  hydrogen bonds       : bond        0.03595 /  1.88 (  125)
  hydrogen bonds       : angle       6.27211 /  7.20 (  324)
  metal coordination   : bond        0.00495 /  0.25 (    4)
  metal coordination   : angle       1.86988 /  0.62 (    6)
  Misc. bond           : bond        0.00060 /  0.03 (    1)

*********************** 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
  45 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 VAL cc_start: 0.4780 (t) cc_final: 0.4565 (t)
REVERT: A   87 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.4775 (mtt180)
REVERT: A   95 LYS cc_start: 0.6806 (tttt) cc_final: 0.6381 (mmmt)
REVERT: A  176 SER cc_start: 0.5061 (m) cc_final: 0.4728 (p)
REVERT: A  177 GLU cc_start: 0.5557 (tt0) cc_final: 0.4538 (mp0)
REVERT: A  225 VAL cc_start: 0.7223 (m) cc_final: 0.6868 (p)
REVERT: A  334 MET cc_start: 0.2464 (OUTLIER) cc_final: 0.1000 (ttp)
  outliers start: 8
  outliers final: 4
  residues processed: 41
  average time/residue: 0.0839
  time to fit residues: 4.0988
Evaluate side-chains
  38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ARG
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0070
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5960

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.131547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.115454 restraints weight = 11684.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.115747 restraints weight = 9072.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.116047 restraints weight = 7057.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.116236 restraints weight = 6404.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.116285 restraints weight = 6015.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5632
moved from start:          0.4870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3147  Z= 0.123
  Angle     :  0.711   9.770   4303  Z= 0.360
  Chirality :  0.046   0.147    451
  Planarity :  0.005   0.052    506
  Dihedral  : 12.688  82.423    501
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 25.58 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.44), residues: 337
  helix:  0.63 (0.49), residues: 110
  sheet: -1.96 (0.60), residues: 63
  loop : -1.30 (0.45), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.023   0.001   TYR A 220 
 PHE   0.009   0.001   PHE A 260 
 TRP   0.100   0.004   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 3142)
  covalent geometry    : angle       0.70861 /  0.36 ( 4297)
  hydrogen bonds       : bond        0.03582 /  1.86 (  125)
  hydrogen bonds       : angle       6.08559 /  7.03 (  324)
  metal coordination   : bond        0.00405 /  0.20 (    4)
  metal coordination   : angle       1.83916 /  0.61 (    6)
  Misc. bond           : bond        0.00054 /  0.03 (    1)

********************** 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
  39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.4796 (mtt180)
REVERT: A   95 LYS cc_start: 0.6788 (tttt) cc_final: 0.6401 (mmmt)
REVERT: A  177 GLU cc_start: 0.5406 (tt0) cc_final: 0.4452 (mp0)
REVERT: A  225 VAL cc_start: 0.7242 (m) cc_final: 0.6926 (p)
REVERT: A  334 MET cc_start: 0.2323 (OUTLIER) cc_final: 0.0881 (ttp)
  outliers start: 6
  outliers final: 2
  residues processed: 36
  average time/residue: 0.1018
  time to fit residues: 4.2823
Evaluate side-chains
  35 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  260 PHE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0870
   chunk 12 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7762

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.131631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.115667 restraints weight = 11874.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.115683 restraints weight = 9482.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.115987 restraints weight = 7110.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.116123 restraints weight = 7105.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.116199 restraints weight = 6177.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5644
moved from start:          0.5053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3147  Z= 0.120
  Angle     :  0.688   9.832   4303  Z= 0.348
  Chirality :  0.046   0.148    451
  Planarity :  0.005   0.052    506
  Dihedral  : 12.634  82.840    501
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 24.92 %
    Favored  : 73.09 %
  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 are not related in a simple way.
  whole: -1.09 (0.44), residues: 337
  helix:  0.76 (0.51), residues: 110
  sheet: -1.86 (0.61), residues: 63
  loop : -1.25 (0.45), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.025   0.001   TYR A 220 
 PHE   0.012   0.001   PHE A 194 
 TRP   0.101   0.004   TRP A 150 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 3142)
  covalent geometry    : angle       0.68554 /  0.35 ( 4297)
  hydrogen bonds       : bond        0.03423 /  1.78 (  125)
  hydrogen bonds       : angle       5.97259 /  6.81 (  324)
  metal coordination   : bond        0.00436 /  0.22 (    4)
  metal coordination   : angle       1.69255 /  0.56 (    6)
  Misc. bond           : bond        0.00045 /  0.02 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 756.15 seconds
wall clock time: 13 minutes 41.42 seconds (821.42 seconds total)