Starting phenix.real_space_refine
on Fri Aug 22 13:41:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dwj_27756/08_2025/8dwj_27756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dwj_27756/08_2025/8dwj_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_27756/08_2025/8dwj_27756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dwj_27756/08_2025/8dwj_27756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dwj_27756/08_2025/8dwj_27756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dwj_27756/08_2025/8dwj_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-2.0-5787/lib/python3.9/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: {'RNA': 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: 1.10, per 1000 atoms: 0.36
  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: 0.28
  Conformation dependent library (CDL) restraints added in 98.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  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: 0.31
  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: 0.36 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: 4121
        2.27 -     4.54: 141
        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=" 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
  angle pdb=" CB  MET A 292 "
        pdb=" CG  MET A 292 "
        pdb=" SD  MET A 292 "
      ideal   model   delta    sigma   weight residual
     112.70  123.89  -11.19 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" C   TYR A  86 "
        pdb=" N   ARG A  87 "
        pdb=" CA  ARG A  87 "
      ideal   model   delta    sigma   weight residual
     120.65  115.88    4.77 1.32e+00 5.74e-01 1.30e+01
  ... (remaining 4292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 1660
       17.58 -    35.16: 166
       35.16 -    52.73: 44
       52.73 -    70.31: 16
       70.31 -    87.88: 7
  Dihedral angle restraints: 1893
    sinusoidal: 895
      harmonic: 998
  Sorted by residual:
  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
  dihedral pdb=" CA  GLU A 114 "
           pdb=" C   GLU A 114 "
           pdb=" N   LYS A 115 "
           pdb=" CA  LYS A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 1890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 274
       0.040 -    0.079: 101
       0.079 -    0.118: 44
       0.118 -    0.158: 22
       0.158 -    0.197: 10
  Chirality restraints: 451
  Sorted by residual:
  chirality pdb=" CA  MET A 281 "
            pdb=" N   MET A 281 "
            pdb=" C   MET A 281 "
            pdb=" CB  MET A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.74e-01
  chirality pdb=" CA  LEU A 336 "
            pdb=" N   LEU A 336 "
            pdb=" C   LEU A 336 "
            pdb=" CB  LEU A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  MET A 307 "
            pdb=" N   MET A 307 "
            pdb=" C   MET A 307 "
            pdb=" CB  MET A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.82e-01
  ... (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:             3.100
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.780
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5760
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= 0.392
  Angle     :  1.176  22.256   4303  Z= 0.591
  Chirality :  0.059   0.197    451
  Planarity :  0.008   0.064    506
  Dihedral  : 16.243  87.883   1251
  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 aren 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
  covalent geometry    : bond        0.00536 ( 3142)
  covalent geometry    : angle       1.05129 ( 4297)
  hydrogen bonds       : bond        0.18315 (  125)
  hydrogen bonds       : angle       9.02912 (  324)
  metal coordination   : bond        0.16030 (    4)
  metal coordination   : angle      14.13845 (    6)
  Misc. bond           : bond        0.05167 (    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  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TRP cc_start: 0.4145 (m100) cc_final: 0.3610 (m100)
REVERT: A   54 TYR cc_start: 0.5764 (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: 0.7190 (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: 0.6151 (tt0) cc_final: 0.5704 (mp0)
REVERT: A  183 PRO cc_start: 0.5777 (Cg_exo) cc_final: 0.5372 (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: 0.8305 (tttt) cc_final: 0.7955 (mtpp)
REVERT: A  292 MET cc_start: 0.8457 (tmm) cc_final: 0.8071 (tpt)
REVERT: A  322 MET cc_start: 0.7559 (mmt) cc_final: 0.7044 (ptp)
REVERT: A  334 MET cc_start: 0.1537 (mmt) cc_final: 0.0137 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0751
  time to fit residues: 8.3556
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  : 0.088 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.132599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.117167 restraints weight = 11871.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.118006 restraints weight = 9830.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.117899 restraints weight = 7662.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.118061 restraints weight = 7405.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.118496 restraints weight = 6629.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5617
moved from start:          0.2806

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= 0.128
  Angle     :  0.674   7.226   4303  Z= 0.338
  Chirality :  0.046   0.156    451
  Planarity :  0.006   0.060    506
  Dihedral  : 14.996  81.097    519
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.28 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.43), residues: 337
  helix: -0.39 (0.47), residues: 110
  sheet: -2.13 (0.70), residues: 47
  loop : -0.84 (0.44), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 264 
 TYR   0.009   0.001   TYR A 185 
 PHE   0.013   0.002   PHE A 260 
 TRP   0.017   0.002   TRP A 294 
 HIS   0.003   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3142)
  covalent geometry    : angle       0.66643 ( 4297)
  hydrogen bonds       : bond        0.04160 (  125)
  hydrogen bonds       : angle       6.91761 (  324)
  metal coordination   : bond        0.00579 (    4)
  metal coordination   : angle       2.79906 (    6)
  Misc. bond           : bond        0.00051 (    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: 7
    poor density    : 52
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.6996 (tt0) cc_final: 0.6521 (pm20)
REVERT: A   87 ARG cc_start: 0.7653 (tmt-80) cc_final: 0.5078 (mtt180)
REVERT: A   95 LYS cc_start: 0.6422 (tttt) cc_final: 0.6180 (mmmt)
REVERT: A  176 SER cc_start: 0.3848 (m) cc_final: 0.3518 (p)
REVERT: A  177 GLU cc_start: 0.5881 (tt0) cc_final: 0.4783 (mp0)
REVERT: A  334 MET cc_start: 0.2364 (mmt) cc_final: 0.0915 (ttp)
  outliers start: 7
  outliers final: 1
  residues processed: 57
  average time/residue: 0.1002
  time to fit residues: 6.5304
Evaluate side-chains
  41 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 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 = 0.4359 r_free = 0.4359 target = 0.129654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.113693 restraints weight = 11685.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.114905 restraints weight = 7535.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.115760 restraints weight = 5834.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.116120 restraints weight = 4946.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.116120 restraints weight = 4549.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5840
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3147  Z= 0.190
  Angle     :  0.748   7.311   4303  Z= 0.385
  Chirality :  0.050   0.186    451
  Planarity :  0.007   0.069    506
  Dihedral  : 15.187  80.597    515
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.93 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.44), residues: 337
  helix:  0.05 (0.48), residues: 109
  sheet: -1.65 (0.63), residues: 62
  loop : -0.82 (0.46), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 280 
 TYR   0.016   0.002   TYR A 220 
 PHE   0.015   0.002   PHE A 241 
 TRP   0.010   0.002   TRP A 266 
 HIS   0.006   0.002   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 3142)
  covalent geometry    : angle       0.73659 ( 4297)
  hydrogen bonds       : bond        0.04633 (  125)
  hydrogen bonds       : angle       6.90526 (  324)
  metal coordination   : bond        0.01494 (    4)
  metal coordination   : angle       3.61955 (    6)
  Misc. bond           : bond        0.00106 (    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
  44 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A   76 ILE cc_start: 0.7396 (mm) cc_final: 0.7180 (mm)
REVERT: A   87 ARG cc_start: 0.7230 (tmt-80) cc_final: 0.4713 (mtt180)
REVERT: A   95 LYS cc_start: 0.7439 (tttt) cc_final: 0.6918 (mmmt)
REVERT: A  176 SER cc_start: 0.5250 (m) cc_final: 0.4884 (p)
REVERT: A  177 GLU cc_start: 0.5983 (tt0) cc_final: 0.4766 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 42
  average time/residue: 0.0651
  time to fit residues: 3.2219
Evaluate side-chains
  36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
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  182 ILE
Chi-restraints excluded: chain A residue  230 VAL
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:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.129032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.114741 restraints weight = 11736.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.115764 restraints weight = 10679.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.115751 restraints weight = 7954.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.115896 restraints weight = 7117.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.116059 restraints weight = 6739.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5782
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3147  Z= 0.156
  Angle     :  0.701  10.670   4303  Z= 0.351
  Chirality :  0.047   0.175    451
  Planarity :  0.007   0.067    506
  Dihedral  : 14.981  82.231    515
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.60 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.43), residues: 337
  helix:  0.25 (0.47), residues: 110
  sheet: -1.80 (0.60), residues: 62
  loop : -0.95 (0.45), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  14 
 TYR   0.018   0.002   TYR A 220 
 PHE   0.012   0.002   PHE A 260 
 TRP   0.025   0.002   TRP A 150 
 HIS   0.004   0.002   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3142)
  covalent geometry    : angle       0.69473 ( 4297)
  hydrogen bonds       : bond        0.04074 (  125)
  hydrogen bonds       : angle       6.69946 (  324)
  metal coordination   : bond        0.01024 (    4)
  metal coordination   : angle       2.52346 (    6)
  Misc. bond           : bond        0.00093 (    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
  46 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.4936 (mtt180)
REVERT: A   95 LYS cc_start: 0.7175 (tttt) cc_final: 0.6773 (tppt)
REVERT: A  177 GLU cc_start: 0.5488 (tt0) cc_final: 0.4520 (mp0)
REVERT: A  225 VAL cc_start: 0.7450 (m) cc_final: 0.7044 (p)
REVERT: A  292 MET cc_start: 0.8029 (tmm) cc_final: 0.7456 (tmm)
REVERT: A  319 MET cc_start: 0.6254 (mpp) cc_final: 0.5916 (mpp)
REVERT: A  334 MET cc_start: 0.2142 (OUTLIER) cc_final: 0.0718 (ttp)
  outliers start: 9
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0573
  time to fit residues: 2.9580
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  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  260 PHE
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:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    0.4980
   chunk 32 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    4.2988

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.127895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.112978 restraints weight = 11836.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.113943 restraints weight = 8527.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.114505 restraints weight = 6853.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.114993 restraints weight = 6181.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.115344 restraints weight = 5568.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5840
moved from start:          0.5999

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= 0.184
  Angle     :  0.729   9.105   4303  Z= 0.370
  Chirality :  0.048   0.163    451
  Planarity :  0.008   0.100    506
  Dihedral  : 15.683  86.629    515
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 20.60 %
    Favored  : 75.08 %
  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 aren not related in a simple way.
  whole: -1.50 (0.43), residues: 337
  helix: -0.03 (0.46), residues: 117
  sheet: -1.99 (0.58), residues: 63
  loop : -1.20 (0.46), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 280 
 TYR   0.015   0.002   TYR A 220 
 PHE   0.011   0.002   PHE A 260 
 TRP   0.036   0.003   TRP A 150 
 HIS   0.005   0.002   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3142)
  covalent geometry    : angle       0.71873 ( 4297)
  hydrogen bonds       : bond        0.04453 (  125)
  hydrogen bonds       : angle       6.88865 (  324)
  metal coordination   : bond        0.01352 (    4)
  metal coordination   : angle       3.31485 (    6)
  Misc. bond           : bond        0.00152 (    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
  48 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.5164 (mtt180)
REVERT: A   95 LYS cc_start: 0.7208 (tttt) cc_final: 0.6863 (tppt)
REVERT: A  177 GLU cc_start: 0.5593 (tt0) cc_final: 0.4600 (mp0)
REVERT: A  292 MET cc_start: 0.8059 (tmm) cc_final: 0.7576 (tmm)
REVERT: A  319 MET cc_start: 0.6184 (mpp) cc_final: 0.5941 (mpp)
  outliers start: 13
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0899
  time to fit residues: 4.4636
Evaluate side-chains
  40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  258 VAL
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:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.128074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.114138 restraints weight = 11793.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.114552 restraints weight = 10282.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.114919 restraints weight = 7379.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.115104 restraints weight = 7456.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.115276 restraints weight = 6336.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5826
moved from start:          0.6317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3147  Z= 0.155
  Angle     :  0.688   6.857   4303  Z= 0.348
  Chirality :  0.046   0.150    451
  Planarity :  0.007   0.065    506
  Dihedral  : 15.496  89.069    515
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 22.26 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.43), residues: 337
  helix:  0.03 (0.46), residues: 118
  sheet: -1.74 (0.62), residues: 61
  loop : -1.27 (0.45), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  36 
 TYR   0.014   0.002   TYR A 220 
 PHE   0.012   0.002   PHE A 260 
 TRP   0.039   0.003   TRP A 150 
 HIS   0.003   0.002   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3142)
  covalent geometry    : angle       0.67694 ( 4297)
  hydrogen bonds       : bond        0.04045 (  125)
  hydrogen bonds       : angle       6.74537 (  324)
  metal coordination   : bond        0.00862 (    4)
  metal coordination   : angle       3.37420 (    6)
  Misc. bond           : bond        0.00135 (    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
  47 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7734 (tmt-80) cc_final: 0.5065 (mtt180)
REVERT: A   95 LYS cc_start: 0.7052 (tttt) cc_final: 0.6661 (tppt)
REVERT: A  292 MET cc_start: 0.8172 (tmm) cc_final: 0.7708 (tmm)
REVERT: A  338 LYS cc_start: 0.6038 (mtmt) cc_final: 0.5633 (mtmt)
  outliers start: 11
  outliers final: 8
  residues processed: 44
  average time/residue: 0.0744
  time to fit residues: 3.8240
Evaluate side-chains
  39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  258 VAL
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:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0270
   chunk 19 optimal weight:    9.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    4.3644

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.126634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.112027 restraints weight = 11640.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.113130 restraints weight = 8200.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.113821 restraints weight = 6371.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.114433 restraints weight = 5490.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.114678 restraints weight = 4864.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5868
moved from start:          0.6805

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= 0.186
  Angle     :  0.738   6.692   4303  Z= 0.378
  Chirality :  0.048   0.160    451
  Planarity :  0.008   0.085    506
  Dihedral  : 15.092  89.692    515
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 20.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.26 %
    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 aren not related in a simple way.
  whole: -1.85 (0.42), residues: 337
  helix: -0.33 (0.44), residues: 118
  sheet: -1.89 (0.60), residues: 63
  loop : -1.55 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  36 
 TYR   0.012   0.002   TYR A  54 
 PHE   0.011   0.002   PHE A 260 
 TRP   0.044   0.003   TRP A 150 
 HIS   0.004   0.002   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 3142)
  covalent geometry    : angle       0.72054 ( 4297)
  hydrogen bonds       : bond        0.04680 (  125)
  hydrogen bonds       : angle       6.84556 (  324)
  metal coordination   : bond        0.01302 (    4)
  metal coordination   : angle       4.34133 (    6)
  Misc. bond           : bond        0.00177 (    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
  49 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 33
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.5267 (mtt180)
REVERT: A   95 LYS cc_start: 0.7233 (tttt) cc_final: 0.6733 (mmmt)
REVERT: A  118 ILE cc_start: -0.1609 (OUTLIER) cc_final: -0.1979 (mt)
REVERT: A  292 MET cc_start: 0.8242 (tmm) cc_final: 0.7750 (tmm)
REVERT: A  338 LYS cc_start: 0.5987 (mtmt) cc_final: 0.5450 (mtmt)
  outliers start: 16
  outliers final: 12
  residues processed: 44
  average time/residue: 0.0830
  time to fit residues: 4.2304
Evaluate side-chains
  47 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  319 MET
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:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 14 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0570
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0570
   overall best weight:    0.5416

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 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 = 0.4354 r_free = 0.4354 target = 0.129900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.115020 restraints weight = 12327.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.115549 restraints weight = 9808.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.115655 restraints weight = 7452.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.115963 restraints weight = 6839.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.116172 restraints weight = 6080.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5865
moved from start:          0.6748

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= 0.122
  Angle     :  0.650   7.051   4303  Z= 0.327
  Chirality :  0.046   0.166    451
  Planarity :  0.006   0.067    506
  Dihedral  : 14.399  87.155    515
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  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 aren not related in a simple way.
  whole: -1.42 (0.43), residues: 337
  helix:  0.19 (0.47), residues: 118
  sheet: -1.76 (0.62), residues: 58
  loop : -1.43 (0.45), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  36 
 TYR   0.012   0.001   TYR A 220 
 PHE   0.012   0.002   PHE A 260 
 TRP   0.044   0.002   TRP A 150 
 HIS   0.005   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3142)
  covalent geometry    : angle       0.63822 ( 4297)
  hydrogen bonds       : bond        0.03651 (  125)
  hydrogen bonds       : angle       6.19603 (  324)
  metal coordination   : bond        0.00410 (    4)
  metal coordination   : angle       3.34634 (    6)
  Misc. bond           : bond        0.00062 (    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
  46 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   18 HIS cc_start: 0.6765 (m-70) cc_final: 0.6184 (p-80)
REVERT: A   87 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.5142 (mtt180)
REVERT: A   95 LYS cc_start: 0.7289 (tttt) cc_final: 0.6602 (mmmt)
REVERT: A  118 ILE cc_start: -0.1088 (OUTLIER) cc_final: -0.1450 (mp)
REVERT: A  292 MET cc_start: 0.8188 (tmm) cc_final: 0.7807 (tmm)
REVERT: A  334 MET cc_start: 0.2219 (mmt) cc_final: 0.0609 (ttp)
  outliers start: 6
  outliers final: 3
  residues processed: 45
  average time/residue: 0.0816
  time to fit residues: 4.2746
Evaluate side-chains
  37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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  156 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  319 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A 134 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 = 0.4329 r_free = 0.4329 target = 0.128901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.113900 restraints weight = 11742.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.114875 restraints weight = 8358.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.115675 restraints weight = 6585.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.116269 restraints weight = 5626.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.116464 restraints weight = 5016.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5807
moved from start:          0.6984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3147  Z= 0.143
  Angle     :  0.681   6.746   4303  Z= 0.345
  Chirality :  0.047   0.173    451
  Planarity :  0.007   0.063    506
  Dihedral  : 14.411  89.741    515
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  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 aren not related in a simple way.
  whole: -1.48 (0.43), residues: 337
  helix:  0.12 (0.48), residues: 118
  sheet: -1.72 (0.59), residues: 63
  loop : -1.45 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  36 
 TYR   0.015   0.002   TYR A 220 
 PHE   0.009   0.002   PHE A 260 
 TRP   0.062   0.003   TRP A 150 
 HIS   0.004   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3142)
  covalent geometry    : angle       0.66458 ( 4297)
  hydrogen bonds       : bond        0.04033 (  125)
  hydrogen bonds       : angle       6.29063 (  324)
  metal coordination   : bond        0.00789 (    4)
  metal coordination   : angle       4.09131 (    6)
  Misc. bond           : bond        0.00100 (    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
  39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   18 HIS cc_start: 0.6730 (m-70) cc_final: 0.6146 (p-80)
REVERT: A   87 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.5252 (mtt180)
REVERT: A   95 LYS cc_start: 0.7313 (tttt) cc_final: 0.6690 (mmmt)
REVERT: A  292 MET cc_start: 0.8188 (tmm) cc_final: 0.7827 (tmm)
REVERT: A  334 MET cc_start: 0.2991 (mmt) cc_final: 0.1269 (ttp)
  outliers start: 6
  outliers final: 3
  residues processed: 38
  average time/residue: 0.0670
  time to fit residues: 3.1308
Evaluate side-chains
  33 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  319 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0030
   overall best weight:    1.3996

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.129530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.112489 restraints weight = 11974.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.113908 restraints weight = 7870.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.114794 restraints weight = 5982.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.115251 restraints weight = 5090.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.115487 restraints weight = 4648.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5834
moved from start:          0.7048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3147  Z= 0.124
  Angle     :  0.653   6.641   4303  Z= 0.329
  Chirality :  0.047   0.189    451
  Planarity :  0.006   0.062    506
  Dihedral  : 14.202  87.974    515
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 26.58 %
    Favored  : 71.43 %
  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 aren not related in a simple way.
  whole: -1.35 (0.43), residues: 337
  helix:  0.27 (0.48), residues: 116
  sheet: -1.72 (0.61), residues: 58
  loop : -1.40 (0.44), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  36 
 TYR   0.015   0.001   TYR A 220 
 PHE   0.015   0.002   PHE A  31 
 TRP   0.070   0.003   TRP A 150 
 HIS   0.004   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3142)
  covalent geometry    : angle       0.63807 ( 4297)
  hydrogen bonds       : bond        0.03892 (  125)
  hydrogen bonds       : angle       6.11123 (  324)
  metal coordination   : bond        0.00551 (    4)
  metal coordination   : angle       3.71817 (    6)
  Misc. bond           : bond        0.00055 (    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
  40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   18 HIS cc_start: 0.6993 (m-70) cc_final: 0.6393 (p-80)
REVERT: A   87 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.5274 (mtt180)
REVERT: A   95 LYS cc_start: 0.7361 (tttt) cc_final: 0.6723 (mmmt)
REVERT: A  292 MET cc_start: 0.8218 (tmm) cc_final: 0.7876 (tmm)
REVERT: A  334 MET cc_start: 0.2797 (mmt) cc_final: 0.0885 (ttp)
  outliers start: 6
  outliers final: 3
  residues processed: 38
  average time/residue: 0.0691
  time to fit residues: 3.2441
Evaluate side-chains
  36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  319 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0050
   overall best weight:    0.7636

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.130437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.115533 restraints weight = 11606.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.116884 restraints weight = 9344.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.117257 restraints weight = 6425.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.117093 restraints weight = 6284.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.117177 restraints weight = 6076.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5753
moved from start:          0.7106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3147  Z= 0.120
  Angle     :  0.651   6.476   4303  Z= 0.329
  Chirality :  0.046   0.196    451
  Planarity :  0.005   0.048    506
  Dihedral  : 14.163  89.044    515
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 27.24 %
    Favored  : 71.43 %
  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 aren not related in a simple way.
  whole: -1.24 (0.43), residues: 337
  helix:  0.41 (0.48), residues: 116
  sheet: -1.66 (0.62), residues: 58
  loop : -1.37 (0.44), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  36 
 TYR   0.016   0.001   TYR A 220 
 PHE   0.015   0.002   PHE A  31 
 TRP   0.050   0.002   TRP A 150 
 HIS   0.005   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3142)
  covalent geometry    : angle       0.63575 ( 4297)
  hydrogen bonds       : bond        0.03738 (  125)
  hydrogen bonds       : angle       6.00716 (  324)
  metal coordination   : bond        0.00439 (    4)
  metal coordination   : angle       3.79539 (    6)
  Misc. bond           : bond        0.00034 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 684.10 seconds
wall clock time: 12 minutes 29.49 seconds (749.49 seconds total)