Starting phenix.real_space_refine
on Tue Feb  3 20:09:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v48_64770/02_2026/9v48_64770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v48_64770/02_2026/9v48_64770.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v48_64770/02_2026/9v48_64770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v48_64770/02_2026/9v48_64770.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v48_64770/02_2026/9v48_64770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v48_64770/02_2026/9v48_64770.cif"
  }
  resolution = 4.75
  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=   0.001 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3028 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      28      5.16       5
     C    2430      2.51       5
     N     753      2.21       5
     O     902      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4153
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "D"
      Number of atoms: 3310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3310
          Classifications: {'peptide': 420}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 405}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 328
          Classifications: {'RNA': 16}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 6, 'rna3p': 9}
    Chain: "F"
      Number of atoms: 515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 515
          Classifications: {'RNA': 24}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 6, 'rna3p': 17}
  Time building chain proxies: 1.10, per 1000 atoms: 0.26
  Number of scatterers: 4153
  At special positions: 0
  Unit cell: (77.76, 103.68, 67.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      40     15.00
     O     902      8.00
     N     753      7.00
     C    2430      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 256.4 milliseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 3 sheets defined
      60.5% alpha, 3.8% beta
      4 base pairs and 12 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'D' and resid 21 through 48
      removed outlier: 4.347A  pdb=" N   ILE D  25 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 55
    Processing helix  chain 'D' and resid 56 through 71
      removed outlier: 4.051A  pdb=" N   SER D  60 " --> pdb=" O   LEU D  56 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL D  67 " --> pdb=" O   ILE D  63 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE D  71 " --> pdb=" O   VAL D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 82
    Processing helix  chain 'D' and resid 113 through 124
    Processing helix  chain 'D' and resid 129 through 148
      removed outlier: 4.321A  pdb=" N   LEU D 133 " --> pdb=" O   ALA D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 158
      removed outlier: 3.795A  pdb=" N   LEU D 154 " --> pdb=" O   ARG D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 167
      removed outlier: 3.998A  pdb=" N   SER D 165 " --> pdb=" O   ARG D 162 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU D 166 " --> pdb=" O   MET D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 183
    Processing helix  chain 'D' and resid 185 through 201
    Processing helix  chain 'D' and resid 209 through 230
    Processing helix  chain 'D' and resid 232 through 244
    Processing helix  chain 'D' and resid 250 through 264
      removed outlier: 3.965A  pdb=" N   GLU D 254 " --> pdb=" O   ASN D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 279
      No H-bonds generated for 'chain 'D' and resid 277 through 279'
    Processing helix  chain 'D' and resid 280 through 288
    Processing helix  chain 'D' and resid 300 through 305
      removed outlier: 4.675A  pdb=" N   PHE D 304 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 335
      removed outlier: 3.526A  pdb=" N   LYS D 325 " --> pdb=" O   ASN D 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 349
    Processing helix  chain 'D' and resid 421 through 427
      removed outlier: 3.843A  pdb=" N   ILE D 425 " --> pdb=" O   ASP D 421 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 428 through 431
    Processing helix  chain 'D' and resid 438 through 438
      No H-bonds generated for 'chain 'D' and resid 438 through 438'
    Processing helix  chain 'D' and resid 439 through 451
      removed outlier: 3.898A  pdb=" N   GLU D 443 " --> pdb=" O   ASP D 439 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   GLY D 450 " --> pdb=" O   ARG D 446 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ALA D 451 " --> pdb=" O   MET D 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 465 through 469
      removed outlier: 3.506A  pdb=" N   GLU D 469 " --> pdb=" O   LEU D 466 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 91 through 92
    Processing sheet with id=AA2, first strand: chain 'D' and resid 95 through 100
      removed outlier: 3.544A  pdb=" N   LYS D  98 " --> pdb=" O   MET D 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 314 through 316
      removed outlier: 4.002A  pdb=" N   SER D 314 " --> pdb=" O   SER D 377 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER D 377 " --> pdb=" O   SER D 314 " (cutoff:3.500A)

    164 hydrogen bonds defined for protein.
    456 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      10 hydrogen bonds
      20 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      12 stacking parallelities
  Total time for adding SS restraints: 0.54

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1075
        1.33 -     1.45: 955
        1.45 -     1.57: 2143
        1.57 -     1.69: 78
        1.69 -     1.81: 50
  Bond restraints: 4301
  Sorted by residual:
  bond pdb=" CA  ARG D 195 "
       pdb=" C   ARG D 195 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.24e-02 6.50e+03 8.19e+00
  bond pdb=" CA  ARG D 174 "
       pdb=" C   ARG D 174 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.031 1.38e-02 5.25e+03 5.07e+00
  bond pdb=" O3'   A F   1 "
       pdb=" P     G F   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.575  0.032 1.50e-02 4.44e+03 4.46e+00
  bond pdb=" O3'   G E 240 "
       pdb=" P     C E 241 "
    ideal  model  delta    sigma   weight residual
    1.607  1.576  0.031 1.50e-02 4.44e+03 4.29e+00
  bond pdb=" C   ARG D 195 "
       pdb=" N   MET D 196 "
    ideal  model  delta    sigma   weight residual
    1.335  1.309  0.026 1.30e-02 5.92e+03 4.13e+00
  ... (remaining 4296 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 5355
        1.35 -     2.71: 485
        2.71 -     4.06: 86
        4.06 -     5.41: 25
        5.41 -     6.76: 16
  Bond angle restraints: 5967
  Sorted by residual:
  angle pdb=" N   ARG D 355 "
        pdb=" CA  ARG D 355 "
        pdb=" C   ARG D 355 "
      ideal   model   delta    sigma   weight residual
     111.75  118.07   -6.32 1.28e+00 6.10e-01 2.44e+01
  angle pdb=" N   LYS D 357 "
        pdb=" CA  LYS D 357 "
        pdb=" C   LYS D 357 "
      ideal   model   delta    sigma   weight residual
     113.23  107.11    6.12 1.24e+00 6.50e-01 2.43e+01
  angle pdb=" N   GLY D  86 "
        pdb=" CA  GLY D  86 "
        pdb=" C   GLY D  86 "
      ideal   model   delta    sigma   weight residual
     111.54  105.19    6.35 1.36e+00 5.41e-01 2.18e+01
  angle pdb=" N   ASN D  76 "
        pdb=" CA  ASN D  76 "
        pdb=" C   ASN D  76 "
      ideal   model   delta    sigma   weight residual
     111.28  106.26    5.02 1.09e+00 8.42e-01 2.12e+01
  angle pdb=" O3'   U E 227 "
        pdb=" C3'   U E 227 "
        pdb=" C2'   U E 227 "
      ideal   model   delta    sigma   weight residual
     109.50  115.65   -6.15 1.50e+00 4.44e-01 1.68e+01
  ... (remaining 5962 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 2477
       35.68 -    71.36: 182
       71.36 -   107.04: 17
      107.04 -   142.72: 3
      142.72 -   178.40: 8
  Dihedral angle restraints: 2687
    sinusoidal: 1484
      harmonic: 1203
  Sorted by residual:
  dihedral pdb=" O4'   U F  21 "
           pdb=" C1'   U F  21 "
           pdb=" N1    U F  21 "
           pdb=" C2    U F  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.14  155.86     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" C5'   C E 241 "
           pdb=" C4'   C E 241 "
           pdb=" C3'   C E 241 "
           pdb=" O3'   C E 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  144.35  -62.35     1      8.00e+00 1.56e-02 8.04e+01
  dihedral pdb=" O4'   C E 241 "
           pdb=" C4'   C E 241 "
           pdb=" C3'   C E 241 "
           pdb=" C2'   C E 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   26.62  -61.62     1      8.00e+00 1.56e-02 7.87e+01
  ... (remaining 2684 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 519
       0.055 -    0.111: 123
       0.111 -    0.166: 31
       0.166 -    0.222: 8
       0.222 -    0.277: 2
  Chirality restraints: 683
  Sorted by residual:
  chirality pdb=" C3'   U E 227 "
            pdb=" C4'   U E 227 "
            pdb=" O3'   U E 227 "
            pdb=" C2'   U E 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.47   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  PHE D 458 "
            pdb=" N   PHE D 458 "
            pdb=" C   PHE D 458 "
            pdb=" CB  PHE D 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" C3'   U F  20 "
            pdb=" C4'   U F  20 "
            pdb=" O3'   U F  20 "
            pdb=" C2'   U F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.70    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 680 not shown)

  Planarity restraints: 630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 353 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO D 354 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO D 354 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 354 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D 356 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" C   GLY D 356 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLY D 356 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS D 357 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 282 "   -0.033 5.00e-02 4.00e+02   5.01e-02 4.01e+00
        pdb=" N   PRO D 283 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO D 283 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 283 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 627 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 614
        2.74 -     3.28: 4758
        3.28 -     3.82: 7303
        3.82 -     4.36: 8352
        4.36 -     4.90: 12126
  Nonbonded interactions: 33153
  Sorted by model distance:
  nonbonded pdb=" O   ARG D  55 "
            pdb=" N   TYR D 313 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" N   ILE D  57 "
            pdb=" O   TYR D 313 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   LEU D 315 "
            pdb=" NZ  LYS D 325 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" ND2 ASN D 417 "
            pdb=" OE1 GLU D 454 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OH  TYR D  52 "
            pdb=" OG  SER D 376 "
     model   vdw
     2.211 3.040
  ... (remaining 33148 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:             4.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.190
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
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      :  0.006   0.056   4301  Z= 0.310
  Angle     :  0.922   6.764   5967  Z= 0.584
  Chirality :  0.055   0.277    683
  Planarity :  0.005   0.060    630
  Dihedral  : 24.490 178.403   1913
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 34.08
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 11.11 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  :  9.94 %
    Favored  : 85.51 %
  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: -4.85 (0.32), residues: 414
  helix: -2.69 (0.26), residues: 213
  sheet: -3.86 (0.79), residues: 26
  loop : -3.72 (0.40), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 416 
 TYR   0.027   0.003   TYR D  97 
 PHE   0.011   0.002   PHE D 464 
 TRP   0.017   0.003   TRP D 330 
 HIS   0.007   0.002   HIS D 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 4301)
  covalent geometry    : angle       0.92185 ( 5967)
  hydrogen bonds       : bond        0.16897 (  174)
  hydrogen bonds       : angle       7.04767 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   78 TYR cc_start: 0.6786 (m-80) cc_final: 0.6052 (m-80)
REVERT: D  103 LYS cc_start: 0.7191 (mmmt) cc_final: 0.6908 (tmtt)
REVERT: D  137 MET cc_start: 0.8931 (mtm) cc_final: 0.8647 (mtm)
REVERT: D  156 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8440 (mmm160)
REVERT: D  168 GLN cc_start: 0.7476 (tt0) cc_final: 0.7078 (tt0)
REVERT: D  208 ARG cc_start: 0.1510 (OUTLIER) cc_final: 0.0547 (ttt180)
REVERT: D  222 MET cc_start: 0.7848 (mmm) cc_final: 0.7617 (mmm)
REVERT: D  235 GLN cc_start: 0.9033 (mt0) cc_final: 0.8775 (mt0)
REVERT: D  331 MET cc_start: 0.5327 (ttp) cc_final: 0.4405 (ttm)
REVERT: D  446 ARG cc_start: 0.9080 (mtm110) cc_final: 0.8857 (ttm110)
REVERT: D  447 MET cc_start: 0.8037 (mtp) cc_final: 0.7348 (tpp)
REVERT: D  448 MET cc_start: 0.8335 (tmm) cc_final: 0.7281 (tmm)
REVERT: D  458 PHE cc_start: 0.8024 (p90) cc_final: 0.7273 (p90)
  outliers start: 16
  outliers final: 4
  residues processed: 97
  average time/residue: 0.1374
  time to fit residues: 15.1041
Evaluate side-chains
  75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
D 135 HIS
D 142 ASN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 417 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.142968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.131142 restraints weight = 11265.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.133581 restraints weight = 7491.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.135322 restraints weight = 5384.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.136497 restraints weight = 4068.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.137424 restraints weight = 3239.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6789
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4301  Z= 0.182
  Angle     :  0.803   7.344   5967  Z= 0.417
  Chirality :  0.044   0.191    683
  Planarity :  0.005   0.050    630
  Dihedral  : 25.973 172.872   1084
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.25 %
    Favored  : 93.18 %
  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: -3.19 (0.37), residues: 414
  helix: -1.17 (0.31), residues: 219
  sheet: -4.05 (0.73), residues: 26
  loop : -3.01 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  75 
 TYR   0.026   0.003   TYR D  78 
 PHE   0.014   0.002   PHE D  71 
 TRP   0.017   0.003   TRP D 330 
 HIS   0.008   0.003   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4301)
  covalent geometry    : angle       0.80326 ( 5967)
  hydrogen bonds       : bond        0.04513 (  174)
  hydrogen bonds       : angle       5.11310 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  136 MET cc_start: 0.8025 (mtp) cc_final: 0.7531 (mtp)
REVERT: D  156 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8269 (mmm160)
REVERT: D  168 GLN cc_start: 0.7399 (tt0) cc_final: 0.6665 (tt0)
REVERT: D  188 THR cc_start: 0.9689 (p) cc_final: 0.8838 (t)
REVERT: D  211 ASN cc_start: 0.9054 (p0) cc_final: 0.8584 (p0)
REVERT: D  216 ARG cc_start: 0.8613 (ttm110) cc_final: 0.8342 (mtt-85)
REVERT: D  240 ASP cc_start: 0.7703 (m-30) cc_final: 0.7222 (m-30)
REVERT: D  277 PRO cc_start: 0.7529 (Cg_endo) cc_final: 0.7027 (Cg_exo)
REVERT: D  443 GLU cc_start: 0.8441 (tt0) cc_final: 0.8059 (tt0)
REVERT: D  447 MET cc_start: 0.7644 (mtp) cc_final: 0.7157 (tpt)
REVERT: D  448 MET cc_start: 0.8722 (tmm) cc_final: 0.8119 (tmm)
REVERT: D  458 PHE cc_start: 0.7921 (p90) cc_final: 0.7201 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1211
  time to fit residues: 11.9091
Evaluate side-chains
  69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0970
   chunk 17 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
D  82 HIS
D 142 ASN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.147519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.135014 restraints weight = 11230.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.137612 restraints weight = 7492.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.139410 restraints weight = 5347.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.140766 restraints weight = 4048.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.141677 restraints weight = 3174.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4301  Z= 0.139
  Angle     :  0.726   7.298   5967  Z= 0.369
  Chirality :  0.040   0.181    683
  Planarity :  0.005   0.052    630
  Dihedral  : 25.893 177.163   1084
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.41 %
    Favored  : 96.31 %
  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: -2.03 (0.40), residues: 414
  helix: -0.09 (0.35), residues: 219
  sheet: -3.61 (1.06), residues: 16
  loop : -2.79 (0.43), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  77 
 TYR   0.024   0.002   TYR D  78 
 PHE   0.007   0.001   PHE D 464 
 TRP   0.017   0.003   TRP D 139 
 HIS   0.007   0.002   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4301)
  covalent geometry    : angle       0.72574 ( 5967)
  hydrogen bonds       : bond        0.03841 (  174)
  hydrogen bonds       : angle       4.49754 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   71 PHE cc_start: 0.6822 (m-80) cc_final: 0.6518 (m-80)
REVERT: D  112 ASP cc_start: 0.6774 (m-30) cc_final: 0.6241 (t70)
REVERT: D  136 MET cc_start: 0.8107 (mtp) cc_final: 0.7879 (mtt)
REVERT: D  137 MET cc_start: 0.8732 (mtm) cc_final: 0.8286 (mtm)
REVERT: D  147 THR cc_start: 0.8465 (p) cc_final: 0.8143 (t)
REVERT: D  156 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8297 (mmm160)
REVERT: D  168 GLN cc_start: 0.7673 (tt0) cc_final: 0.7308 (tt0)
REVERT: D  189 MET cc_start: 0.8400 (tpt) cc_final: 0.8182 (tpt)
REVERT: D  196 MET cc_start: 0.8053 (mtt) cc_final: 0.7795 (mmt)
REVERT: D  211 ASN cc_start: 0.9099 (p0) cc_final: 0.8717 (p0)
REVERT: D  255 ASP cc_start: 0.9125 (m-30) cc_final: 0.8889 (m-30)
REVERT: D  292 GLU cc_start: 0.8282 (pt0) cc_final: 0.7915 (pt0)
REVERT: D  443 GLU cc_start: 0.8529 (tt0) cc_final: 0.7646 (tt0)
REVERT: D  446 ARG cc_start: 0.8930 (mtm180) cc_final: 0.8594 (mtm180)
REVERT: D  448 MET cc_start: 0.8538 (tmm) cc_final: 0.7717 (tmm)
REVERT: D  458 PHE cc_start: 0.7913 (p90) cc_final: 0.7430 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1145
  time to fit residues: 11.0602
Evaluate side-chains
  67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 142 ASN
** D 334 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 = 0.3997 r_free = 0.3997 target = 0.145797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132670 restraints weight = 11033.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.135340 restraints weight = 7322.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.137281 restraints weight = 5210.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.138540 restraints weight = 3893.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.139479 restraints weight = 3087.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4301  Z= 0.149
  Angle     :  0.685   6.608   5967  Z= 0.358
  Chirality :  0.040   0.183    683
  Planarity :  0.005   0.056    630
  Dihedral  : 25.749 178.515   1084
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.69 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.90 (0.40), residues: 414
  helix: -0.08 (0.34), residues: 219
  sheet: -3.49 (0.85), residues: 26
  loop : -2.47 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 216 
 TYR   0.022   0.002   TYR D  78 
 PHE   0.006   0.001   PHE D  39 
 TRP   0.015   0.003   TRP D 104 
 HIS   0.005   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4301)
  covalent geometry    : angle       0.68500 ( 5967)
  hydrogen bonds       : bond        0.03828 (  174)
  hydrogen bonds       : angle       4.49295 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   71 PHE cc_start: 0.6885 (m-80) cc_final: 0.6501 (m-80)
REVERT: D  112 ASP cc_start: 0.6933 (m-30) cc_final: 0.6550 (t70)
REVERT: D  168 GLN cc_start: 0.7539 (tt0) cc_final: 0.6785 (tt0)
REVERT: D  189 MET cc_start: 0.8280 (tpt) cc_final: 0.8015 (tpt)
REVERT: D  196 MET cc_start: 0.8048 (mtt) cc_final: 0.7751 (mmt)
REVERT: D  210 GLU cc_start: 0.8104 (pp20) cc_final: 0.7897 (pm20)
REVERT: D  211 ASN cc_start: 0.9104 (p0) cc_final: 0.8634 (p0)
REVERT: D  255 ASP cc_start: 0.9047 (m-30) cc_final: 0.8839 (m-30)
REVERT: D  443 GLU cc_start: 0.8588 (tt0) cc_final: 0.7622 (tt0)
REVERT: D  446 ARG cc_start: 0.8874 (mtm180) cc_final: 0.8592 (mtm180)
REVERT: D  448 MET cc_start: 0.8540 (tmm) cc_final: 0.7746 (tmm)
REVERT: D  458 PHE cc_start: 0.7921 (p90) cc_final: 0.7095 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1004
  time to fit residues: 9.2972
Evaluate side-chains
  71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0970
   chunk 40 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
D 142 ASN
** D 334 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 = 0.4028 r_free = 0.4028 target = 0.148032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.133970 restraints weight = 12001.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.136751 restraints weight = 8011.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.138775 restraints weight = 5763.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.140187 restraints weight = 4368.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.141201 restraints weight = 3476.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4301  Z= 0.135
  Angle     :  0.667   6.704   5967  Z= 0.343
  Chirality :  0.039   0.180    683
  Planarity :  0.005   0.055    630
  Dihedral  : 25.673 179.928   1084
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  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: -1.60 (0.40), residues: 414
  helix:  0.22 (0.34), residues: 218
  sheet: -3.12 (0.96), residues: 26
  loop : -2.45 (0.45), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 459 
 TYR   0.025   0.002   TYR D  78 
 PHE   0.008   0.001   PHE D 230 
 TRP   0.013   0.003   TRP D 139 
 HIS   0.004   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4301)
  covalent geometry    : angle       0.66671 ( 5967)
  hydrogen bonds       : bond        0.03641 (  174)
  hydrogen bonds       : angle       4.36114 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   71 PHE cc_start: 0.6843 (m-80) cc_final: 0.6566 (m-80)
REVERT: D  112 ASP cc_start: 0.6895 (m-30) cc_final: 0.6416 (t70)
REVERT: D  147 THR cc_start: 0.8510 (p) cc_final: 0.8150 (t)
REVERT: D  156 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8248 (ttt-90)
REVERT: D  189 MET cc_start: 0.8464 (tpt) cc_final: 0.8246 (tpt)
REVERT: D  196 MET cc_start: 0.8224 (mtt) cc_final: 0.7919 (mmt)
REVERT: D  210 GLU cc_start: 0.8393 (pp20) cc_final: 0.8138 (pm20)
REVERT: D  211 ASN cc_start: 0.9142 (p0) cc_final: 0.8729 (p0)
REVERT: D  222 MET cc_start: 0.7867 (mmp) cc_final: 0.7650 (mmt)
REVERT: D  235 GLN cc_start: 0.9194 (mt0) cc_final: 0.8902 (mt0)
REVERT: D  255 ASP cc_start: 0.9119 (m-30) cc_final: 0.8865 (m-30)
REVERT: D  292 GLU cc_start: 0.8272 (pt0) cc_final: 0.7914 (pt0)
REVERT: D  443 GLU cc_start: 0.8486 (tt0) cc_final: 0.7691 (tt0)
REVERT: D  446 ARG cc_start: 0.8999 (mtm180) cc_final: 0.8669 (mtm180)
REVERT: D  448 MET cc_start: 0.8484 (tmm) cc_final: 0.7700 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0977
  time to fit residues: 9.0720
Evaluate side-chains
  73 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 142 ASN
** D 334 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 = 0.4008 r_free = 0.4008 target = 0.146757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.131753 restraints weight = 12161.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.134757 restraints weight = 7969.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.136889 restraints weight = 5652.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138347 restraints weight = 4255.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.139496 restraints weight = 3390.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4301  Z= 0.137
  Angle     :  0.660   6.785   5967  Z= 0.341
  Chirality :  0.039   0.182    683
  Planarity :  0.005   0.059    630
  Dihedral  : 25.600 179.331   1084
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.27 %
    Favored  : 97.44 %
  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: -1.59 (0.40), residues: 414
  helix:  0.15 (0.34), residues: 225
  sheet: -2.89 (1.00), residues: 26
  loop : -2.47 (0.46), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 459 
 TYR   0.022   0.002   TYR D  78 
 PHE   0.010   0.001   PHE D 230 
 TRP   0.018   0.003   TRP D 139 
 HIS   0.004   0.001   HIS D 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4301)
  covalent geometry    : angle       0.66045 ( 5967)
  hydrogen bonds       : bond        0.03686 (  174)
  hydrogen bonds       : angle       4.30625 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  112 ASP cc_start: 0.6878 (m-30) cc_final: 0.6519 (t70)
REVERT: D  189 MET cc_start: 0.8439 (tpt) cc_final: 0.8222 (tpt)
REVERT: D  196 MET cc_start: 0.8222 (mtt) cc_final: 0.7920 (mmt)
REVERT: D  210 GLU cc_start: 0.8337 (pp20) cc_final: 0.8083 (pm20)
REVERT: D  211 ASN cc_start: 0.9143 (p0) cc_final: 0.8739 (p0)
REVERT: D  222 MET cc_start: 0.7821 (mmp) cc_final: 0.7587 (mmt)
REVERT: D  255 ASP cc_start: 0.9127 (m-30) cc_final: 0.8864 (m-30)
REVERT: D  292 GLU cc_start: 0.8353 (pt0) cc_final: 0.8018 (pt0)
REVERT: D  443 GLU cc_start: 0.8509 (tt0) cc_final: 0.7690 (tt0)
REVERT: D  446 ARG cc_start: 0.8975 (mtm180) cc_final: 0.8660 (mtm180)
REVERT: D  448 MET cc_start: 0.8396 (tmm) cc_final: 0.7698 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1035
  time to fit residues: 10.0896
Evaluate side-chains
  74 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 142 ASN
** D 334 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 = 0.4008 r_free = 0.4008 target = 0.146766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.132206 restraints weight = 12339.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.134990 restraints weight = 8285.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.136875 restraints weight = 5974.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.138337 restraints weight = 4616.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.139413 restraints weight = 3716.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4301  Z= 0.145
  Angle     :  0.660   6.616   5967  Z= 0.339
  Chirality :  0.040   0.181    683
  Planarity :  0.006   0.063    630
  Dihedral  : 25.575 178.832   1084
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  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: -1.52 (0.41), residues: 414
  helix:  0.22 (0.34), residues: 226
  sheet: -2.70 (1.05), residues: 26
  loop : -2.50 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 416 
 TYR   0.023   0.002   TYR D  78 
 PHE   0.009   0.001   PHE D 230 
 TRP   0.018   0.003   TRP D 139 
 HIS   0.003   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4301)
  covalent geometry    : angle       0.66012 ( 5967)
  hydrogen bonds       : bond        0.03674 (  174)
  hydrogen bonds       : angle       4.28490 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  112 ASP cc_start: 0.6898 (m-30) cc_final: 0.6520 (t70)
REVERT: D  136 MET cc_start: 0.7861 (ttm) cc_final: 0.7478 (mmm)
REVERT: D  189 MET cc_start: 0.8474 (tpt) cc_final: 0.8170 (tpt)
REVERT: D  196 MET cc_start: 0.8226 (mtt) cc_final: 0.7934 (mmt)
REVERT: D  210 GLU cc_start: 0.8389 (pp20) cc_final: 0.8145 (pm20)
REVERT: D  211 ASN cc_start: 0.9181 (p0) cc_final: 0.8797 (p0)
REVERT: D  222 MET cc_start: 0.7817 (mmp) cc_final: 0.7610 (mmt)
REVERT: D  255 ASP cc_start: 0.9153 (m-30) cc_final: 0.8872 (m-30)
REVERT: D  292 GLU cc_start: 0.8284 (pt0) cc_final: 0.7951 (pt0)
REVERT: D  443 GLU cc_start: 0.8549 (tt0) cc_final: 0.7698 (tt0)
REVERT: D  446 ARG cc_start: 0.9011 (mtm180) cc_final: 0.8690 (mtm180)
REVERT: D  448 MET cc_start: 0.8356 (tmm) cc_final: 0.7605 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1123
  time to fit residues: 10.8587
Evaluate side-chains
  75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0010
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.2980
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 142 ASN
** D 334 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 = 0.4037 r_free = 0.4037 target = 0.148652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.133937 restraints weight = 12243.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.136899 restraints weight = 8171.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.138998 restraints weight = 5846.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.140482 restraints weight = 4426.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.141638 restraints weight = 3520.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4301  Z= 0.124
  Angle     :  0.637   6.677   5967  Z= 0.325
  Chirality :  0.039   0.178    683
  Planarity :  0.005   0.058    630
  Dihedral  : 25.559 179.483   1084
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.57 %
    Favored  : 99.15 %
  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 (0.41), residues: 414
  helix:  0.43 (0.34), residues: 224
  sheet: -2.64 (1.08), residues: 26
  loop : -2.46 (0.45), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 416 
 TYR   0.022   0.002   TYR D  78 
 PHE   0.009   0.001   PHE D 230 
 TRP   0.022   0.003   TRP D 139 
 HIS   0.004   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4301)
  covalent geometry    : angle       0.63732 ( 5967)
  hydrogen bonds       : bond        0.03386 (  174)
  hydrogen bonds       : angle       4.17142 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  112 ASP cc_start: 0.6243 (m-30) cc_final: 0.5868 (t0)
REVERT: D  136 MET cc_start: 0.7848 (ttm) cc_final: 0.7472 (mmm)
REVERT: D  147 THR cc_start: 0.8428 (p) cc_final: 0.8070 (t)
REVERT: D  189 MET cc_start: 0.8521 (tpt) cc_final: 0.8195 (tpt)
REVERT: D  196 MET cc_start: 0.8262 (mtt) cc_final: 0.7958 (mmt)
REVERT: D  210 GLU cc_start: 0.8406 (pp20) cc_final: 0.8170 (pm20)
REVERT: D  211 ASN cc_start: 0.9185 (p0) cc_final: 0.8831 (p0)
REVERT: D  222 MET cc_start: 0.7796 (mmp) cc_final: 0.7467 (mmt)
REVERT: D  235 GLN cc_start: 0.9172 (mt0) cc_final: 0.8956 (mt0)
REVERT: D  255 ASP cc_start: 0.9186 (m-30) cc_final: 0.8878 (m-30)
REVERT: D  448 MET cc_start: 0.8327 (tmm) cc_final: 0.7533 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0940
  time to fit residues: 9.1607
Evaluate side-chains
  72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 142 ASN
** D 334 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 = 0.4012 r_free = 0.4012 target = 0.146594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.131801 restraints weight = 11868.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.134646 restraints weight = 7993.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.136695 restraints weight = 5775.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138064 restraints weight = 4409.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.139181 restraints weight = 3549.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.5391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4301  Z= 0.146
  Angle     :  0.663   6.826   5967  Z= 0.338
  Chirality :  0.040   0.181    683
  Planarity :  0.005   0.059    630
  Dihedral  : 25.522 178.486   1084
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  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: -1.38 (0.41), residues: 414
  helix:  0.37 (0.34), residues: 223
  sheet: -2.77 (1.08), residues: 26
  loop : -2.42 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  55 
 TYR   0.020   0.002   TYR D  97 
 PHE   0.012   0.001   PHE D 230 
 TRP   0.022   0.003   TRP D 139 
 HIS   0.012   0.002   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4301)
  covalent geometry    : angle       0.66273 ( 5967)
  hydrogen bonds       : bond        0.03525 (  174)
  hydrogen bonds       : angle       4.19158 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   90 LYS cc_start: 0.7943 (tptt) cc_final: 0.7722 (tptt)
REVERT: D  112 ASP cc_start: 0.6634 (m-30) cc_final: 0.6356 (m-30)
REVERT: D  189 MET cc_start: 0.8501 (tpt) cc_final: 0.8255 (tpt)
REVERT: D  196 MET cc_start: 0.8258 (mtt) cc_final: 0.7947 (mmt)
REVERT: D  210 GLU cc_start: 0.8374 (pp20) cc_final: 0.8059 (pm20)
REVERT: D  211 ASN cc_start: 0.9129 (p0) cc_final: 0.8691 (p0)
REVERT: D  222 MET cc_start: 0.7782 (mmp) cc_final: 0.7459 (mmt)
REVERT: D  235 GLN cc_start: 0.9118 (mt0) cc_final: 0.8830 (mt0)
REVERT: D  255 ASP cc_start: 0.9156 (m-30) cc_final: 0.8826 (m-30)
REVERT: D  292 GLU cc_start: 0.8265 (pt0) cc_final: 0.7984 (pt0)
REVERT: D  441 ARG cc_start: 0.9018 (mmp80) cc_final: 0.8698 (mmm160)
REVERT: D  443 GLU cc_start: 0.8310 (tt0) cc_final: 0.7536 (tt0)
REVERT: D  446 ARG cc_start: 0.8950 (mtm180) cc_final: 0.8704 (mtm180)
REVERT: D  448 MET cc_start: 0.8469 (tmm) cc_final: 0.7820 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0894
  time to fit residues: 8.5657
Evaluate side-chains
  72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0020
   chunk 23 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 142 ASN
** D 334 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 = 0.4035 r_free = 0.4035 target = 0.148475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.133691 restraints weight = 11459.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.136580 restraints weight = 7687.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.138539 restraints weight = 5520.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.140092 restraints weight = 4235.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.141178 restraints weight = 3396.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6756
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4301  Z= 0.127
  Angle     :  0.650   6.640   5967  Z= 0.330
  Chirality :  0.039   0.178    683
  Planarity :  0.005   0.058    630
  Dihedral  : 25.486 179.218   1084
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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: -1.26 (0.41), residues: 414
  helix:  0.48 (0.34), residues: 223
  sheet: -2.81 (1.09), residues: 26
  loop : -2.38 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 416 
 TYR   0.020   0.002   TYR D  78 
 PHE   0.010   0.001   PHE D 230 
 TRP   0.027   0.003   TRP D 139 
 HIS   0.010   0.002   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4301)
  covalent geometry    : angle       0.65029 ( 5967)
  hydrogen bonds       : bond        0.03297 (  174)
  hydrogen bonds       : angle       4.14973 (  476)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  112 ASP cc_start: 0.6476 (m-30) cc_final: 0.6121 (t0)
REVERT: D  136 MET cc_start: 0.7753 (ttm) cc_final: 0.7430 (mmm)
REVERT: D  189 MET cc_start: 0.8485 (tpt) cc_final: 0.8221 (tpt)
REVERT: D  196 MET cc_start: 0.8179 (mtt) cc_final: 0.7827 (mmt)
REVERT: D  210 GLU cc_start: 0.8248 (pp20) cc_final: 0.7965 (pm20)
REVERT: D  211 ASN cc_start: 0.9111 (p0) cc_final: 0.8685 (p0)
REVERT: D  222 MET cc_start: 0.7743 (mmp) cc_final: 0.7421 (mmt)
REVERT: D  235 GLN cc_start: 0.9133 (mt0) cc_final: 0.8611 (mt0)
REVERT: D  238 MET cc_start: 0.8092 (mtm) cc_final: 0.7830 (mtp)
REVERT: D  255 ASP cc_start: 0.9187 (m-30) cc_final: 0.8934 (m-30)
REVERT: D  292 GLU cc_start: 0.8236 (pt0) cc_final: 0.7948 (pt0)
REVERT: D  448 MET cc_start: 0.8491 (tmm) cc_final: 0.7871 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0891
  time to fit residues: 8.8784
Evaluate side-chains
  71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 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 = 0.4014 r_free = 0.4014 target = 0.146633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.130965 restraints weight = 12127.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.133960 restraints weight = 8123.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.135958 restraints weight = 5833.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.137516 restraints weight = 4502.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.138470 restraints weight = 3612.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.5729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4301  Z= 0.143
  Angle     :  0.665   6.871   5967  Z= 0.339
  Chirality :  0.040   0.181    683
  Planarity :  0.005   0.059    630
  Dihedral  : 25.481 177.648   1084
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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: -1.30 (0.41), residues: 414
  helix:  0.37 (0.34), residues: 224
  sheet: -2.67 (1.12), residues: 26
  loop : -2.29 (0.47), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 416 
 TYR   0.022   0.002   TYR D  97 
 PHE   0.012   0.002   PHE D 230 
 TRP   0.023   0.003   TRP D 139 
 HIS   0.012   0.002   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4301)
  covalent geometry    : angle       0.66525 ( 5967)
  hydrogen bonds       : bond        0.03537 (  174)
  hydrogen bonds       : angle       4.17563 (  476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 926.19 seconds
wall clock time: 16 minutes 41.65 seconds (1001.65 seconds total)