Starting phenix.real_space_refine
on Tue Aug  4 20:53:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v48_64770/08_2026/9v48_64770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v48_64770/08_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_64770/08_2026/9v48_64770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v48_64770/08_2026/9v48_64770.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v48_64770/08_2026/9v48_64770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v48_64770/08_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-2.2rc3-6140/lib/python3.11/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: 1.25, per 1000 atoms: 0.30
  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: 0.43
  Conformation dependent library (CDL) restraints added in 135.1 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: 0.50
  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: 0.61

  Time building geometry restraints manager: 0.55 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=" O3'   A F   1 "
       pdb=" P     G F   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.575  0.032 1.20e-02 6.94e+03 6.96e+00
  bond pdb=" O3'   G E 240 "
       pdb=" P     C E 241 "
    ideal  model  delta    sigma   weight residual
    1.607  1.576  0.031 1.20e-02 6.94e+03 6.71e+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=" 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: 5320
        1.35 -     2.71: 519
        2.71 -     4.06: 87
        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=" N   PHE D 458 "
        pdb=" CA  PHE D 458 "
        pdb=" CB  PHE D 458 "
      ideal   model   delta    sigma   weight residual
     111.66  118.42   -6.76 1.67e+00 3.59e-01 1.64e+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: 514
       0.055 -    0.111: 122
       0.111 -    0.166: 38
       0.166 -    0.222: 7
       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:             4.310
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.530
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
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= 0.347
  Angle     :  0.939   6.764   5967  Z= 0.633
  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/Z
  covalent geometry    : bond        0.00553 /  0.35 ( 4301)
  covalent geometry    : angle       0.93912 /  0.63 ( 5967)
  hydrogen bonds       : bond        0.16897 / 11.54 (  174)
  hydrogen bonds       : angle       7.04767 /  5.12 (  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  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   78 TYR cc_start: 0.6786 (m-80) cc_final: 0.6047 (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: 0.8651 (mtm)
REVERT: D  156 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8391 (mmm160)
REVERT: D  168 GLN cc_start: 0.7476 (tt0) cc_final: 0.7074 (tt0)
REVERT: D  208 ARG cc_start: 0.1510 (OUTLIER) cc_final: 0.0541 (ttt180)
REVERT: D  222 MET cc_start: 0.7848 (mmm) cc_final: 0.7618 (mmm)
REVERT: D  235 GLN cc_start: 0.9033 (mt0) cc_final: 0.8777 (mt0)
REVERT: D  331 MET cc_start: 0.5327 (ttp) cc_final: 0.4407 (ttm)
REVERT: D  446 ARG cc_start: 0.9080 (mtm110) cc_final: 0.8859 (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: 0.7282 (tmm)
REVERT: D  458 PHE cc_start: 0.8024 (p90) cc_final: 0.7271 (p90)
  outliers start: 16
  outliers final: 6
  residues processed: 97
  average time/residue: 0.1364
  time to fit residues: 15.1030
Evaluate side-chains
  78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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...
D  82 HIS
D 135 HIS
** 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 = 0.3962 r_free = 0.3962 target = 0.143387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.131251 restraints weight = 11067.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.133890 restraints weight = 7224.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.135749 restraints weight = 5097.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.137041 restraints weight = 3791.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.137904 restraints weight = 2963.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4301  Z= 0.198
  Angle     :  0.823   6.610   5967  Z= 0.454
  Chirality :  0.050   0.342    683
  Planarity :  0.006   0.053    630
  Dihedral  : 26.206 175.332   1084
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.68 %
    Favored  : 94.03 %
  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: -3.64 (0.36), residues: 414
  helix: -1.50 (0.30), residues: 218
  sheet: -4.28 (0.69), residues: 28
  loop : -3.26 (0.44), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  74 
 TYR   0.022   0.003   TYR D  78 
 PHE   0.017   0.002   PHE D  39 
 TRP   0.018   0.004   TRP D 139 
 HIS   0.008   0.003   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.20 ( 4301)
  covalent geometry    : angle       0.82343 /  0.45 ( 5967)
  hydrogen bonds       : bond        0.05043 /  3.54 (  174)
  hydrogen bonds       : angle       5.51020 /  4.15 (  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
  83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.141 
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   78 TYR cc_start: 0.7117 (m-80) cc_final: 0.6896 (m-80)
REVERT: D  136 MET cc_start: 0.7926 (mtp) cc_final: 0.7483 (mtp)
REVERT: D  168 GLN cc_start: 0.7232 (tt0) cc_final: 0.6609 (tt0)
REVERT: D  188 THR cc_start: 0.9721 (p) cc_final: 0.9421 (t)
REVERT: D  216 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8306 (mtt-85)
REVERT: D  240 ASP cc_start: 0.7777 (m-30) cc_final: 0.7288 (m-30)
REVERT: D  277 PRO cc_start: 0.7446 (Cg_endo) cc_final: 0.6989 (Cg_exo)
REVERT: D  447 MET cc_start: 0.7713 (mtp) cc_final: 0.7177 (tpt)
REVERT: D  448 MET cc_start: 0.8711 (tmm) cc_final: 0.8125 (tmm)
REVERT: D  458 PHE cc_start: 0.7867 (p90) cc_final: 0.7107 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1198
  time to fit residues: 11.5614
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  : 0.147 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.148356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.136059 restraints weight = 10938.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.138627 restraints weight = 7245.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.140550 restraints weight = 5137.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.141895 restraints weight = 3807.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.142826 restraints weight = 2955.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.3193

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= 0.161
  Angle     :  0.720   9.639   5967  Z= 0.397
  Chirality :  0.045   0.335    683
  Planarity :  0.006   0.053    630
  Dihedral  : 26.022 176.489   1084
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  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: -2.63 (0.38), residues: 414
  helix: -0.61 (0.33), residues: 220
  sheet: -3.81 (1.00), residues: 18
  loop : -3.04 (0.41), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 195 
 TYR   0.015   0.002   TYR D  97 
 PHE   0.009   0.001   PHE D 429 
 TRP   0.015   0.003   TRP D 330 
 HIS   0.005   0.001   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.16 ( 4301)
  covalent geometry    : angle       0.71959 /  0.40 ( 5967)
  hydrogen bonds       : bond        0.04287 /  3.00 (  174)
  hydrogen bonds       : angle       4.94704 /  3.77 (  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: 0
    poor density    : 84
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  112 ASP cc_start: 0.7003 (m-30) cc_final: 0.6336 (t70)
REVERT: D  113 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8497 (mtmt)
REVERT: D  137 MET cc_start: 0.8794 (mtm) cc_final: 0.8403 (mtm)
REVERT: D  147 THR cc_start: 0.8406 (p) cc_final: 0.7990 (t)
REVERT: D  168 GLN cc_start: 0.7629 (tt0) cc_final: 0.7265 (tt0)
REVERT: D  255 ASP cc_start: 0.9101 (m-30) cc_final: 0.8865 (m-30)
REVERT: D  292 GLU cc_start: 0.8260 (pt0) cc_final: 0.7872 (pt0)
REVERT: D  443 GLU cc_start: 0.8570 (tt0) cc_final: 0.8162 (tt0)
REVERT: D  447 MET cc_start: 0.7732 (mtp) cc_final: 0.6985 (tpt)
REVERT: D  448 MET cc_start: 0.8681 (tmm) cc_final: 0.7722 (tmm)
REVERT: D  458 PHE cc_start: 0.7965 (p90) cc_final: 0.7526 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1031
  time to fit residues: 10.2941
Evaluate side-chains
  68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3977 r_free = 0.3977 target = 0.144660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.132960 restraints weight = 10607.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.135514 restraints weight = 6990.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.137201 restraints weight = 4905.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.138496 restraints weight = 3658.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.139415 restraints weight = 2820.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4301  Z= 0.168
  Angle     :  0.726   7.162   5967  Z= 0.395
  Chirality :  0.045   0.343    683
  Planarity :  0.006   0.057    630
  Dihedral  : 25.902 177.912   1084
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  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: -2.42 (0.38), residues: 414
  helix: -0.42 (0.33), residues: 220
  sheet: -3.59 (0.85), residues: 26
  loop : -2.88 (0.42), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 216 
 TYR   0.019   0.003   TYR D 219 
 PHE   0.026   0.002   PHE D 464 
 TRP   0.012   0.003   TRP D 330 
 HIS   0.010   0.002   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.17 ( 4301)
  covalent geometry    : angle       0.72561 /  0.39 ( 5967)
  hydrogen bonds       : bond        0.04378 /  3.08 (  174)
  hydrogen bonds       : angle       4.79502 /  3.68 (  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  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  137 MET cc_start: 0.8483 (mtm) cc_final: 0.8152 (mtm)
REVERT: D  147 THR cc_start: 0.8417 (p) cc_final: 0.7973 (t)
REVERT: D  168 GLN cc_start: 0.7508 (tt0) cc_final: 0.7213 (tt0)
REVERT: D  189 MET cc_start: 0.8144 (tpt) cc_final: 0.7861 (tpt)
REVERT: D  196 MET cc_start: 0.7389 (mmt) cc_final: 0.7143 (mmt)
REVERT: D  211 ASN cc_start: 0.8996 (p0) cc_final: 0.8643 (p0)
REVERT: D  292 GLU cc_start: 0.8303 (pt0) cc_final: 0.7945 (pt0)
REVERT: D  443 GLU cc_start: 0.8399 (tt0) cc_final: 0.8068 (tt0)
REVERT: D  446 ARG cc_start: 0.8836 (mtm180) cc_final: 0.8513 (mtt180)
REVERT: D  447 MET cc_start: 0.7575 (mtp) cc_final: 0.6837 (tpt)
REVERT: D  448 MET cc_start: 0.8611 (tmm) cc_final: 0.7646 (tmm)
REVERT: D  458 PHE cc_start: 0.7904 (p90) cc_final: 0.7470 (p90)
  outliers start: 1
  outliers final: 1
  residues processed: 78
  average time/residue: 0.0897
  time to fit residues: 8.4357
Evaluate side-chains
  72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 16 optimal weight:    0.0060
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4041 r_free = 0.4041 target = 0.148728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.135957 restraints weight = 10730.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.138684 restraints weight = 7095.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.140721 restraints weight = 5011.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.141833 restraints weight = 3674.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.142905 restraints weight = 2943.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.4042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4301  Z= 0.139
  Angle     :  0.660   6.850   5967  Z= 0.357
  Chirality :  0.043   0.339    683
  Planarity :  0.005   0.053    630
  Dihedral  : 25.809 179.290   1084
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  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: -2.00 (0.38), residues: 414
  helix: -0.02 (0.34), residues: 219
  sheet: -3.35 (0.88), residues: 26
  loop : -2.78 (0.41), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 416 
 TYR   0.016   0.002   TYR D 313 
 PHE   0.012   0.001   PHE D 464 
 TRP   0.014   0.003   TRP D 139 
 HIS   0.004   0.001   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.14 ( 4301)
  covalent geometry    : angle       0.66009 /  0.36 ( 5967)
  hydrogen bonds       : bond        0.03971 /  2.83 (  174)
  hydrogen bonds       : angle       4.54271 /  3.50 (  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
  81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   71 PHE cc_start: 0.6860 (m-80) cc_final: 0.6428 (m-80)
REVERT: D  112 ASP cc_start: 0.6924 (m-30) cc_final: 0.6316 (t0)
REVERT: D  136 MET cc_start: 0.7396 (ttp) cc_final: 0.7081 (ttm)
REVERT: D  168 GLN cc_start: 0.7538 (tt0) cc_final: 0.6674 (tt0)
REVERT: D  189 MET cc_start: 0.8323 (tpt) cc_final: 0.8120 (tpt)
REVERT: D  210 GLU cc_start: 0.8003 (pp20) cc_final: 0.7743 (pm20)
REVERT: D  211 ASN cc_start: 0.9065 (p0) cc_final: 0.8577 (p0)
REVERT: D  292 GLU cc_start: 0.8304 (pt0) cc_final: 0.7910 (pt0)
REVERT: D  443 GLU cc_start: 0.8537 (tt0) cc_final: 0.8202 (tt0)
REVERT: D  446 ARG cc_start: 0.8923 (mtm180) cc_final: 0.8652 (mtm180)
REVERT: D  448 MET cc_start: 0.8624 (tmm) cc_final: 0.7745 (tmm)
REVERT: D  458 PHE cc_start: 0.7957 (p90) cc_final: 0.7178 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0953
  time to fit residues: 9.2952
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  : 0.141 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4016 r_free = 0.4016 target = 0.146477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.132810 restraints weight = 11592.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.135636 restraints weight = 7593.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.137732 restraints weight = 5338.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.139191 restraints weight = 3899.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.140256 restraints weight = 3015.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.4218

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= 0.157
  Angle     :  0.671   6.796   5967  Z= 0.366
  Chirality :  0.044   0.345    683
  Planarity :  0.005   0.057    630
  Dihedral  : 25.722 179.826   1084
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.84 %
    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: -1.96 (0.39), residues: 414
  helix: -0.05 (0.34), residues: 219
  sheet: -3.25 (0.91), residues: 26
  loop : -2.68 (0.43), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 121 
 TYR   0.025   0.003   TYR D  78 
 PHE   0.006   0.001   PHE D 346 
 TRP   0.017   0.003   TRP D 330 
 HIS   0.015   0.003   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.16 ( 4301)
  covalent geometry    : angle       0.67099 /  0.37 ( 5967)
  hydrogen bonds       : bond        0.04066 /  2.89 (  174)
  hydrogen bonds       : angle       4.54443 /  3.51 (  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
  84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.136 
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: 0.7124 (m-30) cc_final: 0.6537 (t0)
REVERT: D  136 MET cc_start: 0.7470 (ttp) cc_final: 0.7200 (ttm)
REVERT: D  147 THR cc_start: 0.8464 (p) cc_final: 0.8024 (t)
REVERT: D  189 MET cc_start: 0.8363 (tpt) cc_final: 0.8097 (tpt)
REVERT: D  210 GLU cc_start: 0.8129 (pp20) cc_final: 0.7817 (pm20)
REVERT: D  211 ASN cc_start: 0.9078 (p0) cc_final: 0.8629 (p0)
REVERT: D  222 MET cc_start: 0.7811 (mmp) cc_final: 0.7548 (mmp)
REVERT: D  292 GLU cc_start: 0.8309 (pt0) cc_final: 0.7936 (pt0)
REVERT: D  443 GLU cc_start: 0.8540 (tt0) cc_final: 0.8040 (tt0)
REVERT: D  446 ARG cc_start: 0.8945 (mtm180) cc_final: 0.8667 (mtm180)
REVERT: D  448 MET cc_start: 0.8571 (tmm) cc_final: 0.7707 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0923
  time to fit residues: 9.2863
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  : 0.136 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0030
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 142 ASN
D 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.147824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133998 restraints weight = 12016.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.136763 restraints weight = 7961.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.138773 restraints weight = 5711.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.140337 restraints weight = 4303.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.141333 restraints weight = 3336.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4301  Z= 0.146
  Angle     :  0.675   7.136   5967  Z= 0.365
  Chirality :  0.045   0.343    683
  Planarity :  0.005   0.055    630
  Dihedral  : 25.668 179.291   1084
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  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: -1.91 (0.39), residues: 414
  helix: -0.08 (0.33), residues: 219
  sheet: -3.02 (0.97), residues: 26
  loop : -2.59 (0.44), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 459 
 TYR   0.024   0.003   TYR D  78 
 PHE   0.006   0.001   PHE D 230 
 TRP   0.019   0.003   TRP D 330 
 HIS   0.008   0.002   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.15 ( 4301)
  covalent geometry    : angle       0.67486 /  0.36 ( 5967)
  hydrogen bonds       : bond        0.03961 /  2.81 (  174)
  hydrogen bonds       : angle       4.51058 /  3.46 (  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
  84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.144 
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: 0.7068 (m-80) cc_final: 0.6477 (m-80)
REVERT: D  112 ASP cc_start: 0.7127 (m-30) cc_final: 0.6450 (t0)
REVERT: D  137 MET cc_start: 0.8708 (mtm) cc_final: 0.8333 (mtm)
REVERT: D  189 MET cc_start: 0.8390 (tpt) cc_final: 0.8147 (tpt)
REVERT: D  210 GLU cc_start: 0.8229 (pp20) cc_final: 0.7983 (pm20)
REVERT: D  211 ASN cc_start: 0.9094 (p0) cc_final: 0.8689 (p0)
REVERT: D  222 MET cc_start: 0.7825 (mmp) cc_final: 0.7559 (mmp)
REVERT: D  292 GLU cc_start: 0.8301 (pt0) cc_final: 0.7881 (pt0)
REVERT: D  374 MET cc_start: 0.6482 (mmt) cc_final: 0.6263 (mmm)
REVERT: D  441 ARG cc_start: 0.9050 (mmp80) cc_final: 0.8732 (mmp80)
REVERT: D  443 GLU cc_start: 0.8578 (tt0) cc_final: 0.7915 (tt0)
REVERT: D  446 ARG cc_start: 0.8935 (mtm180) cc_final: 0.8706 (mtm180)
REVERT: D  448 MET cc_start: 0.8540 (tmm) cc_final: 0.7654 (tmm)
REVERT: D  459 ARG cc_start: 0.6823 (mtm180) cc_final: 0.6332 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1011
  time to fit residues: 10.1919
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  : 0.130 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 HIS
D 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.144979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.131376 restraints weight = 12006.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.133856 restraints weight = 8171.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.135745 restraints weight = 5994.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.137225 restraints weight = 4624.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.138152 restraints weight = 3633.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.4639

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= 0.152
  Angle     :  0.686   9.897   5967  Z= 0.369
  Chirality :  0.044   0.344    683
  Planarity :  0.005   0.057    630
  Dihedral  : 25.577 178.653   1084
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.70 %
    Favored  : 98.01 %
  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: -1.80 (0.39), residues: 414
  helix: -0.01 (0.33), residues: 219
  sheet: -3.08 (0.98), residues: 26
  loop : -2.47 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 416 
 TYR   0.026   0.003   TYR D  78 
 PHE   0.009   0.002   PHE D 230 
 TRP   0.019   0.003   TRP D 139 
 HIS   0.012   0.003   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.15 ( 4301)
  covalent geometry    : angle       0.68644 /  0.37 ( 5967)
  hydrogen bonds       : bond        0.03991 /  2.83 (  174)
  hydrogen bonds       : angle       4.48085 /  3.44 (  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
  85 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.132 
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: 0.6999 (m-80) cc_final: 0.6478 (m-80)
REVERT: D  112 ASP cc_start: 0.7098 (m-30) cc_final: 0.6572 (t0)
REVERT: D  189 MET cc_start: 0.8328 (tpt) cc_final: 0.8002 (tpt)
REVERT: D  210 GLU cc_start: 0.8177 (pp20) cc_final: 0.7952 (pm20)
REVERT: D  211 ASN cc_start: 0.9024 (p0) cc_final: 0.8636 (p0)
REVERT: D  222 MET cc_start: 0.7716 (mmp) cc_final: 0.7509 (mmp)
REVERT: D  235 GLN cc_start: 0.9184 (mt0) cc_final: 0.8866 (mt0)
REVERT: D  292 GLU cc_start: 0.8318 (pt0) cc_final: 0.7978 (pt0)
REVERT: D  443 GLU cc_start: 0.8427 (tt0) cc_final: 0.7819 (tt0)
REVERT: D  448 MET cc_start: 0.8610 (tmm) cc_final: 0.7953 (tmm)
REVERT: D  459 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6549 (mtm-85)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1001
  time to fit residues: 10.0854
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  : 0.154 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 14 optimal weight:    0.0570
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 142 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.146542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.132581 restraints weight = 11703.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.135465 restraints weight = 7683.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.137382 restraints weight = 5376.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.138844 restraints weight = 4049.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.139853 restraints weight = 3173.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.4829

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= 0.145
  Angle     :  0.703   9.936   5967  Z= 0.372
  Chirality :  0.043   0.341    683
  Planarity :  0.008   0.158    630
  Dihedral  : 25.585 178.136   1084
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  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: -1.62 (0.40), residues: 414
  helix:  0.21 (0.34), residues: 218
  sheet: -2.99 (1.00), residues: 26
  loop : -2.51 (0.44), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 461 
 TYR   0.026   0.003   TYR D  78 
 PHE   0.009   0.001   PHE D 230 
 TRP   0.018   0.003   TRP D 330 
 HIS   0.008   0.002   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.15 ( 4301)
  covalent geometry    : angle       0.70317 /  0.37 ( 5967)
  hydrogen bonds       : bond        0.03948 /  2.77 (  174)
  hydrogen bonds       : angle       4.45706 /  3.42 (  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
  86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.142 
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: 0.7120 (m-80) cc_final: 0.6583 (m-80)
REVERT: D  189 MET cc_start: 0.8465 (tpt) cc_final: 0.8125 (tpt)
REVERT: D  210 GLU cc_start: 0.8216 (pp20) cc_final: 0.7979 (pm20)
REVERT: D  211 ASN cc_start: 0.9052 (p0) cc_final: 0.8725 (p0)
REVERT: D  222 MET cc_start: 0.7842 (mmp) cc_final: 0.7595 (mmp)
REVERT: D  235 GLN cc_start: 0.9167 (mt0) cc_final: 0.8859 (mt0)
REVERT: D  292 GLU cc_start: 0.8294 (pt0) cc_final: 0.7924 (pt0)
REVERT: D  441 ARG cc_start: 0.8599 (mmp80) cc_final: 0.8389 (mmp80)
REVERT: D  448 MET cc_start: 0.8532 (tmm) cc_final: 0.7849 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0837
  time to fit residues: 8.8298
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  : 0.130 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.6960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 HIS
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.146596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.132524 restraints weight = 11211.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.135380 restraints weight = 7348.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.137338 restraints weight = 5199.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.138827 restraints weight = 3934.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.139751 restraints weight = 3082.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4301  Z= 0.142
  Angle     :  0.683  11.912   5967  Z= 0.366
  Chirality :  0.043   0.342    683
  Planarity :  0.008   0.131    630
  Dihedral  : 25.554 177.926   1084
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  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: -1.66 (0.40), residues: 414
  helix:  0.16 (0.33), residues: 223
  sheet: -3.00 (1.02), residues: 26
  loop : -2.56 (0.45), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 461 
 TYR   0.026   0.003   TYR D  78 
 PHE   0.012   0.001   PHE D 230 
 TRP   0.019   0.003   TRP D 139 
 HIS   0.010   0.003   HIS D 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 ( 4301)
  covalent geometry    : angle       0.68301 /  0.37 ( 5967)
  hydrogen bonds       : bond        0.03988 /  2.81 (  174)
  hydrogen bonds       : angle       4.39830 /  3.37 (  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
  85 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.138 
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: 0.7309 (ttp) cc_final: 0.7064 (ttm)
REVERT: D  137 MET cc_start: 0.8739 (mtm) cc_final: 0.8284 (mtm)
REVERT: D  189 MET cc_start: 0.8431 (tpt) cc_final: 0.8118 (tpt)
REVERT: D  210 GLU cc_start: 0.8145 (pp20) cc_final: 0.7917 (pm20)
REVERT: D  211 ASN cc_start: 0.9012 (p0) cc_final: 0.8644 (p0)
REVERT: D  222 MET cc_start: 0.7770 (mmp) cc_final: 0.7560 (mmp)
REVERT: D  235 GLN cc_start: 0.9102 (mt0) cc_final: 0.8720 (mt0)
REVERT: D  448 MET cc_start: 0.8514 (tmm) cc_final: 0.7836 (tmm)
REVERT: D  459 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6910 (mtm180)
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 0.0789
  time to fit residues: 8.1370
Evaluate side-chains
  74 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0570
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 44 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 142 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.146937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.132657 restraints weight = 11751.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.135609 restraints weight = 7730.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.137520 restraints weight = 5465.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.139047 restraints weight = 4163.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.140156 restraints weight = 3290.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6699
moved from start:          0.5215

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     :  0.680  10.154   5967  Z= 0.367
  Chirality :  0.044   0.340    683
  Planarity :  0.007   0.116    630
  Dihedral  : 25.535 177.878   1084
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    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: -1.58 (0.40), residues: 414
  helix:  0.19 (0.34), residues: 224
  sheet: -2.86 (1.05), residues: 26
  loop : -2.51 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 461 
 TYR   0.026   0.002   TYR D  78 
 PHE   0.022   0.002   PHE D 258 
 TRP   0.020   0.003   TRP D 139 
 HIS   0.007   0.002   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 ( 4301)
  covalent geometry    : angle       0.68026 /  0.37 ( 5967)
  hydrogen bonds       : bond        0.03981 /  2.80 (  174)
  hydrogen bonds       : angle       4.37668 /  3.35 (  476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 919.53 seconds
wall clock time: 16 minutes 34.37 seconds (994.37 seconds total)