Starting phenix.real_space_refine
on Fri Aug 22 14:13:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b6z_15893/08_2025/8b6z_15893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b6z_15893/08_2025/8b6z_15893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2025/8b6z_15893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2025/8b6z_15893.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2025/8b6z_15893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2025/8b6z_15893.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      16      5.16       5
     C    2240      2.51       5
     N     624      2.21       5
     O     693      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3581
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3406
          Classifications: {'peptide': 442}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 175
          Classifications: {'RNA': 8}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY A  50 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A  50 " occ=0.00
  Time building chain proxies: 1.23, per 1000 atoms: 0.34
  Number of scatterers: 3581
  At special positions: 0
  Unit cell: (65.934, 93.906, 67.932, 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      16     16.00
     P       8     15.00
     O     693      8.00
     N     624      7.00
     C    2240      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: 0.34
  Conformation dependent library (CDL) restraints added in 179.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  806

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 5 sheets defined
      25.1% alpha, 33.3% beta
      1 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 32
    Processing helix  chain 'A' and resid 35 through 50
    Processing helix  chain 'A' and resid 57 through 66
    Processing helix  chain 'A' and resid 97 through 105
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.703A  pdb=" N   ILE A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 154 through 158
      removed outlier: 3.836A  pdb=" N   SER A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR A 158 " --> pdb=" O   MET A 155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 154 through 158'
    Processing helix  chain 'A' and resid 163 through 182
      removed outlier: 3.601A  pdb=" N   TYR A 177 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 227 through 234
      removed outlier: 3.715A  pdb=" N   ALA A 231 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81
      removed outlier: 6.557A  pdb=" N   ILE A   8 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   ILE A  90 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   ILE A  10 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   CYS A 111 " --> pdb=" O   HIS A   7 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ASN A   9 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   VAL A 113 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL A  11 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   ILE A 115 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ILE A  13 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   ALA A 117 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 191 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216
    Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.659A  pdb=" N   ASN A 311 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   VAL A 292 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY A 309 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   MET A 294 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
      removed outlier: 9.275A  pdb=" N   ASN A 307 " --> pdb=" O   MET A 294 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR A 261 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 249
    Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389
      removed outlier: 6.610A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL A 405 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU A 375 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   GLU A 403 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   ALA A 338 " --> pdb=" O   PRO A 406 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLN A 339 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN A 343 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE A 438 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   ILE A 345 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   GLY A 436 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   THR A 432 " --> pdb=" O   ASP A 428 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ASP A 428 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL A 360 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    366 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      2 hydrogen bonds
      4 hydrogen bond angles
      0 basepair planarities
      1 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 0.58

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1126
        1.34 -     1.46: 522
        1.46 -     1.57: 1984
        1.57 -     1.69: 15
        1.69 -     1.81: 26
  Bond restraints: 3673
  Sorted by residual:
  bond pdb=" C   ILE A 235 "
       pdb=" N   LEU A 236 "
    ideal  model  delta    sigma   weight residual
    1.327  1.339 -0.012 1.39e-02 5.18e+03 7.88e-01
  bond pdb=" N   VAL A 152 "
       pdb=" CA  VAL A 152 "
    ideal  model  delta    sigma   weight residual
    1.465  1.476 -0.011 1.38e-02 5.25e+03 5.94e-01
  bond pdb=" CA  GLY A 351 "
       pdb=" C   GLY A 351 "
    ideal  model  delta    sigma   weight residual
    1.514  1.505  0.010 1.41e-02 5.03e+03 4.55e-01
  bond pdb=" CA  HIS A 364 "
       pdb=" CB  HIS A 364 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.69e-02 3.50e+03 4.23e-01
  bond pdb=" C   LYS A 165 "
       pdb=" O   LYS A 165 "
    ideal  model  delta    sigma   weight residual
    1.236  1.228  0.008 1.26e-02 6.30e+03 4.09e-01
  ... (remaining 3668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 4915
        1.47 -     2.93: 71
        2.93 -     4.40: 20
        4.40 -     5.86: 1
        5.86 -     7.33: 1
  Bond angle restraints: 5008
  Sorted by residual:
  angle pdb=" N   GLY A 182 "
        pdb=" CA  GLY A 182 "
        pdb=" C   GLY A 182 "
      ideal   model   delta    sigma   weight residual
     113.18  120.51   -7.33 2.37e+00 1.78e-01 9.56e+00
  angle pdb=" N   SER A 157 "
        pdb=" CA  SER A 157 "
        pdb=" C   SER A 157 "
      ideal   model   delta    sigma   weight residual
     112.88  115.26   -2.38 1.29e+00 6.01e-01 3.40e+00
  angle pdb=" CB  LYS A 172 "
        pdb=" CG  LYS A 172 "
        pdb=" CD  LYS A 172 "
      ideal   model   delta    sigma   weight residual
     111.30  115.15   -3.85 2.30e+00 1.89e-01 2.80e+00
  angle pdb=" CA  GLY A 182 "
        pdb=" C   GLY A 182 "
        pdb=" N   TYR A 183 "
      ideal   model   delta    sigma   weight residual
     116.69  119.99   -3.30 2.04e+00 2.40e-01 2.62e+00
  angle pdb=" N   ASN A 200 "
        pdb=" CA  ASN A 200 "
        pdb=" CB  ASN A 200 "
      ideal   model   delta    sigma   weight residual
     113.15  110.58    2.57 1.63e+00 3.76e-01 2.48e+00
  ... (remaining 5003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.56: 2078
       14.56 -    29.12: 95
       29.12 -    43.68: 36
       43.68 -    58.25: 16
       58.25 -    72.81: 11
  Dihedral angle restraints: 2236
    sinusoidal: 977
      harmonic: 1259
  Sorted by residual:
  dihedral pdb=" CA  VAL A 152 "
           pdb=" C   VAL A 152 "
           pdb=" N   ASN A 153 "
           pdb=" CA  ASN A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.01  -18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  PRO A 160 "
           pdb=" C   PRO A 160 "
           pdb=" N   ALA A 161 "
           pdb=" CA  ALA A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.08  -17.92     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  ILE A 178 "
           pdb=" C   ILE A 178 "
           pdb=" N   LYS A 179 "
           pdb=" CA  LYS A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.10   17.90     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 2233 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 309
       0.025 -    0.050: 155
       0.050 -    0.075: 37
       0.075 -    0.100: 31
       0.100 -    0.125: 37
  Chirality restraints: 569
  Sorted by residual:
  chirality pdb=" CA  ILE A 401 "
            pdb=" N   ILE A 401 "
            pdb=" C   ILE A 401 "
            pdb=" CB  ILE A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  VAL A 405 "
            pdb=" N   VAL A 405 "
            pdb=" C   VAL A 405 "
            pdb=" CB  VAL A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  VAL A 292 "
            pdb=" N   VAL A 292 "
            pdb=" C   VAL A 292 "
            pdb=" CB  VAL A 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 566 not shown)

  Planarity restraints: 613
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 419 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A 420 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 420 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 420 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 418 "   -0.021 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 419 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 419 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 419 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 358 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.41e-01
        pdb=" N   PRO A 359 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 359 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 359 "    0.013 5.00e-02 4.00e+02
  ... (remaining 610 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 924
        2.81 -     3.33: 3215
        3.33 -     3.85: 5926
        3.85 -     4.38: 6908
        4.38 -     4.90: 11870
  Nonbonded interactions: 28843
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  74 "
            pdb=" OG  SER A  76 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   ALA A 231 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   VAL A 277 "
            pdb=" OG  SER A 329 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" OH  TYR A  29 "
            pdb=" NE1 TRP A  58 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" OE2 GLU A  68 "
            pdb=" N   ARG A  96 "
     model   vdw
     2.413 3.120
  ... (remaining 28838 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=0.00 max=1.00 mean=0.70
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.090
  Find NCS groups from input model:        0.010
  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:8.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5668
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      :  0.002   0.023   3673  Z= 0.109
  Angle     :  0.507   7.329   5008  Z= 0.273
  Chirality :  0.044   0.125    569
  Planarity :  0.004   0.041    613
  Dihedral  : 12.065  72.808   1430
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.14 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.37), residues: 440
  helix: -0.07 (0.48), residues: 93
  sheet: -0.11 (0.60), residues: 83
  loop : -0.67 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.012   0.002   TYR A 167 
 PHE   0.005   0.001   PHE A 123 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3673)
  covalent geometry    : angle       0.50747 ( 5008)
  hydrogen bonds       : bond        0.21255 (  128)
  hydrogen bonds       : angle       8.23571 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 THR cc_start: 0.6986 (p) cc_final: 0.5496 (t)
REVERT: A  243 ASP cc_start: 0.5976 (m-30) cc_final: 0.5723 (t0)
REVERT: A  254 TYR cc_start: 0.4476 (m-80) cc_final: 0.4154 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.7227
  time to fit residues: 51.8488
Evaluate side-chains
  34 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:   30.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:   30.0000
   chunk 25 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:   50.0000
   chunk 37 optimal weight:   40.0000
   overall best weight:    9.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.104924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.087016 restraints weight = 14467.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.66
r_work: 0.3772 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3684 r_free = 0.3684    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1041 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1056 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3673  Z= 0.183
  Angle     :  0.707  12.555   5008  Z= 0.361
  Chirality :  0.048   0.150    569
  Planarity :  0.005   0.043    613
  Dihedral  : 11.749  73.571    590
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.67 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.39), residues: 440
  helix:  0.45 (0.52), residues: 96
  sheet:  0.16 (0.51), residues: 103
  loop : -0.58 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  37 
 TYR   0.016   0.002   TYR A 183 
 PHE   0.008   0.001   PHE A 310 
 TRP   0.006   0.002   TRP A  78 
 HIS   0.010   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3673)
  covalent geometry    : angle       0.70718 ( 5008)
  hydrogen bonds       : bond        0.05212 (  128)
  hydrogen bonds       : angle       6.01421 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: -0.2418 (mmt) cc_final: -0.2783 (mmm)
REVERT: A  243 ASP cc_start: 0.7229 (m-30) cc_final: 0.6992 (t0)
REVERT: A  294 MET cc_start: 0.5282 (tpt) cc_final: 0.5024 (tmm)
  outliers start: 7
  outliers final: 0
  residues processed: 36
  average time/residue: 0.7861
  time to fit residues: 29.0539
Evaluate side-chains
  22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:   50.0000
   chunk 13 optimal weight:   50.0000
   chunk 41 optimal weight:    9.9990
   chunk 2 optimal weight:   50.0000
   chunk 12 optimal weight:   10.0000
   chunk 28 optimal weight:   40.0000
   chunk 33 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 0 optimal weight:   50.0000
   chunk 9 optimal weight:   30.0000
   chunk 15 optimal weight:    7.9990
   overall best weight:    9.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.102897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.085448 restraints weight = 13935.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.54
r_work: 0.3763 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3674 r_free = 0.3674    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1056 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3673  Z= 0.181
  Angle     :  0.693  12.436   5008  Z= 0.354
  Chirality :  0.048   0.142    569
  Planarity :  0.005   0.050    613
  Dihedral  : 11.748  73.490    590
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.28 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.38), residues: 440
  helix:  0.53 (0.51), residues: 95
  sheet:  0.11 (0.53), residues: 99
  loop : -0.70 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  37 
 TYR   0.014   0.002   TYR A 183 
 PHE   0.028   0.003   PHE A 211 
 TRP   0.004   0.001   TRP A 214 
 HIS   0.007   0.002   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3673)
  covalent geometry    : angle       0.69347 ( 5008)
  hydrogen bonds       : bond        0.04640 (  128)
  hydrogen bonds       : angle       5.57658 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6020 (mtp) cc_final: 0.5279 (ttm)
REVERT: A  290 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5220 (tppt)
REVERT: A  294 MET cc_start: 0.5445 (tpt) cc_final: 0.5196 (tmm)
REVERT: A  310 PHE cc_start: 0.8644 (p90) cc_final: 0.7861 (p90)
REVERT: A  315 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7470 (m)
REVERT: A  404 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7302 (mmm)
  outliers start: 7
  outliers final: 0
  residues processed: 30
  average time/residue: 0.6304
  time to fit residues: 19.5876
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 43 optimal weight:   50.0000
   chunk 6 optimal weight:   50.0000
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:   50.0000
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 19 optimal weight:   40.0000
   chunk 0 optimal weight:   30.0000
   chunk 34 optimal weight:   30.0000
   overall best weight:   13.1994

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.101128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.082862 restraints weight = 13928.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.60
r_work: 0.3711 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3673  Z= 0.225
  Angle     :  0.713   9.928   5008  Z= 0.364
  Chirality :  0.048   0.141    569
  Planarity :  0.006   0.061    613
  Dihedral  : 11.732  73.438    590
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.28 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.38), residues: 440
  helix:  0.45 (0.49), residues: 95
  sheet: -0.08 (0.51), residues: 105
  loop : -0.83 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 266 
 TYR   0.013   0.002   TYR A 162 
 PHE   0.031   0.003   PHE A 211 
 TRP   0.007   0.001   TRP A 196 
 HIS   0.006   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 3673)
  covalent geometry    : angle       0.71254 ( 5008)
  hydrogen bonds       : bond        0.04720 (  128)
  hydrogen bonds       : angle       5.47979 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 MET cc_start: -0.2658 (mmt) cc_final: -0.2893 (mmm)
REVERT: A  276 MET cc_start: 0.6220 (mtp) cc_final: 0.5523 (ttm)
REVERT: A  290 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.4627 (tppt)
REVERT: A  294 MET cc_start: 0.5377 (tpt) cc_final: 0.5033 (tmm)
REVERT: A  310 PHE cc_start: 0.8654 (p90) cc_final: 0.7696 (p90)
  outliers start: 7
  outliers final: 1
  residues processed: 28
  average time/residue: 0.6438
  time to fit residues: 18.6913
Evaluate side-chains
  21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  290 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 2 optimal weight:   30.0000
   chunk 10 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 15 optimal weight:   50.0000
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:   50.0000
   chunk 42 optimal weight:    6.9990
   chunk 20 optimal weight:   30.0000
   chunk 43 optimal weight:   30.0000
   chunk 34 optimal weight:   30.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:   11.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.100777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.082234 restraints weight = 13759.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.60
r_work: 0.3705 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3673  Z= 0.197
  Angle     :  0.674   9.750   5008  Z= 0.347
  Chirality :  0.047   0.141    569
  Planarity :  0.006   0.061    613
  Dihedral  : 11.944  73.407    590
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.28 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.39), residues: 440
  helix:  0.50 (0.51), residues: 95
  sheet:  0.14 (0.50), residues: 112
  loop : -0.82 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  37 
 TYR   0.012   0.002   TYR A 162 
 PHE   0.036   0.003   PHE A 211 
 TRP   0.017   0.002   TRP A  58 
 HIS   0.006   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3673)
  covalent geometry    : angle       0.67390 ( 5008)
  hydrogen bonds       : bond        0.04362 (  128)
  hydrogen bonds       : angle       5.36074 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 VAL cc_start: 0.8956 (t) cc_final: 0.8394 (m)
REVERT: A  165 LYS cc_start: 0.8423 (mmpt) cc_final: 0.8009 (pmtt)
REVERT: A  276 MET cc_start: 0.6096 (mtp) cc_final: 0.5374 (ttm)
REVERT: A  290 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.4599 (tppt)
REVERT: A  294 MET cc_start: 0.5509 (tpt) cc_final: 0.5118 (tmm)
REVERT: A  310 PHE cc_start: 0.8687 (p90) cc_final: 0.7848 (p90)
  outliers start: 7
  outliers final: 1
  residues processed: 24
  average time/residue: 0.6525
  time to fit residues: 16.2318
Evaluate side-chains
  20 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  429 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 41 optimal weight:    0.5980
   chunk 29 optimal weight:   30.0000
   chunk 6 optimal weight:   40.0000
   chunk 28 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 1 optimal weight:   50.0000
   chunk 8 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:   50.0000
   overall best weight:    6.9190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.101045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.082550 restraints weight = 13713.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.63
r_work: 0.3713 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3673  Z= 0.141
  Angle     :  0.627   8.967   5008  Z= 0.320
  Chirality :  0.046   0.140    569
  Planarity :  0.006   0.058    613
  Dihedral  : 11.447  73.522    590
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.35 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.39), residues: 440
  helix:  0.71 (0.52), residues: 95
  sheet: -0.11 (0.58), residues: 87
  loop : -0.91 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  37 
 TYR   0.010   0.001   TYR A 357 
 PHE   0.012   0.002   PHE A 340 
 TRP   0.009   0.001   TRP A  58 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3673)
  covalent geometry    : angle       0.62749 ( 5008)
  hydrogen bonds       : bond        0.03721 (  128)
  hydrogen bonds       : angle       5.14109 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 VAL cc_start: 0.8955 (t) cc_final: 0.8373 (m)
REVERT: A  165 LYS cc_start: 0.8519 (mmpt) cc_final: 0.8077 (ptpp)
REVERT: A  276 MET cc_start: 0.6265 (mtp) cc_final: 0.5580 (ttm)
REVERT: A  290 LYS cc_start: 0.6030 (OUTLIER) cc_final: 0.4515 (tppt)
REVERT: A  294 MET cc_start: 0.5423 (tpt) cc_final: 0.5056 (tmm)
REVERT: A  310 PHE cc_start: 0.8688 (p90) cc_final: 0.7805 (p90)
REVERT: A  404 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6966 (mmm)
  outliers start: 6
  outliers final: 0
  residues processed: 26
  average time/residue: 0.6047
  time to fit residues: 16.3191
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 29 optimal weight:   40.0000
   chunk 20 optimal weight:   50.0000
   chunk 21 optimal weight:   40.0000
   chunk 7 optimal weight:   30.0000
   chunk 31 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   overall best weight:    8.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.101024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.082705 restraints weight = 14031.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 2.48
r_work: 0.3717 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3657 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.5862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3673  Z= 0.155
  Angle     :  0.629   8.952   5008  Z= 0.322
  Chirality :  0.046   0.137    569
  Planarity :  0.006   0.059    613
  Dihedral  : 11.212  73.495    590
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 17.43 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.40), residues: 440
  helix:  0.78 (0.53), residues: 95
  sheet:  0.19 (0.53), residues: 105
  loop : -0.95 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 430 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.011   0.002   PHE A 340 
 TRP   0.009   0.001   TRP A  58 
 HIS   0.005   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3673)
  covalent geometry    : angle       0.62934 ( 5008)
  hydrogen bonds       : bond        0.03867 (  128)
  hydrogen bonds       : angle       5.08022 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: -0.1687 (mmt) cc_final: -0.2032 (mpt)
REVERT: A  165 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8165 (pmtt)
REVERT: A  276 MET cc_start: 0.6112 (mtp) cc_final: 0.5402 (ttm)
REVERT: A  290 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.4393 (tppt)
REVERT: A  294 MET cc_start: 0.5529 (tpt) cc_final: 0.5149 (tmm)
REVERT: A  310 PHE cc_start: 0.8693 (p90) cc_final: 0.7876 (p90)
REVERT: A  404 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6876 (mmm)
  outliers start: 3
  outliers final: 1
  residues processed: 23
  average time/residue: 0.5364
  time to fit residues: 12.8675
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:   30.0000
   chunk 0 optimal weight:   60.0000
   chunk 39 optimal weight:   40.0000
   chunk 5 optimal weight:   20.0000
   chunk 37 optimal weight:   30.0000
   chunk 10 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.100914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.082700 restraints weight = 14123.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.54
r_work: 0.3718 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.6049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3673  Z= 0.132
  Angle     :  0.610   9.385   5008  Z= 0.309
  Chirality :  0.045   0.138    569
  Planarity :  0.005   0.058    613
  Dihedral  : 11.129  73.506    590
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 17.43 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.40), residues: 440
  helix:  0.92 (0.54), residues: 95
  sheet:  0.09 (0.52), residues: 108
  loop : -0.79 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  37 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.011   0.001   PHE A 340 
 TRP   0.007   0.001   TRP A  58 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3673)
  covalent geometry    : angle       0.61009 ( 5008)
  hydrogen bonds       : bond        0.03513 (  128)
  hydrogen bonds       : angle       5.03356 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 MET cc_start: -0.1689 (mmt) cc_final: -0.2158 (mpt)
REVERT: A  165 LYS cc_start: 0.8469 (mmpt) cc_final: 0.8142 (pmtt)
REVERT: A  276 MET cc_start: 0.6068 (mtp) cc_final: 0.5292 (ttm)
REVERT: A  290 LYS cc_start: 0.5946 (OUTLIER) cc_final: 0.4175 (tppt)
REVERT: A  294 MET cc_start: 0.5577 (tpt) cc_final: 0.5233 (tmm)
REVERT: A  310 PHE cc_start: 0.8706 (p90) cc_final: 0.7948 (p90)
REVERT: A  404 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6728 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 21
  average time/residue: 0.5121
  time to fit residues: 11.2987
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 2 optimal weight:   50.0000
   chunk 10 optimal weight:    9.9990
   chunk 8 optimal weight:   40.0000
   chunk 43 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 6 optimal weight:   50.0000
   chunk 23 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   overall best weight:    9.1190

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.100635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.082459 restraints weight = 13891.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.46
r_work: 0.3715 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3655 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.6356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3673  Z= 0.162
  Angle     :  0.639  11.495   5008  Z= 0.322
  Chirality :  0.045   0.136    569
  Planarity :  0.006   0.060    613
  Dihedral  : 11.255  73.585    590
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.89 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.39), residues: 440
  helix:  0.79 (0.53), residues: 97
  sheet:  0.02 (0.53), residues: 105
  loop : -0.90 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 266 
 TYR   0.013   0.001   TYR A 162 
 PHE   0.036   0.002   PHE A 211 
 TRP   0.006   0.001   TRP A  58 
 HIS   0.008   0.002   HIS A  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3673)
  covalent geometry    : angle       0.63887 ( 5008)
  hydrogen bonds       : bond        0.03875 (  128)
  hydrogen bonds       : angle       5.07256 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 HIS cc_start: 0.8039 (t70) cc_final: 0.7657 (t-90)
REVERT: A   49 MET cc_start: -0.1541 (mmt) cc_final: -0.1949 (mpt)
REVERT: A  165 LYS cc_start: 0.8489 (mmpt) cc_final: 0.8157 (pmtt)
REVERT: A  276 MET cc_start: 0.6083 (mtp) cc_final: 0.5380 (ttm)
REVERT: A  290 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.4418 (tppt)
REVERT: A  294 MET cc_start: 0.5763 (tpt) cc_final: 0.5373 (tmm)
REVERT: A  310 PHE cc_start: 0.8685 (p90) cc_final: 0.7903 (p90)
REVERT: A  404 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6851 (mmm)
  outliers start: 5
  outliers final: 1
  residues processed: 23
  average time/residue: 0.5859
  time to fit residues: 14.0325
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:   20.0000
   chunk 5 optimal weight:   50.0000
   chunk 24 optimal weight:   20.0000
   chunk 35 optimal weight:   40.0000
   chunk 10 optimal weight:    7.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.101206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.085471 restraints weight = 13904.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 4.85
r_work: 0.3688 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.6448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3673  Z= 0.116
  Angle     :  0.607  11.327   5008  Z= 0.302
  Chirality :  0.045   0.138    569
  Planarity :  0.005   0.057    613
  Dihedral  : 11.012  73.474    590
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 17.96 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.39), residues: 440
  helix:  0.94 (0.54), residues: 97
  sheet:  0.01 (0.53), residues: 105
  loop : -0.78 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  37 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.012   0.001   PHE A 340 
 TRP   0.007   0.001   TRP A  58 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3673)
  covalent geometry    : angle       0.60716 ( 5008)
  hydrogen bonds       : bond        0.03264 (  128)
  hydrogen bonds       : angle       4.94661 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 HIS cc_start: 0.8093 (t70) cc_final: 0.7814 (t-90)
REVERT: A  165 LYS cc_start: 0.8456 (mmpt) cc_final: 0.8147 (pmtt)
REVERT: A  290 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.4232 (tppt)
REVERT: A  294 MET cc_start: 0.5791 (tpt) cc_final: 0.5436 (tmm)
REVERT: A  310 PHE cc_start: 0.8731 (p90) cc_final: 0.7936 (p90)
REVERT: A  319 ASP cc_start: 0.8364 (p0) cc_final: 0.8011 (p0)
REVERT: A  404 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6629 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 20
  average time/residue: 0.6039
  time to fit residues: 12.5655
Evaluate side-chains
  20 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 34 optimal weight:   40.0000
   chunk 8 optimal weight:   40.0000
   chunk 32 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:   40.0000
   chunk 3 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 35 optimal weight:   40.0000
   overall best weight:    7.5992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.100652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.084726 restraints weight = 13814.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 4.39
r_work: 0.3681 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3651
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3651 r_free = 0.3651    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3651 r_free = 0.3651    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
r_final: 0.3651
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.6554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3673  Z= 0.144
  Angle     :  0.638  11.669   5008  Z= 0.317
  Chirality :  0.045   0.136    569
  Planarity :  0.005   0.057    613
  Dihedral  : 11.051  73.535    590
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 17.96 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.39), residues: 440
  helix:  0.79 (0.53), residues: 97
  sheet:  0.20 (0.51), residues: 112
  loop : -0.80 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 423 
 TYR   0.011   0.001   TYR A 162 
 PHE   0.011   0.001   PHE A 340 
 TRP   0.006   0.001   TRP A  58 
 HIS   0.005   0.002   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3673)
  covalent geometry    : angle       0.63809 ( 5008)
  hydrogen bonds       : bond        0.03610 (  128)
  hydrogen bonds       : angle       5.16601 (  370)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2013.02 seconds
wall clock time: 34 minutes 56.56 seconds (2096.56 seconds total)