Starting phenix.real_space_refine
on Tue Aug  4 15:55:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rha_53963/08_2026/9rha_53963.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rha_53963/08_2026/9rha_53963.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rha_53963/08_2026/9rha_53963.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rha_53963/08_2026/9rha_53963.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rha_53963/08_2026/9rha_53963.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rha_53963/08_2026/9rha_53963.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2965      2.51       5
     N     740      2.21       5
     O     826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  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: 4550
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 2827
          Classifications: {'peptide': 378}
          Link IDs: {'PTRANS': 15, 'TRANS': 362}
    Chain: "B"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 907
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "C"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 816
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101}
  Time building chain proxies: 1.04, per 1000 atoms: 0.23
  Number of scatterers: 4550
  At special positions: 0
  Unit cell: (66.123, 77.004, 102.951, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     826      8.00
     N     740      7.00
     C    2965      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03

  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: 0.27
  Conformation dependent library (CDL) restraints added in 130.0 milliseconds
  

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1092

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      53.3% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 31
    Processing helix  chain 'A' and resid 33 through 43
      removed outlier: 4.662A  pdb=" N   TRP A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A  42 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 86
      removed outlier: 3.654A  pdb=" N   ALA A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 5.434A  pdb=" N   PHE A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      Proline residue:  A 108  - end of helix
      removed outlier: 3.863A  pdb=" N   PHE A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
      removed outlier: 4.235A  pdb=" N   GLU A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 128
    Processing helix  chain 'A' and resid 133 through 145
      removed outlier: 3.852A  pdb=" N   LEU A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 148
      No H-bonds generated for 'chain 'A' and resid 146 through 148'
    Processing helix  chain 'A' and resid 149 through 175
    Processing helix  chain 'A' and resid 180 through 200
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 3.645A  pdb=" N   TYR A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 237
      removed outlier: 4.181A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 262
      Proline residue:  A 257  - end of helix
    Processing helix  chain 'A' and resid 262 through 272
    Processing helix  chain 'A' and resid 282 through 285
    Processing helix  chain 'A' and resid 286 through 298
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 324 through 335
      removed outlier: 3.711A  pdb=" N   VAL A 330 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 351
    Processing helix  chain 'A' and resid 354 through 382
      removed outlier: 3.687A  pdb=" N   VAL A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.726A  pdb=" N   ASP B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.364A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.544A  pdb=" N   LYS B  98 " --> pdb=" O   TYR B 107 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   TYR B 107 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.512A  pdb=" N   SER C  65 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12
      removed outlier: 7.102A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE C  48 " --> pdb=" O   TRP C  35 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   GLN C  37 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   ARG C  46 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
      removed outlier: 7.102A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    801 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.75

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1416
        1.34 -     1.46: 1073
        1.46 -     1.58: 2130
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 4650
  Sorted by residual:
  bond pdb=" N   ILE A 337 "
       pdb=" CA  ILE A 337 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.018 1.57e-02 4.06e+03 1.38e+00
  bond pdb=" CB  VAL A  79 "
       pdb=" CG2 VAL A  79 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  bond pdb=" CB  LYS A 240 "
       pdb=" CG  LYS A 240 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.02e+00
  bond pdb=" C   THR C   7 "
       pdb=" N   PRO C   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.024 2.34e-02 1.83e+03 1.01e+00
  bond pdb=" CB  ILE A 161 "
       pdb=" CG2 ILE A 161 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.74e-01
  ... (remaining 4645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 6141
        1.32 -     2.64: 140
        2.64 -     3.96: 33
        3.96 -     5.28: 9
        5.28 -     6.60: 4
  Bond angle restraints: 6327
  Sorted by residual:
  angle pdb=" C   GLU B  89 "
        pdb=" N   ASP B  90 "
        pdb=" CA  ASP B  90 "
      ideal   model   delta    sigma   weight residual
     123.15  119.40    3.75 1.21e+00 6.83e-01 9.62e+00
  angle pdb=" N   ILE A 337 "
        pdb=" CA  ILE A 337 "
        pdb=" C   ILE A 337 "
      ideal   model   delta    sigma   weight residual
     106.21  109.24   -3.03 1.07e+00 8.73e-01 8.01e+00
  angle pdb=" N   ILE C  29 "
        pdb=" CA  ILE C  29 "
        pdb=" CB  ILE C  29 "
      ideal   model   delta    sigma   weight residual
     112.35  108.71    3.64 1.38e+00 5.25e-01 6.94e+00
  angle pdb=" N   ASP B  90 "
        pdb=" CA  ASP B  90 "
        pdb=" C   ASP B  90 "
      ideal   model   delta    sigma   weight residual
     108.94  113.10   -4.16 1.76e+00 3.23e-01 5.59e+00
  angle pdb=" C   ILE A 337 "
        pdb=" CA  ILE A 337 "
        pdb=" CB  ILE A 337 "
      ideal   model   delta    sigma   weight residual
     113.22  110.69    2.53 1.12e+00 7.97e-01 5.11e+00
  ... (remaining 6322 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 2413
       14.86 -    29.73: 220
       29.73 -    44.59: 68
       44.59 -    59.46: 20
       59.46 -    74.32: 3
  Dihedral angle restraints: 2724
    sinusoidal: 1010
      harmonic: 1714
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.58   38.42     1      1.00e+01 1.00e-02 2.08e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.13   37.87     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CG  ARG A 381 "
           pdb=" CD  ARG A 381 "
           pdb=" NE  ARG A 381 "
           pdb=" CZ  ARG A 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.82  -44.18     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 2721 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 518
       0.035 -    0.070: 172
       0.070 -    0.104: 42
       0.104 -    0.139: 17
       0.139 -    0.174: 2
  Chirality restraints: 751
  Sorted by residual:
  chirality pdb=" CG  LEU C  33 "
            pdb=" CB  LEU C  33 "
            pdb=" CD1 LEU C  33 "
            pdb=" CD2 LEU C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  THR C   7 "
            pdb=" N   THR C   7 "
            pdb=" C   THR C   7 "
            pdb=" CB  THR C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  VAL C  58 "
            pdb=" N   VAL C  58 "
            pdb=" C   VAL C  58 "
            pdb=" CB  VAL C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 748 not shown)

  Planarity restraints: 779
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  58 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.90e+00
        pdb=" N   PRO C  59 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO C  59 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C  59 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 319 "    0.016 5.00e-02 4.00e+02   2.42e-02 9.33e-01
        pdb=" N   PRO A 320 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 320 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 320 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  13 "    0.016 5.00e-02 4.00e+02   2.39e-02 9.12e-01
        pdb=" N   PRO B  14 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO B  14 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B  14 "    0.013 5.00e-02 4.00e+02
  ... (remaining 776 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 570
        2.75 -     3.29: 4426
        3.29 -     3.82: 7528
        3.82 -     4.36: 8625
        4.36 -     4.90: 15569
  Nonbonded interactions: 36718
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  55 "
            pdb=" N   SER C  56 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   GLU A 124 "
            pdb=" OH  TYR A 175 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" NZ  LYS A  80 "
            pdb=" O   PHE A 235 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   SER B  85 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OD2 ASP A 163 "
            pdb=" NZ  LYS A 300 "
     model   vdw
     2.326 3.120
  ... (remaining 36713 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.920
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
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      :  0.004   0.034   4652  Z= 0.155
  Angle     :  0.557   6.603   6331  Z= 0.306
  Chirality :  0.040   0.174    751
  Planarity :  0.003   0.034    779
  Dihedral  : 13.504  74.319   1626
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.79 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.17 (0.35), residues: 596
  helix:  1.30 (0.30), residues: 272
  sheet:  1.02 (0.49), residues: 114
  loop :  0.10 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.011   0.001   TYR A 325 
 PHE   0.013   0.001   PHE A  72 
 TRP   0.006   0.001   TRP A 216 
 HIS   0.003   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.15 ( 4650)
  covalent geometry    : angle       0.55746 /  0.31 ( 6327)
  SS BOND              : bond        0.00335 /  0.17 (    2)
  SS BOND              : angle       0.25973 /  0.15 (    4)
  hydrogen bonds       : bond        0.22582 / 14.94 (  280)
  hydrogen bonds       : angle       7.92578 /  5.71 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.168 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0689
  time to fit residues: 6.3730
Evaluate side-chains
  67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:   30.0000
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0770
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A  58 ASN
A 177 ASN
A 256 HIS
B   5 HIS
C  37 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.184184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.123287 restraints weight = 5705.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.121748 restraints weight = 2940.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122766 restraints weight = 2574.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.122890 restraints weight = 2094.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.123351 restraints weight = 1964.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4652  Z= 0.114
  Angle     :  0.535   6.815   6331  Z= 0.276
  Chirality :  0.040   0.153    751
  Planarity :  0.004   0.037    779
  Dihedral  :  4.206  17.848    641
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.00 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.35), residues: 596
  helix:  2.01 (0.31), residues: 279
  sheet:  1.01 (0.48), residues: 113
  loop : -0.20 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.012   0.001   TYR C  71 
 PHE   0.011   0.001   PHE A 136 
 TRP   0.008   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 4650)
  covalent geometry    : angle       0.53527 /  0.28 ( 6327)
  SS BOND              : bond        0.00552 /  0.26 (    2)
  SS BOND              : angle       0.43650 /  0.33 (    4)
  hydrogen bonds       : bond        0.04324 /  2.89 (  280)
  hydrogen bonds       : angle       5.36569 /  3.85 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7499 (mt-10)
REVERT: C    7 THR cc_start: 0.6193 (OUTLIER) cc_final: 0.5928 (t)
  outliers start: 5
  outliers final: 1
  residues processed: 80
  average time/residue: 0.0647
  time to fit residues: 6.9521
Evaluate side-chains
  74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.0470
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 39 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.7080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN
A 177 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.184667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.124165 restraints weight = 5723.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.122540 restraints weight = 3029.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.123633 restraints weight = 2497.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.123686 restraints weight = 2147.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.124238 restraints weight = 1950.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4652  Z= 0.104
  Angle     :  0.493   6.666   6331  Z= 0.250
  Chirality :  0.039   0.153    751
  Planarity :  0.003   0.036    779
  Dihedral  :  4.062  17.161    641
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.00 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.87 (0.35), residues: 596
  helix:  2.24 (0.31), residues: 277
  sheet:  1.23 (0.48), residues: 110
  loop : -0.10 (0.45), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  81 
 TYR   0.014   0.001   TYR C  71 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.008   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.10 ( 4650)
  covalent geometry    : angle       0.49274 /  0.25 ( 6327)
  SS BOND              : bond        0.00425 /  0.20 (    2)
  SS BOND              : angle       0.39786 /  0.32 (    4)
  hydrogen bonds       : bond        0.03558 /  2.36 (  280)
  hydrogen bonds       : angle       4.89554 /  3.51 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   82 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8166 (mm-30)
REVERT: A  181 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6795 (tmm)
REVERT: C    7 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5806 (t)
REVERT: C   47 LEU cc_start: 0.8407 (mm) cc_final: 0.8098 (tt)
  outliers start: 10
  outliers final: 3
  residues processed: 87
  average time/residue: 0.0534
  time to fit residues: 6.3785
Evaluate side-chains
  83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0030
   chunk 49 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A  58 ASN
A 177 ASN
C   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.185498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125228 restraints weight = 5735.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.123668 restraints weight = 3140.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124855 restraints weight = 2591.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.125006 restraints weight = 2050.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.125263 restraints weight = 1904.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4652  Z= 0.103
  Angle     :  0.495   6.720   6331  Z= 0.248
  Chirality :  0.039   0.152    751
  Planarity :  0.003   0.036    779
  Dihedral  :  4.035  16.808    641
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.49 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.92 (0.35), residues: 596
  helix:  2.33 (0.31), residues: 277
  sheet:  1.19 (0.49), residues: 113
  loop : -0.11 (0.46), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.009   0.001   TYR A 112 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.009   0.001   TRP C  35 
 HIS   0.002   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.10 ( 4650)
  covalent geometry    : angle       0.49498 /  0.25 ( 6327)
  SS BOND              : bond        0.00549 /  0.26 (    2)
  SS BOND              : angle       0.64877 /  0.47 (    4)
  hydrogen bonds       : bond        0.03281 /  2.16 (  280)
  hydrogen bonds       : angle       4.79350 /  3.43 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6738 (tmm)
REVERT: C    7 THR cc_start: 0.5879 (OUTLIER) cc_final: 0.5603 (t)
  outliers start: 8
  outliers final: 3
  residues processed: 83
  average time/residue: 0.0457
  time to fit residues: 5.0282
Evaluate side-chains
  80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 46 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.184868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124769 restraints weight = 5725.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.123211 restraints weight = 3200.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124139 restraints weight = 2615.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.124270 restraints weight = 2101.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.125035 restraints weight = 1949.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4652  Z= 0.105
  Angle     :  0.505   6.742   6331  Z= 0.251
  Chirality :  0.039   0.151    751
  Planarity :  0.003   0.037    779
  Dihedral  :  3.982  16.569    641
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.49 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.97 (0.36), residues: 596
  helix:  2.37 (0.31), residues: 278
  sheet:  1.22 (0.49), residues: 113
  loop : -0.11 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.008   0.001   TYR A 112 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.007   0.001   TRP A 216 
 HIS   0.005   0.001   HIS A 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.10 ( 4650)
  covalent geometry    : angle       0.50518 /  0.25 ( 6327)
  SS BOND              : bond        0.00461 /  0.22 (    2)
  SS BOND              : angle       0.57338 /  0.39 (    4)
  hydrogen bonds       : bond        0.03225 /  2.14 (  280)
  hydrogen bonds       : angle       4.73895 /  3.39 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8457 (ttm) cc_final: 0.8235 (ttp)
REVERT: A  181 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6767 (tmm)
REVERT: A  252 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: C    7 THR cc_start: 0.5810 (OUTLIER) cc_final: 0.5527 (t)
REVERT: C   47 LEU cc_start: 0.8466 (mm) cc_final: 0.8155 (tt)
  outliers start: 8
  outliers final: 3
  residues processed: 81
  average time/residue: 0.0450
  time to fit residues: 4.8847
Evaluate side-chains
  78 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 42 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.185288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124699 restraints weight = 5797.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.123218 restraints weight = 3373.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124288 restraints weight = 2708.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.124393 restraints weight = 2158.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.124780 restraints weight = 1942.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4652  Z= 0.108
  Angle     :  0.512   6.883   6331  Z= 0.254
  Chirality :  0.039   0.151    751
  Planarity :  0.003   0.037    779
  Dihedral  :  3.980  16.490    641
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.32 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.99 (0.36), residues: 596
  helix:  2.40 (0.31), residues: 278
  sheet:  1.25 (0.49), residues: 113
  loop : -0.13 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.027   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.007   0.001   TRP A 216 
 HIS   0.002   0.000   HIS A 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 4650)
  covalent geometry    : angle       0.51208 /  0.25 ( 6327)
  SS BOND              : bond        0.00478 /  0.23 (    2)
  SS BOND              : angle       0.66682 /  0.43 (    4)
  hydrogen bonds       : bond        0.03156 /  2.07 (  280)
  hydrogen bonds       : angle       4.70476 /  3.35 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8474 (ttm) cc_final: 0.8255 (ttp)
REVERT: A  181 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6805 (tmm)
REVERT: C    7 THR cc_start: 0.5823 (OUTLIER) cc_final: 0.5536 (t)
REVERT: C   55 ASP cc_start: 0.6903 (t70) cc_final: 0.6683 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 73
  average time/residue: 0.0636
  time to fit residues: 6.2149
Evaluate side-chains
  77 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.183242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.122547 restraints weight = 5679.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.121407 restraints weight = 3000.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.121771 restraints weight = 2554.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.121973 restraints weight = 2143.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.122573 restraints weight = 2022.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4652  Z= 0.137
  Angle     :  0.512   6.773   6331  Z= 0.260
  Chirality :  0.040   0.150    751
  Planarity :  0.003   0.038    779
  Dihedral  :  4.042  17.077    641
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.52 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.98 (0.35), residues: 596
  helix:  2.38 (0.31), residues: 277
  sheet:  1.30 (0.48), residues: 113
  loop : -0.15 (0.46), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  46 
 TYR   0.022   0.001   TYR A 117 
 PHE   0.015   0.001   PHE A  72 
 TRP   0.006   0.001   TRP B  36 
 HIS   0.002   0.001   HIS A 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 4650)
  covalent geometry    : angle       0.51205 /  0.26 ( 6327)
  SS BOND              : bond        0.00383 /  0.18 (    2)
  SS BOND              : angle       0.51328 /  0.33 (    4)
  hydrogen bonds       : bond        0.03368 /  2.21 (  280)
  hydrogen bonds       : angle       4.75361 /  3.38 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8431 (ttm) cc_final: 0.8221 (ttp)
REVERT: A  181 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6832 (tmm)
REVERT: C    7 THR cc_start: 0.5833 (OUTLIER) cc_final: 0.5535 (t)
REVERT: C   47 LEU cc_start: 0.8512 (mm) cc_final: 0.8018 (tt)
REVERT: C   55 ASP cc_start: 0.6995 (t70) cc_final: 0.6408 (t0)
REVERT: C   56 SER cc_start: 0.5986 (t) cc_final: 0.5524 (p)
  outliers start: 10
  outliers final: 5
  residues processed: 71
  average time/residue: 0.0628
  time to fit residues: 5.9519
Evaluate side-chains
  74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 52 optimal weight:    8.9990
   chunk 27 optimal weight:    0.3980
   chunk 37 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 24 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.185943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.125666 restraints weight = 5735.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.124870 restraints weight = 3070.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.125432 restraints weight = 2522.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.125662 restraints weight = 2138.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.126137 restraints weight = 1957.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4652  Z= 0.098
  Angle     :  0.510   9.288   6331  Z= 0.250
  Chirality :  0.039   0.150    751
  Planarity :  0.003   0.038    779
  Dihedral  :  3.963  16.356    641
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.77 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.07 (0.35), residues: 596
  helix:  2.47 (0.31), residues: 278
  sheet:  1.43 (0.49), residues: 113
  loop : -0.20 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.010   0.001   TRP C  35 
 HIS   0.003   0.001   HIS B  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 ( 4650)
  covalent geometry    : angle       0.50969 /  0.25 ( 6327)
  SS BOND              : bond        0.00519 /  0.25 (    2)
  SS BOND              : angle       0.83825 /  0.61 (    4)
  hydrogen bonds       : bond        0.03045 /  1.99 (  280)
  hydrogen bonds       : angle       4.66855 /  3.30 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8440 (ttm) cc_final: 0.8238 (ttp)
REVERT: A  181 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6767 (tmm)
REVERT: B   31 ASP cc_start: 0.7673 (m-30) cc_final: 0.7046 (t70)
REVERT: B   34 MET cc_start: 0.7359 (mtp) cc_final: 0.7026 (mtp)
REVERT: C    7 THR cc_start: 0.5941 (OUTLIER) cc_final: 0.5663 (t)
REVERT: C   47 LEU cc_start: 0.8471 (mm) cc_final: 0.7992 (tt)
REVERT: C   55 ASP cc_start: 0.6864 (t70) cc_final: 0.6614 (t0)
REVERT: C  104 LEU cc_start: 0.5155 (tt) cc_final: 0.4953 (tp)
  outliers start: 6
  outliers final: 3
  residues processed: 73
  average time/residue: 0.0725
  time to fit residues: 6.8944
Evaluate side-chains
  74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  383 ARG
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 47 optimal weight:    0.2980
   chunk 52 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A 177 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.183705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124087 restraints weight = 5703.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.123189 restraints weight = 3659.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.124576 restraints weight = 2495.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.124415 restraints weight = 2376.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124688 restraints weight = 1976.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4652  Z= 0.135
  Angle     :  0.521   8.553   6331  Z= 0.258
  Chirality :  0.040   0.150    751
  Planarity :  0.003   0.039    779
  Dihedral  :  4.011  17.029    641
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.77 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 (0.35), residues: 596
  helix:  2.40 (0.31), residues: 277
  sheet:  1.44 (0.49), residues: 113
  loop : -0.25 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.022   0.001   TYR A 117 
 PHE   0.015   0.001   PHE A  72 
 TRP   0.008   0.001   TRP C  35 
 HIS   0.002   0.001   HIS A 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 4650)
  covalent geometry    : angle       0.52095 /  0.26 ( 6327)
  SS BOND              : bond        0.00482 /  0.23 (    2)
  SS BOND              : angle       0.75967 /  0.53 (    4)
  hydrogen bonds       : bond        0.03302 /  2.17 (  280)
  hydrogen bonds       : angle       4.71485 /  3.33 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8454 (ttm) cc_final: 0.8249 (ttp)
REVERT: A  181 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6889 (tmm)
REVERT: C    7 THR cc_start: 0.5441 (OUTLIER) cc_final: 0.5139 (t)
REVERT: C   47 LEU cc_start: 0.8445 (mm) cc_final: 0.7902 (tt)
REVERT: C   55 ASP cc_start: 0.6895 (t70) cc_final: 0.6275 (t0)
REVERT: C   56 SER cc_start: 0.6024 (t) cc_final: 0.5566 (p)
  outliers start: 7
  outliers final: 3
  residues processed: 71
  average time/residue: 0.0639
  time to fit residues: 6.0597
Evaluate side-chains
  71 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.184636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.125404 restraints weight = 5667.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.126264 restraints weight = 3781.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.126935 restraints weight = 2327.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.127175 restraints weight = 1938.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.127351 restraints weight = 1792.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4652  Z= 0.109
  Angle     :  0.513   9.271   6331  Z= 0.250
  Chirality :  0.039   0.151    751
  Planarity :  0.003   0.040    779
  Dihedral  :  3.915  16.554    641
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 16.39 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.05 (0.35), residues: 596
  helix:  2.47 (0.31), residues: 277
  sheet:  1.43 (0.49), residues: 113
  loop : -0.25 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.023   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.012   0.001   TRP C  35 
 HIS   0.002   0.001   HIS A 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 4650)
  covalent geometry    : angle       0.51221 /  0.25 ( 6327)
  SS BOND              : bond        0.00497 /  0.24 (    2)
  SS BOND              : angle       1.39927 /  0.89 (    4)
  hydrogen bonds       : bond        0.03113 /  2.03 (  280)
  hydrogen bonds       : angle       4.62861 /  3.28 (  801)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8424 (ttm) cc_final: 0.8221 (ttp)
REVERT: A  181 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6864 (tmm)
REVERT: C    7 THR cc_start: 0.5383 (OUTLIER) cc_final: 0.5068 (t)
REVERT: C   47 LEU cc_start: 0.8397 (mm) cc_final: 0.7880 (tt)
REVERT: C   55 ASP cc_start: 0.6834 (t70) cc_final: 0.6219 (t0)
REVERT: C   56 SER cc_start: 0.5963 (t) cc_final: 0.5523 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 67
  average time/residue: 0.0627
  time to fit residues: 5.5692
Evaluate side-chains
  70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0170
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    2.1824

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.181177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.122086 restraints weight = 5762.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119387 restraints weight = 3293.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120706 restraints weight = 3020.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.120989 restraints weight = 2345.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121178 restraints weight = 2079.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4652  Z= 0.186
  Angle     :  0.565   8.858   6331  Z= 0.279
  Chirality :  0.041   0.151    751
  Planarity :  0.003   0.043    779
  Dihedral  :  4.151  17.580    641
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.56 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.84 (0.35), residues: 596
  helix:  2.26 (0.31), residues: 277
  sheet:  1.40 (0.48), residues: 111
  loop : -0.31 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 383 
 TYR   0.020   0.002   TYR A 117 
 PHE   0.017   0.002   PHE A  72 
 TRP   0.009   0.001   TRP C  35 
 HIS   0.003   0.001   HIS A 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.19 ( 4650)
  covalent geometry    : angle       0.56440 /  0.28 ( 6327)
  SS BOND              : bond        0.00573 /  0.27 (    2)
  SS BOND              : angle       1.18432 /  0.79 (    4)
  hydrogen bonds       : bond        0.03616 /  2.39 (  280)
  hydrogen bonds       : angle       4.80758 /  3.41 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 869.20 seconds
wall clock time: 15 minutes 39.17 seconds (939.17 seconds total)