Starting phenix.real_space_refine
on Fri Aug 22 15:47:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p70_17513/08_2025/8p70_17513.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p70_17513/08_2025/8p70_17513.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p70_17513/08_2025/8p70_17513.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p70_17513/08_2025/8p70_17513.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p70_17513/08_2025/8p70_17513.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p70_17513/08_2025/8p70_17513.map"
  }
  resolution = 2.0
  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      31      5.16       5
     C    3309      2.51       5
     N     876      2.21       5
     O    1066      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  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: 5282
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2281
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 279, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2283
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 52
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 26
          Unusual residues: {'X4Q': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 26
          Unusual residues: {'X4Q': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 16
          Classifications: {'water': 16}
          Link IDs: {None: 15}
    Chain: "I"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 62
          Classifications: {'water': 62}
          Link IDs: {None: 61}
    Chain: "J"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 76
          Classifications: {'water': 76}
          Link IDs: {None: 75}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C01AX4Q J 401 " occ=0.81
      ... (50 atoms not shown)
      pdb=" N25BX4Q J 401 " occ=0.19
  Time building chain proxies: 1.52, per 1000 atoms: 0.29
  Number of scatterers: 5282
  At special positions: 0
  Unit cell: (84.7875, 93.3375, 66.975, 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      31     16.00
     O    1066      8.00
     N     876      7.00
     C    3309      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: 0.38
  Conformation dependent library (CDL) restraints added in 180.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1196

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      62.4% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'H' and resid 263 through 267
      removed outlier: 3.514A  pdb=" N   LEU H 266 " --> pdb=" O   LEU H 263 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY H 267 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 263 through 267'
    Processing helix  chain 'H' and resid 270 through 275
      removed outlier: 3.537A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 285
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.834A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
      removed outlier: 3.621A  pdb=" N   ASN I   4 " --> pdb=" O   MET I   1 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 1 through 4'
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
      removed outlier: 3.543A  pdb=" N   LEU I  19 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 70
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 3.982A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.794A  pdb=" N   LEU I 106 " --> pdb=" O   ARG I 102 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 127
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.622A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.649A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 4.419A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 262
      removed outlier: 3.869A  pdb=" N   ILE I 251 " --> pdb=" O   GLN I 247 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 266 through 284
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.366A  pdb=" N   LEU J 158 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.514A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.707A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20
      removed outlier: 6.552A  pdb=" N   LYS J  28 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   PHE J  17 " --> pdb=" O   VAL J  26 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   VAL J  26 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134

    272 hydrogen bonds defined for protein.
    762 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: 0.63

  Time building geometry restraints manager: 0.49 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: 1644
        1.34 -     1.46: 1122
        1.46 -     1.58: 2438
        1.58 -     1.69: 2
        1.69 -     1.81: 49
  Bond restraints: 5255
  Sorted by residual:
  bond pdb=" C15BX4Q J 401 "
       pdb=" N16BX4Q J 401 "
    ideal  model  delta    sigma   weight residual
    1.357  1.491 -0.134 2.00e-02 2.50e+03 4.48e+01
  bond pdb=" C15AX4Q J 401 "
       pdb=" N16AX4Q J 401 "
    ideal  model  delta    sigma   weight residual
    1.357  1.491 -0.134 2.00e-02 2.50e+03 4.47e+01
  bond pdb=" C02BX4Q J 401 "
       pdb=" C04BX4Q J 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.598 -0.102 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" C02AX4Q J 401 "
       pdb=" C04AX4Q J 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.598 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C07AX4Q J 401 "
       pdb=" N08AX4Q J 401 "
    ideal  model  delta    sigma   weight residual
    1.367  1.453 -0.086 2.00e-02 2.50e+03 1.84e+01
  ... (remaining 5250 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 6917
        1.52 -     3.05: 141
        3.05 -     4.57: 39
        4.57 -     6.10: 10
        6.10 -     7.62: 6
  Bond angle restraints: 7113
  Sorted by residual:
  angle pdb=" CA  MET I 237 "
        pdb=" CB  MET I 237 "
        pdb=" CG  MET I 237 "
      ideal   model   delta    sigma   weight residual
     114.10  121.72   -7.62 2.00e+00 2.50e-01 1.45e+01
  angle pdb=" N   MET I 237 "
        pdb=" CA  MET I 237 "
        pdb=" CB  MET I 237 "
      ideal   model   delta    sigma   weight residual
     113.65  109.48    4.17 1.47e+00 4.63e-01 8.06e+00
  angle pdb=" CA  TYR I  91 "
        pdb=" CB  TYR I  91 "
        pdb=" CG  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     113.90  109.27    4.63 1.80e+00 3.09e-01 6.63e+00
  angle pdb=" CB  MET I  75 "
        pdb=" CG  MET I  75 "
        pdb=" SD  MET I  75 "
      ideal   model   delta    sigma   weight residual
     112.70  106.11    6.59 3.00e+00 1.11e-01 4.83e+00
  angle pdb=" C   PHE I  90 "
        pdb=" N   TYR I  91 "
        pdb=" CA  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     122.56  118.83    3.73 1.72e+00 3.38e-01 4.69e+00
  ... (remaining 7108 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.38: 2879
       22.38 -    44.77: 252
       44.77 -    67.15: 35
       67.15 -    89.53: 11
       89.53 -   111.92: 2
  Dihedral angle restraints: 3179
    sinusoidal: 1332
      harmonic: 1847
  Sorted by residual:
  dihedral pdb=" C07BX4Q J 401 "
           pdb=" C09BX4Q J 401 "
           pdb=" N08BX4Q J 401 "
           pdb=" C10BX4Q J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.54  179.62  111.92     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" C07BX4Q J 401 "
           pdb=" C09BX4Q J 401 "
           pdb=" N08BX4Q J 401 "
           pdb=" C13BX4Q J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.58   62.87  111.71     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" CA  TYR I  91 "
           pdb=" C   TYR I  91 "
           pdb=" N   LEU I  92 "
           pdb=" CA  LEU I  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.23   16.77     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 3176 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 472
       0.029 -    0.058: 198
       0.058 -    0.087: 59
       0.087 -    0.116: 37
       0.116 -    0.145: 11
  Chirality restraints: 777
  Sorted by residual:
  chirality pdb=" CA  TYR I  91 "
            pdb=" N   TYR I  91 "
            pdb=" C   TYR I  91 "
            pdb=" CB  TYR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  PRO J 238 "
            pdb=" N   PRO J 238 "
            pdb=" C   PRO J 238 "
            pdb=" CB  PRO J 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  PRO J 140 "
            pdb=" N   PRO J 140 "
            pdb=" C   PRO J 140 "
            pdb=" CB  PRO J 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 774 not shown)

  Planarity restraints: 905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET I 237 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   MET I 237 "    0.030 2.00e-02 2.50e+03
        pdb=" O   MET I 237 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU I 238 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU I  49 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.74e+00
        pdb=" N   PRO I  50 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO I  50 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO I  50 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 139 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO J 140 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO J 140 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO J 140 "    0.021 5.00e-02 4.00e+02
  ... (remaining 902 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 529
        2.74 -     3.28: 5489
        3.28 -     3.82: 10018
        3.82 -     4.36: 11931
        4.36 -     4.90: 19411
  Nonbonded interactions: 47378
  Sorted by model distance:
  nonbonded pdb=" O   GLY H 285 "
            pdb=" O   HOH H 401 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ARG I   9 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   LEU I 144 "
            pdb=" O   HOH I 402 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OD1 ASP J 104 "
            pdb=" OG  SER J 106 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OE2 GLU J  62 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.235 3.040
  ... (remaining 47373 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=0.19 max=1.00 mean=1.00
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:             4.320
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.140
  Find NCS groups from input model:        0.030
  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:8.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.134   5255  Z= 0.276
  Angle     :  0.617   7.621   7113  Z= 0.297
  Chirality :  0.040   0.145    777
  Planarity :  0.005   0.041    905
  Dihedral  : 16.718 111.917   1983
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.43 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.34), residues: 618
  helix:  1.97 (0.29), residues: 334
  sheet:  0.84 (1.05), residues: 15
  loop :  0.08 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  63 
 TYR   0.020   0.002   TYR I 231 
 PHE   0.016   0.002   PHE I  30 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.003   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 5255)
  covalent geometry    : angle       0.61741 ( 7113)
  hydrogen bonds       : bond        0.13506 (  272)
  hydrogen bonds       : angle       6.11540 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.146 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 95
  average time/residue: 0.6500
  time to fit residues: 63.7884
Evaluate side-chains
  92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  279 SER
Chi-restraints excluded: chain I residue   78 SER
Chi-restraints excluded: chain I residue  254 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.170791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142380 restraints weight = 24180.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.78
r_work: 0.3612 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.0653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5255  Z= 0.128
  Angle     :  0.527   6.326   7113  Z= 0.275
  Chirality :  0.040   0.138    777
  Planarity :  0.005   0.040    905
  Dihedral  :  7.316  92.391    725
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  0.97 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.62 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.34), residues: 618
  helix:  2.06 (0.29), residues: 345
  sheet:  0.69 (1.06), residues: 15
  loop :  0.19 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  63 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.016   0.002   PHE I  30 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5255)
  covalent geometry    : angle       0.52690 ( 7113)
  hydrogen bonds       : bond        0.04582 (  272)
  hydrogen bonds       : angle       4.78042 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.215 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 102
  average time/residue: 0.6223
  time to fit residues: 65.5787
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.170219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.143536 restraints weight = 17753.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.23
r_work: 0.3636 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.0845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5255  Z= 0.132
  Angle     :  0.537   9.103   7113  Z= 0.275
  Chirality :  0.040   0.140    777
  Planarity :  0.005   0.040    905
  Dihedral  :  6.267  58.569    722
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.52 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.34), residues: 618
  helix:  2.05 (0.28), residues: 345
  sheet:  0.50 (1.09), residues: 15
  loop :  0.17 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  63 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.016   0.002   PHE I  30 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5255)
  covalent geometry    : angle       0.53654 ( 7113)
  hydrogen bonds       : bond        0.04469 (  272)
  hydrogen bonds       : angle       4.69076 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.138 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6843 (ttmt)
  outliers start: 13
  outliers final: 5
  residues processed: 109
  average time/residue: 0.5605
  time to fit residues: 63.1562
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Chi-restraints excluded: chain J residue  266 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN
J 259 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.167381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.138977 restraints weight = 23899.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.72
r_work: 0.3572 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   5255  Z= 0.243
  Angle     :  0.674   7.606   7113  Z= 0.343
  Chirality :  0.045   0.155    777
  Planarity :  0.006   0.046    905
  Dihedral  :  7.248  80.333    722
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.44 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.34), residues: 618
  helix:  1.56 (0.28), residues: 343
  sheet:  0.42 (1.20), residues: 15
  loop :  0.04 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  23 
 TYR   0.020   0.003   TYR I 231 
 PHE   0.019   0.003   PHE I  30 
 TRP   0.016   0.003   TRP I  11 
 HIS   0.007   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 5255)
  covalent geometry    : angle       0.67366 ( 7113)
  hydrogen bonds       : bond        0.05549 (  272)
  hydrogen bonds       : angle       5.03530 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.133 
Fit side-chains
REVERT: H  251 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.5066 (mp)
REVERT: H  268 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.6032 (mtm-85)
REVERT: I  250 ASP cc_start: 0.7485 (p0) cc_final: 0.7122 (m-30)
  outliers start: 14
  outliers final: 4
  residues processed: 101
  average time/residue: 0.5316
  time to fit residues: 55.3942
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  251 LEU
Chi-restraints excluded: chain H residue  268 ARG
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN

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 = 0.168517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.140300 restraints weight = 22567.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.63
r_work: 0.3584 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5255  Z= 0.175
  Angle     :  0.600   7.723   7113  Z= 0.307
  Chirality :  0.042   0.148    777
  Planarity :  0.005   0.045    905
  Dihedral  :  6.487  57.242    722
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.52 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.34), residues: 618
  helix:  1.71 (0.28), residues: 343
  sheet:  0.38 (1.22), residues: 15
  loop :  0.08 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  63 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.018   0.002   PHE I  30 
 TRP   0.014   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5255)
  covalent geometry    : angle       0.59991 ( 7113)
  hydrogen bonds       : bond        0.04946 (  272)
  hydrogen bonds       : angle       4.88130 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.171 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6337 (ptp-170)
REVERT: I  250 ASP cc_start: 0.7406 (p0) cc_final: 0.7042 (m-30)
REVERT: I  260 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7140 (ttmt)
REVERT: J  293 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8404 (mtmt)
  outliers start: 12
  outliers final: 4
  residues processed: 99
  average time/residue: 0.5599
  time to fit residues: 57.2377
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   77 ARG
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Chi-restraints excluded: chain J residue  293 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.169221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.141793 restraints weight = 17798.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.33
r_work: 0.3608 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5255  Z= 0.157
  Angle     :  0.583   8.608   7113  Z= 0.299
  Chirality :  0.041   0.147    777
  Planarity :  0.005   0.044    905
  Dihedral  :  6.256  59.183    722
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.70 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.34), residues: 618
  helix:  1.84 (0.28), residues: 343
  sheet:  0.32 (1.20), residues: 15
  loop :  0.10 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  63 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.017   0.002   PHE I  30 
 TRP   0.013   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5255)
  covalent geometry    : angle       0.58304 ( 7113)
  hydrogen bonds       : bond        0.04740 (  272)
  hydrogen bonds       : angle       4.81122 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.147 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6306 (ptp-170)
REVERT: I  228 MET cc_start: 0.8113 (ptm) cc_final: 0.7893 (ptm)
REVERT: I  250 ASP cc_start: 0.7372 (p0) cc_final: 0.7030 (m-30)
REVERT: I  260 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7137 (ttmt)
REVERT: J  227 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6805 (pt0)
  outliers start: 11
  outliers final: 5
  residues processed: 98
  average time/residue: 0.6039
  time to fit residues: 61.2092
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   77 ARG
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   70 SER
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    0.4980
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.170397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.142052 restraints weight = 23145.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.69
r_work: 0.3611 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3513 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5255  Z= 0.128
  Angle     :  0.547   9.981   7113  Z= 0.279
  Chirality :  0.040   0.144    777
  Planarity :  0.005   0.043    905
  Dihedral  :  5.759  53.473    722
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.43 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.34), residues: 618
  helix:  2.02 (0.28), residues: 345
  sheet:  0.31 (1.18), residues: 15
  loop :  0.14 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  63 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.015   0.002   PHE I  30 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5255)
  covalent geometry    : angle       0.54686 ( 7113)
  hydrogen bonds       : bond        0.04332 (  272)
  hydrogen bonds       : angle       4.68781 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.134 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6296 (ptp-170)
REVERT: I  228 MET cc_start: 0.8125 (ptm) cc_final: 0.7921 (ptm)
REVERT: I  250 ASP cc_start: 0.7335 (p0) cc_final: 0.7003 (m-30)
REVERT: I  260 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7104 (ttmt)
REVERT: J  227 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6773 (pt0)
  outliers start: 10
  outliers final: 4
  residues processed: 100
  average time/residue: 0.5894
  time to fit residues: 60.9965
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   77 ARG
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0270
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.9240

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.170186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.141899 restraints weight = 23152.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.68
r_work: 0.3607 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5255  Z= 0.131
  Angle     :  0.547   6.376   7113  Z= 0.281
  Chirality :  0.040   0.143    777
  Planarity :  0.005   0.042    905
  Dihedral  :  5.732  53.915    722
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.15 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.34), residues: 618
  helix:  2.07 (0.29), residues: 345
  sheet:  0.39 (1.17), residues: 15
  loop :  0.14 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  63 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.016   0.002   PHE I  30 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5255)
  covalent geometry    : angle       0.54735 ( 7113)
  hydrogen bonds       : bond        0.04391 (  272)
  hydrogen bonds       : angle       4.67546 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.213 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6289 (ptp-170)
REVERT: I  228 MET cc_start: 0.8121 (ptm) cc_final: 0.7918 (ptm)
REVERT: I  250 ASP cc_start: 0.7370 (p0) cc_final: 0.7024 (m-30)
REVERT: I  260 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7161 (ttmt)
REVERT: J  227 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6771 (pt0)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 0.6132
  time to fit residues: 62.0660
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   77 ARG
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   70 SER
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 47 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 39 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.170931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.142809 restraints weight = 21585.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.61
r_work: 0.3620 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3516
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3516
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5255  Z= 0.120
  Angle     :  0.535   6.704   7113  Z= 0.275
  Chirality :  0.040   0.142    777
  Planarity :  0.005   0.042    905
  Dihedral  :  5.566  56.660    722
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.15 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.35), residues: 618
  helix:  2.16 (0.29), residues: 344
  sheet:  0.42 (1.16), residues: 15
  loop :  0.12 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  63 
 TYR   0.017   0.002   TYR I  91 
 PHE   0.015   0.001   PHE I  30 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5255)
  covalent geometry    : angle       0.53470 ( 7113)
  hydrogen bonds       : bond        0.04211 (  272)
  hydrogen bonds       : angle       4.60176 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.143 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6261 (ptp-170)
REVERT: I  250 ASP cc_start: 0.7362 (p0) cc_final: 0.7014 (m-30)
REVERT: I  260 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6962 (ttmt)
  outliers start: 8
  outliers final: 3
  residues processed: 101
  average time/residue: 0.5946
  time to fit residues: 62.1855
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   77 ARG
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 59 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0570
   chunk 2 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.172008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.144756 restraints weight = 22507.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.62
r_work: 0.3641 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5255  Z= 0.111
  Angle     :  0.546  13.056   7113  Z= 0.275
  Chirality :  0.039   0.141    777
  Planarity :  0.005   0.042    905
  Dihedral  :  5.307  51.627    722
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.69 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.35), residues: 618
  helix:  2.21 (0.29), residues: 344
  sheet:  0.46 (1.14), residues: 15
  loop :  0.17 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  63 
 TYR   0.015   0.002   TYR I  91 
 PHE   0.013   0.001   PHE I  30 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5255)
  covalent geometry    : angle       0.54638 ( 7113)
  hydrogen bonds       : bond        0.03970 (  272)
  hydrogen bonds       : angle       4.55833 (  762)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.192 
Fit side-chains
REVERT: I   16 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7097 (mm-30)
REVERT: I   77 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6266 (ptp-170)
REVERT: J  227 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6711 (pt0)
  outliers start: 6
  outliers final: 3
  residues processed: 99
  average time/residue: 0.5901
  time to fit residues: 60.3615
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   77 ARG
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   96 THR
Chi-restraints excluded: chain J residue  251 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 49 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.171262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.143123 restraints weight = 24293.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.84
r_work: 0.3621 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5255  Z= 0.119
  Angle     :  0.553   8.176   7113  Z= 0.281
  Chirality :  0.040   0.149    777
  Planarity :  0.005   0.042    905
  Dihedral  :  5.350  52.212    722
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.87 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.34), residues: 618
  helix:  2.21 (0.29), residues: 344
  sheet:  0.48 (1.14), residues: 15
  loop :  0.12 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  63 
 TYR   0.017   0.002   TYR I  91 
 PHE   0.014   0.001   PHE I  30 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5255)
  covalent geometry    : angle       0.55260 ( 7113)
  hydrogen bonds       : bond        0.04176 (  272)
  hydrogen bonds       : angle       4.57752 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2686.17 seconds
wall clock time: 46 minutes 15.31 seconds (2775.31 seconds total)