Starting phenix.real_space_refine
on Sat May 10 05:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p70_17513/05_2025/8p70_17513.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p70_17513/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p70_17513/05_2025/8p70_17513.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p70_17513/05_2025/8p70_17513.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p70_17513/05_2025/8p70_17513.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p70_17513/05_2025/8p70_17513.cif"
  }
  resolution = 2.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.79, per 1000 atoms: 0.91
  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: 1.43
  Conformation dependent library (CDL) restraints added in 613.1 milliseconds
  

  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: 0.55
  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: 1.48

  Time building geometry restraints manager: 1.66 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:             3.120
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.760
  Find NCS groups from input model:        0.080
  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:13.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.940
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.011   0.002   TRP I  11 
 HIS   0.003   0.001   HIS J 131 
 PHE   0.016   0.002   PHE I  30 
 TYR   0.020   0.002   TYR I 231 
 ARG   0.006   0.000   ARG I  63 

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

*********************** 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  : 0.663 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 95
  average time/residue: 1.4900
  time to fit residues: 146.5736
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  : 0.638 
-------------------------------------------------------------------------------
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 52 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.170519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.142894 restraints weight = 19552.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.48
r_work: 0.3620 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    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 = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.0656

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= 0.135
  Angle     :  0.534   6.407   7113  Z= 0.278
  Chirality :  0.040   0.139    777
  Planarity :  0.005   0.041    905
  Dihedral  :  7.326  92.203    725
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.34), residues: 618
  helix:  2.04 (0.29), residues: 345
  sheet:  0.72 (1.08), residues: 15
  loop :  0.18 (0.39), residues: 258

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  272)
  hydrogen bonds       : angle       4.79272 (  762)
  covalent geometry    : bond        0.00294 ( 5255)
  covalent geometry    : angle       0.53357 ( 7113)

*********************** 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  : 0.522 
Fit side-chains
REVERT: I  189 LYS cc_start: 0.7485 (mmmm) cc_final: 0.7272 (mptm)
REVERT: J  246 TYR cc_start: 0.6760 (t80) cc_final: 0.6521 (t80)
  outliers start: 9
  outliers final: 3
  residues processed: 102
  average time/residue: 1.4519
  time to fit residues: 153.3409
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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 39 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
I  93 ASN
J 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.171569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.144227 restraints weight = 18169.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.39
r_work: 0.3637 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3539 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.0883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5255  Z= 0.118
  Angle     :  0.526   8.573   7113  Z= 0.267
  Chirality :  0.039   0.137    777
  Planarity :  0.005   0.039    905
  Dihedral  :  6.069  54.388    722
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.34), residues: 618
  helix:  2.15 (0.28), residues: 345
  sheet:  0.58 (1.07), residues: 15
  loop :  0.19 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.015   0.001   PHE I  30 
 TYR   0.017   0.002   TYR I  91 
 ARG   0.005   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04258 (  272)
  hydrogen bonds       : angle       4.61990 (  762)
  covalent geometry    : bond        0.00262 ( 5255)
  covalent geometry    : angle       0.52582 ( 7113)

*********************** 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: 12
    poor density    : 101
  time to evaluate  : 0.584 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6926 (ttmt)
  outliers start: 12
  outliers final: 5
  residues processed: 110
  average time/residue: 1.5069
  time to fit residues: 171.6072
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  : 0.653 
-------------------------------------------------------------------------------
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 18 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0870
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.1964

-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.169981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.142656 restraints weight = 16699.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.26
r_work: 0.3626 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5255  Z= 0.147
  Angle     :  0.555   7.239   7113  Z= 0.284
  Chirality :  0.041   0.141    777
  Planarity :  0.005   0.041    905
  Dihedral  :  6.153  58.015    722
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.52 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.34), residues: 618
  helix:  2.07 (0.28), residues: 344
  sheet:  0.58 (1.13), residues: 15
  loop :  0.18 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I  30 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.005   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  272)
  hydrogen bonds       : angle       4.69227 (  762)
  covalent geometry    : bond        0.00327 ( 5255)
  covalent geometry    : angle       0.55488 ( 7113)

*********************** 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: 9
    poor density    : 96
  time to evaluate  : 0.682 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6885 (ttmt)
  outliers start: 9
  outliers final: 5
  residues processed: 102
  average time/residue: 1.5750
  time to fit residues: 166.2017
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    0.0470
   chunk 59 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.1882

-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.169992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.142501 restraints weight = 17989.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.30
r_work: 0.3626 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5255  Z= 0.145
  Angle     :  0.549   6.450   7113  Z= 0.282
  Chirality :  0.041   0.142    777
  Planarity :  0.005   0.041    905
  Dihedral  :  5.956  54.444    722
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  0.97 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.34), residues: 618
  helix:  2.03 (0.28), residues: 344
  sheet:  0.54 (1.14), residues: 15
  loop :  0.18 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I  30 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.006   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04555 (  272)
  hydrogen bonds       : angle       4.67944 (  762)
  covalent geometry    : bond        0.00322 ( 5255)
  covalent geometry    : angle       0.54910 ( 7113)

*********************** 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
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.675 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6255 (ptp-170)
REVERT: I  260 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6871 (ttmt)
  outliers start: 11
  outliers final: 5
  residues processed: 106
  average time/residue: 1.5334
  time to fit residues: 168.1976
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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  266 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0970
   chunk 16 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.171422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.143457 restraints weight = 20631.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.55
r_work: 0.3630 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5255  Z= 0.116
  Angle     :  0.524   8.947   7113  Z= 0.267
  Chirality :  0.039   0.141    777
  Planarity :  0.005   0.040    905
  Dihedral  :  5.599  55.655    722
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.34), residues: 618
  helix:  2.24 (0.28), residues: 344
  sheet:  0.45 (1.14), residues: 15
  loop :  0.18 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.014   0.001   PHE I  30 
 TYR   0.017   0.002   TYR I  91 
 ARG   0.006   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  272)
  hydrogen bonds       : angle       4.57828 (  762)
  covalent geometry    : bond        0.00260 ( 5255)
  covalent geometry    : angle       0.52380 ( 7113)

*********************** 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: 10
    poor density    : 92
  time to evaluate  : 0.600 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6245 (ptp-170)
REVERT: I  260 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6910 (ttmt)
REVERT: J  227 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6792 (pt0)
  outliers start: 10
  outliers final: 4
  residues processed: 99
  average time/residue: 1.5250
  time to fit residues: 156.1969
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  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  266 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.169873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142499 restraints weight = 17140.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.30
r_work: 0.3618 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5255  Z= 0.154
  Angle     :  0.566   7.915   7113  Z= 0.289
  Chirality :  0.041   0.142    777
  Planarity :  0.005   0.040    905
  Dihedral  :  5.855  55.204    722
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.34), residues: 618
  helix:  2.08 (0.28), residues: 344
  sheet:  0.45 (1.16), residues: 15
  loop :  0.18 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I  30 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.005   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  272)
  hydrogen bonds       : angle       4.72702 (  762)
  covalent geometry    : bond        0.00350 ( 5255)
  covalent geometry    : angle       0.56588 ( 7113)

*********************** 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: 9
    poor density    : 95
  time to evaluate  : 0.581 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6279 (ptp-170)
REVERT: I  260 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6868 (ttmt)
REVERT: J  227 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6784 (pt0)
  outliers start: 9
  outliers final: 5
  residues processed: 101
  average time/residue: 1.5734
  time to fit residues: 164.2717
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
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  266 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0170
   chunk 7 optimal weight:    0.0970
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.9620

-------------------------------------------------------------------------------
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 = 0.4097 r_free = 0.4097 target = 0.170614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.142145 restraints weight = 23596.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.72
r_work: 0.3608 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    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 = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5255  Z= 0.133
  Angle     :  0.549   7.539   7113  Z= 0.280
  Chirality :  0.040   0.142    777
  Planarity :  0.005   0.040    905
  Dihedral  :  5.710  57.471    722
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.79 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.34), residues: 618
  helix:  2.16 (0.28), residues: 344
  sheet:  0.37 (1.15), residues: 15
  loop :  0.12 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.016   0.002   PHE I  30 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.007   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  272)
  hydrogen bonds       : angle       4.65426 (  762)
  covalent geometry    : bond        0.00301 ( 5255)
  covalent geometry    : angle       0.54869 ( 7113)

*********************** 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
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.604 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6312 (ptp-170)
REVERT: I  260 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6898 (ttmt)
REVERT: J  227 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6778 (pt0)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 1.5921
  time to fit residues: 159.7344
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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  266 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4086 r_free = 0.4086 target = 0.169597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.141817 restraints weight = 19074.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.44
r_work: 0.3608 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5255  Z= 0.156
  Angle     :  0.583   6.398   7113  Z= 0.298
  Chirality :  0.041   0.142    777
  Planarity :  0.005   0.041    905
  Dihedral  :  5.857  55.029    722
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.34), residues: 618
  helix:  2.02 (0.28), residues: 344
  sheet:  0.38 (1.17), residues: 15
  loop :  0.14 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I  30 
 TYR   0.020   0.002   TYR J 178 
 ARG   0.006   0.001   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  272)
  hydrogen bonds       : angle       4.74808 (  762)
  covalent geometry    : bond        0.00352 ( 5255)
  covalent geometry    : angle       0.58291 ( 7113)

*********************** 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
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.640 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6342 (ptp-170)
REVERT: I  260 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6907 (ttmt)
REVERT: J  246 TYR cc_start: 0.6804 (t80) cc_final: 0.6546 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 1.5073
  time to fit residues: 151.5998
Evaluate side-chains
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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  266 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    0.3980
   chunk 51 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0170
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6420

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.171632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.143357 restraints weight = 22264.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.66
r_work: 0.3627 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1079

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= 0.116
  Angle     :  0.532   6.571   7113  Z= 0.274
  Chirality :  0.040   0.143    777
  Planarity :  0.005   0.040    905
  Dihedral  :  5.487  56.418    722
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 17.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.34), residues: 618
  helix:  2.25 (0.29), residues: 344
  sheet:  0.44 (1.16), residues: 15
  loop :  0.13 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.014   0.001   PHE I  30 
 TYR   0.017   0.002   TYR I  91 
 ARG   0.006   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  272)
  hydrogen bonds       : angle       4.56753 (  762)
  covalent geometry    : bond        0.00257 ( 5255)
  covalent geometry    : angle       0.53192 ( 7113)

********************** 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: 7
    poor density    : 94
  time to evaluate  : 0.657 
Fit side-chains
REVERT: I   77 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6039 (ptp-170)
REVERT: I  260 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6791 (ttmt)
REVERT: J  227 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6647 (pt0)
  outliers start: 7
  outliers final: 4
  residues processed: 97
  average time/residue: 1.4990
  time to fit residues: 150.7156
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  266 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 59 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0980
   chunk 44 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.172599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.144679 restraints weight = 20711.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.56
r_work: 0.3645 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5255  Z= 0.108
  Angle     :  0.522   5.982   7113  Z= 0.269
  Chirality :  0.039   0.140    777
  Planarity :  0.005   0.040    905
  Dihedral  :  5.230  50.217    722
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.34), residues: 618
  helix:  2.30 (0.29), residues: 344
  sheet:  0.42 (1.12), residues: 15
  loop :  0.17 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 
 PHE   0.013   0.001   PHE I  30 
 TYR   0.016   0.002   TYR I  91 
 ARG   0.007   0.000   ARG I  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  272)
  hydrogen bonds       : angle       4.47627 (  762)
  covalent geometry    : bond        0.00239 ( 5255)
  covalent geometry    : angle       0.52168 ( 7113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6462.19 seconds
wall clock time: 111 minutes 28.09 seconds (6688.09 seconds total)