Starting phenix.real_space_refine
on Tue Feb 11 12:17:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n62_24192/02_2025/7n62_24192_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n62_24192/02_2025/7n62_24192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n62_24192/02_2025/7n62_24192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n62_24192/02_2025/7n62_24192.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n62_24192/02_2025/7n62_24192_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n62_24192/02_2025/7n62_24192_neut.cif"
  }
  resolution = 4.0
  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=   0.002
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      17      5.16       5
     C    3569      2.51       5
     N     933      2.21       5
     O    1094      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5613
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2235
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 14, 'TRANS': 262}
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1689
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211}
    Chain: "L"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1619
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 3.83, per 1000 atoms: 0.68
  Number of scatterers: 5613
  At special positions: 0
  Unit cell: (64.35, 95.7, 122.925, 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      17     16.00
     O    1094      8.00
     N     933      7.00
     C    3569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A  17 "
      " NAG A1302 " - " ASN A  61 "
      " NAG A1303 " - " ASN A 122 "
      " NAG A1304 " - " ASN A 165 "
      " NAG A1305 " - " ASN A 234 "
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 647.9 milliseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1314

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 16 sheets defined
      5.3% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.558A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 195 through 199
    Processing helix  chain 'L' and resid 29 through 32
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.775A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 182 through 188
      removed outlier: 4.097A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28
      removed outlier: 3.628A  pdb=" N   LYS A 195 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.649A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 5.651A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145
      removed outlier: 4.062A  pdb=" N   TYR A 144 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   MET A 153 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.865A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 132 through 133
      removed outlier: 4.376A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL H 192 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 132 through 133
      removed outlier: 4.376A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL H 192 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER H 187 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12
    Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.530A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.631A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.731A  pdb=" N   LYS L 145 " --> pdb=" O   THR L 197 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   CYS L 194 " --> pdb=" O   LYS L 207 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL L 205 " --> pdb=" O   VAL L 196 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    429 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: 1.55

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1779
        1.34 -     1.46: 1526
        1.46 -     1.59: 2431
        1.59 -     1.71: 0
        1.71 -     1.83: 22
  Bond restraints: 5758
  Sorted by residual:
  bond pdb=" N   GLU H   6 "
       pdb=" CA  GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.23e-02 6.61e+03 6.33e+00
  bond pdb=" N   ASP A 253 "
       pdb=" CA  ASP A 253 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.50e-02 4.44e+03 5.06e+00
  bond pdb=" C   ALA H  92 "
       pdb=" N   VAL H  93 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.24e-02 6.50e+03 2.83e+00
  bond pdb=" CB  PRO H 159 "
       pdb=" CG  PRO H 159 "
    ideal  model  delta    sigma   weight residual
    1.506  1.567 -0.061 3.90e-02 6.57e+02 2.41e+00
  bond pdb=" CB  TRP H  36 "
       pdb=" CG  TRP H  36 "
    ideal  model  delta    sigma   weight residual
    1.498  1.455  0.043 3.10e-02 1.04e+03 1.97e+00
  ... (remaining 5753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 7408
        1.64 -     3.28: 354
        3.28 -     4.92: 51
        4.92 -     6.56: 14
        6.56 -     8.20: 5
  Bond angle restraints: 7832
  Sorted by residual:
  angle pdb=" C   GLU H 158 "
        pdb=" N   PRO H 159 "
        pdb=" CD  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     120.60  113.12    7.48 2.20e+00 2.07e-01 1.16e+01
  angle pdb=" N   TYR A 144 "
        pdb=" CA  TYR A 144 "
        pdb=" C   TYR A 144 "
      ideal   model   delta    sigma   weight residual
     108.46  113.39   -4.93 1.51e+00 4.39e-01 1.07e+01
  angle pdb=" CA  PRO H 159 "
        pdb=" N   PRO H 159 "
        pdb=" CD  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     111.50  107.46    4.04 1.40e+00 5.10e-01 8.34e+00
  angle pdb=" CA  GLU A  96 "
        pdb=" CB  GLU A  96 "
        pdb=" CG  GLU A  96 "
      ideal   model   delta    sigma   weight residual
     114.10  119.83   -5.73 2.00e+00 2.50e-01 8.21e+00
  angle pdb=" C   GLU H 158 "
        pdb=" N   PRO H 159 "
        pdb=" CA  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     127.00  133.63   -6.63 2.40e+00 1.74e-01 7.62e+00
  ... (remaining 7827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3112
       17.83 -    35.66: 280
       35.66 -    53.49: 54
       53.49 -    71.32: 8
       71.32 -    89.14: 4
  Dihedral angle restraints: 3458
    sinusoidal: 1396
      harmonic: 2062
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.85   56.15     1      1.00e+01 1.00e-02 4.25e+01
  dihedral pdb=" CA  THR A  19 "
           pdb=" C   THR A  19 "
           pdb=" N   THR A  20 "
           pdb=" CA  THR A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.77   27.23     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  PRO A  82 "
           pdb=" C   PRO A  82 "
           pdb=" N   VAL A  83 "
           pdb=" CA  VAL A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.13   25.87     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 3455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 839
       0.106 -    0.213: 32
       0.213 -    0.319: 2
       0.319 -    0.425: 1
       0.425 -    0.532: 1
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" C1  NAG A1304 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1304 "
            pdb=" O5  NAG A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.07e+00
  chirality pdb=" CB  ILE A 210 "
            pdb=" CA  ILE A 210 "
            pdb=" CG1 ILE A 210 "
            pdb=" CG2 ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE L  76 "
            pdb=" CA  ILE L  76 "
            pdb=" CG1 ILE L  76 "
            pdb=" CG2 ILE L  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 872 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L 119 "   -0.061 5.00e-02 4.00e+02   9.15e-02 1.34e+01
        pdb=" N   PRO L 120 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO L 120 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO L 120 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "   -0.057 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO H 159 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H 135 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO H 136 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO H 136 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 136 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 764
        2.74 -     3.28: 6066
        3.28 -     3.82: 9555
        3.82 -     4.36: 11231
        4.36 -     4.90: 18714
  Nonbonded interactions: 46330
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 156 "
            pdb=" OH  TYR A 160 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLN L 166 "
            pdb=" OG  SER L 171 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" NH2 ARG A 158 "
            pdb=" OD1 ASP H 101 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   GLN A  14 "
            pdb=" NH1 ARG A 158 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   TYR L 186 "
            pdb=" OH  TYR L 192 "
     model   vdw
     2.229 3.040
  ... (remaining 46325 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.620
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
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   0.061   5758  Z= 0.418
  Angle     :  0.825   8.203   7832  Z= 0.444
  Chirality :  0.053   0.532    875
  Planarity :  0.006   0.092   1000
  Dihedral  : 13.902  89.144   2126
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 21.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.74 (0.31), residues: 706
  helix: -2.65 (1.15), residues: 14
  sheet: -1.13 (0.31), residues: 269
  loop : -2.35 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 258 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.020   0.002   PHE L  72 
 TYR   0.035   0.002   TYR A 144 
 ARG   0.005   0.001   ARG H  72 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.6470 (t) cc_final: 0.6260 (t)
REVERT: A   56 LEU cc_start: 0.9064 (tp) cc_final: 0.8691 (tp)
REVERT: A  100 ILE cc_start: 0.9421 (tt) cc_final: 0.9202 (tt)
REVERT: H   90 ASP cc_start: 0.9094 (m-30) cc_final: 0.8846 (m-30)
REVERT: H   99 ASP cc_start: 0.9256 (t0) cc_final: 0.8997 (t0)
REVERT: H  104 TYR cc_start: 0.8107 (t80) cc_final: 0.7561 (t80)
REVERT: L   88 TYR cc_start: 0.9417 (m-80) cc_final: 0.9138 (m-80)
REVERT: L  139 PHE cc_start: 0.8581 (p90) cc_final: 0.8362 (p90)
REVERT: L  142 ARG cc_start: 0.8410 (tpt90) cc_final: 0.8165 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1632
  time to fit residues: 27.0233
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:   40.0000
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 ASN
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 138 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.103171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.073763 restraints weight = 13961.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.076824 restraints weight = 6968.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.078811 restraints weight = 4520.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5758  Z= 0.271
  Angle     :  0.773   9.241   7832  Z= 0.403
  Chirality :  0.051   0.461    875
  Planarity :  0.006   0.071   1000
  Dihedral  :  6.957  56.935    880
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.48 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.60 (0.30), residues: 706
  helix: -1.77 (1.17), residues: 14
  sheet: -1.03 (0.29), residues: 273
  loop : -2.30 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 258 
 HIS   0.008   0.001   HIS A 146 
 PHE   0.017   0.002   PHE L  72 
 TYR   0.022   0.002   TYR A 144 
 ARG   0.006   0.001   ARG L 108 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9062 (tp) cc_final: 0.8672 (tp)
REVERT: A   91 TYR cc_start: 0.9286 (t80) cc_final: 0.8894 (t80)
REVERT: A  156 GLU cc_start: 0.8620 (pt0) cc_final: 0.8239 (pt0)
REVERT: A  157 PHE cc_start: 0.8876 (m-80) cc_final: 0.8647 (m-10)
REVERT: H   90 ASP cc_start: 0.8984 (m-30) cc_final: 0.8665 (m-30)
REVERT: L   88 TYR cc_start: 0.9413 (m-80) cc_final: 0.9186 (m-80)
REVERT: L   90 GLN cc_start: 0.8662 (tt0) cc_final: 0.8336 (tt0)
REVERT: L  139 PHE cc_start: 0.8644 (p90) cc_final: 0.8304 (p90)
REVERT: L  142 ARG cc_start: 0.8472 (tpt90) cc_final: 0.8113 (tpt90)
  outliers start: 4
  outliers final: 3
  residues processed: 119
  average time/residue: 0.2086
  time to fit residues: 32.4403
Evaluate side-chains
  98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0670
   chunk 10 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.7918

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.106813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.077470 restraints weight = 13789.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.080544 restraints weight = 6824.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.082587 restraints weight = 4414.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5758  Z= 0.184
  Angle     :  0.716   8.006   7832  Z= 0.367
  Chirality :  0.049   0.417    875
  Planarity :  0.006   0.062   1000
  Dihedral  :  6.244  50.398    880
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.72 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.33 (0.30), residues: 706
  helix: -1.36 (1.26), residues: 14
  sheet: -0.83 (0.28), residues: 296
  loop : -2.19 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.025   0.002   PHE L 209 
 TYR   0.016   0.001   TYR A 145 
 ARG   0.004   0.001   ARG A 214 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9045 (p)
REVERT: A   56 LEU cc_start: 0.8989 (tp) cc_final: 0.8597 (tp)
REVERT: A  140 PHE cc_start: 0.9630 (p90) cc_final: 0.9057 (p90)
REVERT: A  154 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7894 (mt-10)
REVERT: A  156 GLU cc_start: 0.8522 (pt0) cc_final: 0.8153 (pt0)
REVERT: A  157 PHE cc_start: 0.8743 (m-80) cc_final: 0.8478 (m-10)
REVERT: A  248 TYR cc_start: 0.7481 (m-10) cc_final: 0.7275 (m-80)
REVERT: H   74 ASN cc_start: 0.8528 (m-40) cc_final: 0.7649 (m-40)
REVERT: H   90 ASP cc_start: 0.8963 (m-30) cc_final: 0.8572 (m-30)
REVERT: H  161 THR cc_start: 0.8961 (m) cc_final: 0.8629 (p)
REVERT: L   88 TYR cc_start: 0.9381 (m-80) cc_final: 0.9069 (m-80)
REVERT: L   90 GLN cc_start: 0.8667 (tt0) cc_final: 0.8446 (tt0)
REVERT: L  139 PHE cc_start: 0.8595 (p90) cc_final: 0.8335 (p90)
REVERT: L  140 TYR cc_start: 0.7825 (t80) cc_final: 0.7415 (t80)
REVERT: L  142 ARG cc_start: 0.8457 (tpt90) cc_final: 0.8013 (tpt90)
  outliers start: 11
  outliers final: 7
  residues processed: 138
  average time/residue: 0.1914
  time to fit residues: 33.5668
Evaluate side-chains
  111 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 ASN
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.078466 restraints weight = 14154.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.081587 restraints weight = 6959.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.083646 restraints weight = 4471.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5758  Z= 0.191
  Angle     :  0.713   9.678   7832  Z= 0.357
  Chirality :  0.049   0.405    875
  Planarity :  0.006   0.078   1000
  Dihedral  :  5.723  35.802    880
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.80 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.26 (0.30), residues: 706
  helix: -1.02 (1.36), residues: 14
  sheet: -0.82 (0.29), residues: 296
  loop : -2.11 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 258 
 HIS   0.007   0.001   HIS A 146 
 PHE   0.020   0.002   PHE L  72 
 TYR   0.014   0.001   TYR A 145 
 ARG   0.005   0.000   ARG A 214 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8937 (t0) cc_final: 0.8688 (t0)
REVERT: A   36 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9050 (p)
REVERT: A   56 LEU cc_start: 0.8987 (tp) cc_final: 0.8581 (tp)
REVERT: A  140 PHE cc_start: 0.9620 (p90) cc_final: 0.9065 (p90)
REVERT: A  154 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7838 (mt-10)
REVERT: A  156 GLU cc_start: 0.8496 (pt0) cc_final: 0.8117 (pt0)
REVERT: A  157 PHE cc_start: 0.8663 (m-80) cc_final: 0.8435 (m-10)
REVERT: A  191 GLU cc_start: 0.8617 (tt0) cc_final: 0.8320 (mt-10)
REVERT: H   36 TRP cc_start: 0.8562 (m100) cc_final: 0.8303 (m100)
REVERT: H   90 ASP cc_start: 0.8913 (m-30) cc_final: 0.8580 (m-30)
REVERT: H  161 THR cc_start: 0.8881 (m) cc_final: 0.8579 (p)
REVERT: L   88 TYR cc_start: 0.9402 (m-80) cc_final: 0.9071 (m-80)
REVERT: L   90 GLN cc_start: 0.8700 (tt0) cc_final: 0.8410 (tt0)
REVERT: L  139 PHE cc_start: 0.8570 (p90) cc_final: 0.8339 (p90)
REVERT: L  158 ASN cc_start: 0.7434 (p0) cc_final: 0.6667 (t0)
REVERT: L  192 TYR cc_start: 0.8642 (m-10) cc_final: 0.8382 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1781
  time to fit residues: 28.9733
Evaluate side-chains
  119 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 174 HIS
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.108380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.078714 restraints weight = 13929.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.081927 restraints weight = 7000.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.083969 restraints weight = 4543.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5758  Z= 0.182
  Angle     :  0.686   8.468   7832  Z= 0.347
  Chirality :  0.049   0.391    875
  Planarity :  0.005   0.059   1000
  Dihedral  :  5.406  25.356    880
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.29 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.21 (0.30), residues: 706
  helix: -0.93 (1.44), residues: 14
  sheet: -0.87 (0.28), residues: 315
  loop : -2.03 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 258 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.018   0.002   PHE L  47 
 TYR   0.023   0.001   TYR L 140 
 ARG   0.005   0.001   ARG A 246 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8913 (t0) cc_final: 0.8644 (t0)
REVERT: A   56 LEU cc_start: 0.8946 (tp) cc_final: 0.8547 (tp)
REVERT: A  140 PHE cc_start: 0.9591 (p90) cc_final: 0.9046 (p90)
REVERT: A  156 GLU cc_start: 0.8412 (pt0) cc_final: 0.8066 (pt0)
REVERT: A  157 PHE cc_start: 0.8567 (m-80) cc_final: 0.8320 (m-10)
REVERT: H   90 ASP cc_start: 0.8841 (m-30) cc_final: 0.8544 (m-30)
REVERT: H  101 ASP cc_start: 0.8390 (t0) cc_final: 0.8095 (t0)
REVERT: H  161 THR cc_start: 0.8911 (m) cc_final: 0.8614 (p)
REVERT: H  222 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8188 (mm-30)
REVERT: L   88 TYR cc_start: 0.9387 (m-80) cc_final: 0.8990 (m-80)
REVERT: L   90 GLN cc_start: 0.8578 (tt0) cc_final: 0.8292 (tt0)
REVERT: L  139 PHE cc_start: 0.8551 (p90) cc_final: 0.8335 (p90)
REVERT: L  142 ARG cc_start: 0.8351 (tpt90) cc_final: 0.7869 (tpt90)
REVERT: L  145 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8620 (mmmm)
  outliers start: 18
  outliers final: 14
  residues processed: 133
  average time/residue: 0.1827
  time to fit residues: 31.5158
Evaluate side-chains
  123 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 239 GLN
H  39 GLN
L  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.107644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.078049 restraints weight = 13789.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.081153 restraints weight = 7060.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083113 restraints weight = 4611.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5758  Z= 0.208
  Angle     :  0.683   8.303   7832  Z= 0.348
  Chirality :  0.048   0.387    875
  Planarity :  0.005   0.058   1000
  Dihedral  :  5.315  24.324    880
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.26 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.25 (0.30), residues: 706
  helix: -0.83 (1.50), residues: 14
  sheet: -0.91 (0.27), residues: 322
  loop : -2.07 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  36 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.020   0.002   PHE L  72 
 TYR   0.013   0.001   TYR L 140 
 ARG   0.005   0.001   ARG L 108 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8949 (tp) cc_final: 0.8565 (tp)
REVERT: A  140 PHE cc_start: 0.9590 (p90) cc_final: 0.9095 (p90)
REVERT: A  154 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: A  156 GLU cc_start: 0.8471 (pt0) cc_final: 0.8106 (pt0)
REVERT: A  157 PHE cc_start: 0.8607 (m-80) cc_final: 0.8322 (m-10)
REVERT: A  191 GLU cc_start: 0.8650 (mt-10) cc_final: 0.7972 (mm-30)
REVERT: H   90 ASP cc_start: 0.8860 (m-30) cc_final: 0.8569 (m-30)
REVERT: H  101 ASP cc_start: 0.8448 (t0) cc_final: 0.8125 (t0)
REVERT: H  161 THR cc_start: 0.8903 (m) cc_final: 0.8595 (p)
REVERT: L   37 TYR cc_start: 0.9200 (m-80) cc_final: 0.8724 (m-80)
REVERT: L   88 TYR cc_start: 0.9406 (m-80) cc_final: 0.9082 (m-80)
REVERT: L  142 ARG cc_start: 0.8352 (tpt90) cc_final: 0.7796 (tpt90)
  outliers start: 20
  outliers final: 14
  residues processed: 134
  average time/residue: 0.1977
  time to fit residues: 34.0547
Evaluate side-chains
  121 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    8.9990
   chunk 64 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.077503 restraints weight = 14237.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.080648 restraints weight = 7015.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.082673 restraints weight = 4525.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5758  Z= 0.247
  Angle     :  0.682   8.676   7832  Z= 0.351
  Chirality :  0.048   0.384    875
  Planarity :  0.005   0.045   1000
  Dihedral  :  5.397  24.369    880
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.56 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.20 (0.30), residues: 706
  helix: -0.73 (1.53), residues: 14
  sheet: -0.95 (0.27), residues: 330
  loop : -1.96 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.017   0.002   PHE L  72 
 TYR   0.027   0.002   TYR L 140 
 ARG   0.007   0.001   ARG L 108 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9019 (tp) cc_final: 0.8646 (tp)
REVERT: A  140 PHE cc_start: 0.9598 (p90) cc_final: 0.9041 (p90)
REVERT: A  154 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7801 (mt-10)
REVERT: A  156 GLU cc_start: 0.8578 (pt0) cc_final: 0.8159 (pt0)
REVERT: A  157 PHE cc_start: 0.8724 (m-80) cc_final: 0.8428 (m-10)
REVERT: A  191 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7997 (mm-30)
REVERT: H   90 ASP cc_start: 0.8903 (m-30) cc_final: 0.8581 (m-30)
REVERT: H  101 ASP cc_start: 0.8497 (t0) cc_final: 0.8197 (t0)
REVERT: H  161 THR cc_start: 0.8910 (m) cc_final: 0.8594 (p)
REVERT: L   37 TYR cc_start: 0.9249 (m-80) cc_final: 0.8720 (m-80)
REVERT: L   88 TYR cc_start: 0.9419 (m-80) cc_final: 0.9127 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1774
  time to fit residues: 30.6598
Evaluate side-chains
  121 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 5 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A 115 GLN
** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.106206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.076088 restraints weight = 14141.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.079216 restraints weight = 7022.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.081233 restraints weight = 4569.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   5758  Z= 0.284
  Angle     :  0.714   9.302   7832  Z= 0.370
  Chirality :  0.050   0.377    875
  Planarity :  0.005   0.047   1000
  Dihedral  :  5.576  28.613    880
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.53 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.19 (0.31), residues: 706
  helix: -0.72 (1.54), residues: 14
  sheet: -0.92 (0.27), residues: 325
  loop : -1.98 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.020   0.002   PHE L  47 
 TYR   0.030   0.002   TYR L 140 
 ARG   0.004   0.001   ARG L 142 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9049 (tp) cc_final: 0.8674 (tp)
REVERT: A  140 PHE cc_start: 0.9605 (p90) cc_final: 0.8976 (p90)
REVERT: A  154 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7907 (mt-10)
REVERT: A  156 GLU cc_start: 0.8549 (pt0) cc_final: 0.8130 (pt0)
REVERT: A  157 PHE cc_start: 0.8744 (m-80) cc_final: 0.8446 (m-10)
REVERT: A  191 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8227 (mt-10)
REVERT: H   90 ASP cc_start: 0.8919 (m-30) cc_final: 0.8618 (m-30)
REVERT: H  101 ASP cc_start: 0.8549 (t0) cc_final: 0.8249 (t0)
REVERT: L   37 TYR cc_start: 0.9250 (m-80) cc_final: 0.8796 (m-80)
REVERT: L   88 TYR cc_start: 0.9432 (m-80) cc_final: 0.9191 (m-80)
REVERT: L  139 PHE cc_start: 0.8439 (p90) cc_final: 0.8174 (p90)
REVERT: L  142 ARG cc_start: 0.8237 (tpt90) cc_final: 0.7783 (tpt90)
REVERT: L  192 TYR cc_start: 0.8629 (m-10) cc_final: 0.8350 (m-10)
  outliers start: 21
  outliers final: 19
  residues processed: 125
  average time/residue: 0.1709
  time to fit residues: 27.8175
Evaluate side-chains
  126 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0030
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0050
   overall best weight:    0.9406

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.079386 restraints weight = 14000.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.082619 restraints weight = 6816.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.084701 restraints weight = 4355.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5758  Z= 0.200
  Angle     :  0.707   9.399   7832  Z= 0.362
  Chirality :  0.049   0.360    875
  Planarity :  0.005   0.048   1000
  Dihedral  :  5.323  24.244    880
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.69 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -2.07 (0.31), residues: 706
  helix: -0.69 (1.52), residues: 14
  sheet: -0.84 (0.28), residues: 317
  loop : -1.89 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 258 
 HIS   0.001   0.001   HIS A 245 
 PHE   0.022   0.002   PHE L  47 
 TYR   0.030   0.001   TYR L 140 
 ARG   0.005   0.001   ARG A 214 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8996 (tp) cc_final: 0.8622 (tp)
REVERT: A  140 PHE cc_start: 0.9581 (p90) cc_final: 0.9030 (p90)
REVERT: A  156 GLU cc_start: 0.8584 (pt0) cc_final: 0.8145 (pt0)
REVERT: A  191 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8070 (mm-30)
REVERT: A  212 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8013 (tt)
REVERT: H   90 ASP cc_start: 0.8859 (m-30) cc_final: 0.8605 (m-30)
REVERT: H  161 THR cc_start: 0.8942 (m) cc_final: 0.8638 (p)
REVERT: H  204 TYR cc_start: 0.6091 (m-80) cc_final: 0.5780 (m-10)
REVERT: L   88 TYR cc_start: 0.9388 (m-80) cc_final: 0.9042 (m-80)
REVERT: L  142 ARG cc_start: 0.8197 (tpt90) cc_final: 0.7741 (tpt90)
REVERT: L  192 TYR cc_start: 0.8559 (m-10) cc_final: 0.8308 (m-10)
REVERT: L  195 GLU cc_start: 0.7804 (pm20) cc_final: 0.7311 (pm20)
  outliers start: 20
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1885
  time to fit residues: 32.6259
Evaluate side-chains
  120 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 56 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 44 optimal weight:    8.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.109909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.080211 restraints weight = 14066.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.083357 restraints weight = 7146.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.085380 restraints weight = 4676.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5758  Z= 0.200
  Angle     :  0.712  10.156   7832  Z= 0.363
  Chirality :  0.048   0.358    875
  Planarity :  0.005   0.050   1000
  Dihedral  :  5.200  25.957    880
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.69 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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 (0.31), residues: 706
  helix: -0.58 (1.55), residues: 14
  sheet: -0.60 (0.29), residues: 317
  loop : -2.02 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.025   0.002   PHE L  72 
 TYR   0.034   0.001   TYR L 140 
 ARG   0.004   0.001   ARG L  62 

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8946 (tp) cc_final: 0.8542 (tp)
REVERT: A  140 PHE cc_start: 0.9563 (p90) cc_final: 0.9088 (p90)
REVERT: A  156 GLU cc_start: 0.8300 (pt0) cc_final: 0.7895 (pt0)
REVERT: A  191 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7997 (mm-30)
REVERT: H   36 TRP cc_start: 0.8546 (m100) cc_final: 0.8324 (m100)
REVERT: H   90 ASP cc_start: 0.8843 (m-30) cc_final: 0.8629 (m-30)
REVERT: H  161 THR cc_start: 0.8923 (m) cc_final: 0.8610 (p)
REVERT: H  204 TYR cc_start: 0.6028 (m-80) cc_final: 0.5743 (m-10)
REVERT: L   37 TYR cc_start: 0.9163 (m-80) cc_final: 0.8742 (m-80)
REVERT: L   88 TYR cc_start: 0.9379 (m-80) cc_final: 0.9042 (m-80)
REVERT: L  140 TYR cc_start: 0.7382 (t80) cc_final: 0.7116 (t80)
REVERT: L  142 ARG cc_start: 0.8243 (tpt90) cc_final: 0.7763 (tpt90)
REVERT: L  192 TYR cc_start: 0.8629 (m-10) cc_final: 0.8392 (m-10)
REVERT: L  195 GLU cc_start: 0.7789 (pm20) cc_final: 0.7291 (pm20)
  outliers start: 18
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1771
  time to fit residues: 30.7241
Evaluate side-chains
  127 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0000
   chunk 4 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.111088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.081384 restraints weight = 14081.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.084642 restraints weight = 6856.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.086764 restraints weight = 4409.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5758  Z= 0.190
  Angle     :  0.715   8.945   7832  Z= 0.360
  Chirality :  0.048   0.353    875
  Planarity :  0.005   0.050   1000
  Dihedral  :  5.095  23.524    880
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.50 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    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: -1.94 (0.31), residues: 706
  helix: -0.61 (1.53), residues: 14
  sheet: -0.62 (0.29), residues: 312
  loop : -1.93 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 258 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.027   0.002   PHE L  72 
 TYR   0.030   0.001   TYR L 140 
 ARG   0.006   0.001   ARG A 214 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2150.50 seconds
wall clock time: 39 minutes 21.67 seconds (2361.67 seconds total)