Starting phenix.real_space_refine
on Thu Mar  6 07:25:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exr_28660/03_2025/8exr_28660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exr_28660/03_2025/8exr_28660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exr_28660/03_2025/8exr_28660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exr_28660/03_2025/8exr_28660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exr_28660/03_2025/8exr_28660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exr_28660/03_2025/8exr_28660.cif"
  }
  resolution = 3.8
  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=   0.014
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       5      5.49       5
     S      20      5.16       5
     C    3438      2.51       5
     N     802      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5111
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2496
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 6, 'TRANS': 288}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 2051
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 6, 'TRANS': 234}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 445
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.52, per 1000 atoms: 0.69
  Number of scatterers: 5111
  At special positions: 0
  Unit cell: (72.38, 85.47, 93.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      20     16.00
     P       5     15.00
     O     844      8.00
     N     802      7.00
     C    3438      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: 1.36
  Conformation dependent library (CDL) restraints added in 534.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "


  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      70.7% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 3.858A  pdb=" N   TYR B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 48
      removed outlier: 4.065A  pdb=" N   LEU B  43 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 100 through 133
      removed outlier: 4.624A  pdb=" N   VAL B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 194 through 208
      removed outlier: 4.327A  pdb=" N   LEU B 200 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ASN B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.197A  pdb=" N   ILE B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 251
      removed outlier: 3.501A  pdb=" N   ILE B 232 " --> pdb=" O   PRO B 228 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ILE B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   HIS B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 271
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 329
      removed outlier: 3.534A  pdb=" N   PHE B 328 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 336
    Processing helix  chain 'A' and resid 2 through 31
      removed outlier: 3.529A  pdb=" N   ILE A  15 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 47
      removed outlier: 4.125A  pdb=" N   LEU A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.566A  pdb=" N   VAL A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 194 through 208
      removed outlier: 3.814A  pdb=" N   ASN A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 227 through 251
      removed outlier: 3.857A  pdb=" N   HIS A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LYS A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG A 235 " --> pdb=" O   HIS A 231 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 253
      No H-bonds generated for 'chain 'A' and resid 252 through 253'
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 257 through 271
      removed outlier: 3.752A  pdb=" N   VAL A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 299
      removed outlier: 3.734A  pdb=" N   LYS C 299 " --> pdb=" O   LEU C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 329
      removed outlier: 4.354A  pdb=" N   LEU C 311 " --> pdb=" O   SER C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 336
      removed outlier: 4.040A  pdb=" N   THR C 335 " --> pdb=" O   GLN C 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 164
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.685A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)

    299 hydrogen bonds defined for protein.
    870 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: 1.13

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.18 -     1.33: 1301
        1.33 -     1.47: 1570
        1.47 -     1.61: 2315
        1.61 -     1.75: 3
        1.75 -     1.89: 34
  Bond restraints: 5223
  Sorted by residual:
  bond pdb=" CB  HIS B 213 "
       pdb=" CG  HIS B 213 "
    ideal  model  delta    sigma   weight residual
    1.497  1.371  0.126 1.40e-02 5.10e+03 8.05e+01
  bond pdb=" CB  HIS B 153 "
       pdb=" CG  HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.372  0.125 1.40e-02 5.10e+03 7.94e+01
  bond pdb=" CB  PHE A 173 "
       pdb=" CG  PHE A 173 "
    ideal  model  delta    sigma   weight residual
    1.502  1.321  0.181 2.30e-02 1.89e+03 6.18e+01
  bond pdb=" NE1 TRP B  39 "
       pdb=" CE2 TRP B  39 "
    ideal  model  delta    sigma   weight residual
    1.370  1.285  0.085 1.10e-02 8.26e+03 6.00e+01
  bond pdb=" CB  HIS A 205 "
       pdb=" CG  HIS A 205 "
    ideal  model  delta    sigma   weight residual
    1.497  1.389  0.108 1.40e-02 5.10e+03 5.93e+01
  ... (remaining 5218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 6387
        3.28 -     6.57: 574
        6.57 -     9.85: 51
        9.85 -    13.13: 6
       13.13 -    16.42: 3
  Bond angle restraints: 7021
  Sorted by residual:
  angle pdb=" N   VAL A 160 "
        pdb=" CA  VAL A 160 "
        pdb=" C   VAL A 160 "
      ideal   model   delta    sigma   weight residual
     108.46  122.06  -13.60 1.49e+00 4.50e-01 8.33e+01
  angle pdb=" N   ARG A 194 "
        pdb=" CA  ARG A 194 "
        pdb=" C   ARG A 194 "
      ideal   model   delta    sigma   weight residual
     114.04  102.97   11.07 1.24e+00 6.50e-01 7.97e+01
  angle pdb=" N   VAL B 160 "
        pdb=" CA  VAL B 160 "
        pdb=" C   VAL B 160 "
      ideal   model   delta    sigma   weight residual
     108.46  121.66  -13.20 1.49e+00 4.50e-01 7.84e+01
  angle pdb=" CA  PHE B  30 "
        pdb=" CB  PHE B  30 "
        pdb=" CG  PHE B  30 "
      ideal   model   delta    sigma   weight residual
     113.80  105.18    8.62 1.00e+00 1.00e+00 7.44e+01
  angle pdb=" N   TRP B 174 "
        pdb=" CA  TRP B 174 "
        pdb=" C   TRP B 174 "
      ideal   model   delta    sigma   weight residual
     110.56  126.98  -16.42 1.94e+00 2.66e-01 7.16e+01
  ... (remaining 7016 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.09: 2907
       14.09 -    28.17: 148
       28.17 -    42.25: 49
       42.25 -    56.34: 30
       56.34 -    70.42: 11
  Dihedral angle restraints: 3145
    sinusoidal: 1362
      harmonic: 1783
  Sorted by residual:
  dihedral pdb=" C   PHE B 258 "
           pdb=" N   PHE B 258 "
           pdb=" CA  PHE B 258 "
           pdb=" CB  PHE B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.82   -7.78     0      2.50e+00 1.60e-01 9.68e+00
  dihedral pdb=" N   TYR B 155 "
           pdb=" C   TYR B 155 "
           pdb=" CA  TYR B 155 "
           pdb=" CB  TYR B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.57   -7.77     0      2.50e+00 1.60e-01 9.66e+00
  dihedral pdb=" CG  ARG A 235 "
           pdb=" CD  ARG A 235 "
           pdb=" NE  ARG A 235 "
           pdb=" CZ  ARG A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  143.09   36.91     2      1.50e+01 4.44e-03 7.69e+00
  ... (remaining 3142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 564
       0.117 -    0.234: 200
       0.234 -    0.351: 31
       0.351 -    0.468: 4
       0.468 -    0.584: 1
  Chirality restraints: 800
  Sorted by residual:
  chirality pdb=" C5  P6L A 702 "
            pdb=" C6  P6L A 702 "
            pdb=" C7  P6L A 702 "
            pdb=" O4  P6L A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.73   -0.58 2.00e-01 2.50e+01 8.54e+00
  chirality pdb=" CA  TRP B 174 "
            pdb=" N   TRP B 174 "
            pdb=" C   TRP B 174 "
            pdb=" CB  TRP B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CA  TYR B 155 "
            pdb=" N   TYR B 155 "
            pdb=" C   TYR B 155 "
            pdb=" CB  TYR B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 797 not shown)

  Planarity restraints: 823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 P6L B 702 "    0.079 2.00e-02 2.50e+03   1.61e-01 2.59e+02
        pdb=" C22 P6L B 702 "   -0.213 2.00e-02 2.50e+03
        pdb=" C23 P6L B 702 "    0.213 2.00e-02 2.50e+03
        pdb=" C24 P6L B 702 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 P6L A 702 "    0.077 2.00e-02 2.50e+03   1.53e-01 2.35e+02
        pdb=" C22 P6L A 702 "   -0.203 2.00e-02 2.50e+03
        pdb=" C23 P6L A 702 "    0.203 2.00e-02 2.50e+03
        pdb=" C24 P6L A 702 "   -0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C32 P6L A 702 "   -0.074 2.00e-02 2.50e+03   1.48e-01 2.18e+02
        pdb=" C33 P6L A 702 "    0.195 2.00e-02 2.50e+03
        pdb=" C34 P6L A 702 "   -0.195 2.00e-02 2.50e+03
        pdb=" C35 P6L A 702 "    0.074 2.00e-02 2.50e+03
  ... (remaining 820 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 76
        2.59 -     3.17: 5122
        3.17 -     3.75: 7615
        3.75 -     4.32: 10357
        4.32 -     4.90: 15033
  Nonbonded interactions: 38203
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.016 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.017 2.230
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.038 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.050 2.230
  nonbonded pdb=" O   GLY B 286 "
            pdb=" CG  LYS B 287 "
     model   vdw
     2.142 3.440
  ... (remaining 38198 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
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      :  0.026   0.181   5223  Z= 1.652
  Angle     :  1.944  16.416   7021  Z= 1.328
  Chirality :  0.115   0.584    800
  Planarity :  0.013   0.161    823
  Dihedral  : 12.156  70.423   1981
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.76 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.66 (0.32), residues: 580
  helix: -0.13 (0.24), residues: 383
  sheet: -0.25 (0.87), residues: 26
  loop : -0.87 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.009   TRP B  99 
 HIS   0.012   0.003   HIS A 153 
 PHE   0.033   0.006   PHE B 284 
 TYR   0.099   0.012   TYR A 203 
 ARG   0.006   0.001   ARG A  23 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 LEU cc_start: 0.8542 (mt) cc_final: 0.7864 (tt)
REVERT: B  136 LEU cc_start: 0.6840 (tp) cc_final: 0.6454 (tp)
REVERT: B  255 LYS cc_start: 0.8736 (mttt) cc_final: 0.8205 (mmtm)
REVERT: A  141 ASN cc_start: 0.7362 (m-40) cc_final: 0.6924 (p0)
REVERT: A  187 PHE cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80)
REVERT: A  219 ILE cc_start: 0.8605 (mm) cc_final: 0.8397 (mt)
REVERT: A  276 ASN cc_start: 0.6779 (p0) cc_final: 0.6314 (m-40)
REVERT: C  295 LEU cc_start: 0.8700 (mt) cc_final: 0.8423 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1923
  time to fit residues: 44.5331
Evaluate side-chains
  119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 271 ASN
A 271 ASN
C 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.187074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.165619 restraints weight = 10958.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.169805 restraints weight = 6817.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.172760 restraints weight = 4712.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5223  Z= 0.231
  Angle     :  0.727   7.174   7021  Z= 0.406
  Chirality :  0.045   0.222    800
  Planarity :  0.005   0.050    823
  Dihedral  : 13.274  72.724    725
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.41 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 11.52 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.97 (0.34), residues: 580
  helix:  1.39 (0.25), residues: 375
  sheet: -0.02 (1.00), residues: 35
  loop : -0.82 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 110 
 HIS   0.006   0.002   HIS B 213 
 PHE   0.026   0.002   PHE B  16 
 TYR   0.019   0.002   TYR B 127 
 ARG   0.006   0.001   ARG A 247 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 MET cc_start: 0.7427 (mmt) cc_final: 0.6892 (ptp)
REVERT: B   22 PHE cc_start: 0.7004 (m-80) cc_final: 0.6740 (m-80)
REVERT: B  136 LEU cc_start: 0.7343 (tp) cc_final: 0.6718 (mp)
REVERT: B  168 GLN cc_start: 0.6725 (mp10) cc_final: 0.6207 (mm-40)
REVERT: B  240 ASP cc_start: 0.8395 (m-30) cc_final: 0.8024 (t0)
REVERT: A  122 LEU cc_start: 0.8393 (mt) cc_final: 0.8160 (tp)
REVERT: A  138 LEU cc_start: 0.6470 (pt) cc_final: 0.6175 (pt)
REVERT: A  141 ASN cc_start: 0.7698 (m-40) cc_final: 0.7247 (p0)
REVERT: A  194 ARG cc_start: 0.6976 (ptt180) cc_final: 0.6620 (ptt180)
REVERT: C  295 LEU cc_start: 0.8603 (mt) cc_final: 0.7924 (tt)
  outliers start: 18
  outliers final: 9
  residues processed: 163
  average time/residue: 0.1520
  time to fit residues: 32.0825
Evaluate side-chains
  125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  328 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.188037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.166096 restraints weight = 11067.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.170331 restraints weight = 6885.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.173342 restraints weight = 4791.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5223  Z= 0.192
  Angle     :  0.648  11.169   7021  Z= 0.352
  Chirality :  0.043   0.193    800
  Planarity :  0.004   0.051    823
  Dihedral  : 12.012  88.966    725
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 15.96 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.98 (0.34), residues: 580
  helix:  1.49 (0.25), residues: 380
  sheet: -0.33 (1.09), residues: 32
  loop : -1.06 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.020   0.002   PHE A 173 
 TYR   0.023   0.002   TYR A 261 
 ARG   0.003   0.001   ARG A 247 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 MET cc_start: 0.7279 (mmt) cc_final: 0.7030 (ptm)
REVERT: B   22 PHE cc_start: 0.7077 (m-80) cc_final: 0.6769 (m-80)
REVERT: B  136 LEU cc_start: 0.7501 (tp) cc_final: 0.7100 (mp)
REVERT: B  162 ARG cc_start: 0.6480 (mtt180) cc_final: 0.6140 (ttm170)
REVERT: B  240 ASP cc_start: 0.8349 (m-30) cc_final: 0.8047 (t0)
REVERT: B  266 MET cc_start: 0.7001 (tpt) cc_final: 0.6718 (tpt)
REVERT: A   22 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7868 (t80)
REVERT: A  141 ASN cc_start: 0.7704 (m-40) cc_final: 0.7351 (p0)
REVERT: A  165 GLU cc_start: 0.6913 (pm20) cc_final: 0.6590 (pt0)
REVERT: A  246 ASP cc_start: 0.7212 (m-30) cc_final: 0.6987 (t0)
REVERT: C  300 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7956 (tm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 139
  average time/residue: 0.1452
  time to fit residues: 26.5483
Evaluate side-chains
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  328 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4272 r_free = 0.4272 target = 0.184725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.163468 restraints weight = 10210.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.167851 restraints weight = 6368.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.171065 restraints weight = 4365.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5223  Z= 0.188
  Angle     :  0.607   9.331   7021  Z= 0.334
  Chirality :  0.042   0.197    800
  Planarity :  0.004   0.050    823
  Dihedral  : 11.242  82.627    725
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.73 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.09 (0.34), residues: 580
  helix:  1.64 (0.26), residues: 378
  sheet: -0.58 (0.96), residues: 37
  loop : -1.09 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.019   0.002   PHE A 173 
 TYR   0.025   0.002   TYR A 186 
 ARG   0.003   0.000   ARG A 247 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: B   22 PHE cc_start: 0.6983 (m-80) cc_final: 0.6694 (m-80)
REVERT: B   23 ARG cc_start: 0.7704 (ttm170) cc_final: 0.7207 (ttm-80)
REVERT: B  240 ASP cc_start: 0.8551 (m-30) cc_final: 0.8231 (t0)
REVERT: A  141 ASN cc_start: 0.7454 (m-40) cc_final: 0.7237 (p0)
REVERT: A  165 GLU cc_start: 0.6940 (pm20) cc_final: 0.6721 (pt0)
REVERT: A  246 ASP cc_start: 0.7366 (m-30) cc_final: 0.7095 (t0)
REVERT: C  300 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8058 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1494
  time to fit residues: 26.8987
Evaluate side-chains
  129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4278 r_free = 0.4278 target = 0.185776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.164236 restraints weight = 10224.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.168588 restraints weight = 6373.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.171774 restraints weight = 4411.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.5935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5223  Z= 0.183
  Angle     :  0.624   8.628   7021  Z= 0.336
  Chirality :  0.042   0.206    800
  Planarity :  0.004   0.053    823
  Dihedral  : 10.652  76.622    725
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.04 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.18 (0.35), residues: 580
  helix:  1.77 (0.26), residues: 373
  sheet: -0.84 (0.92), residues: 37
  loop : -1.07 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.023   0.002   PHE C 328 
 TYR   0.020   0.002   TYR A 130 
 ARG   0.002   0.000   ARG B 162 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 PHE cc_start: 0.7008 (m-80) cc_final: 0.6690 (m-80)
REVERT: B  240 ASP cc_start: 0.8524 (m-30) cc_final: 0.8263 (t0)
REVERT: B  266 MET cc_start: 0.6917 (tpt) cc_final: 0.6673 (tpt)
REVERT: A  100 ASP cc_start: 0.4566 (m-30) cc_final: 0.3928 (t0)
REVERT: A  165 GLU cc_start: 0.7018 (pm20) cc_final: 0.6768 (pt0)
REVERT: A  246 ASP cc_start: 0.7308 (m-30) cc_final: 0.7015 (t0)
REVERT: A  271 ASN cc_start: 0.6425 (m-40) cc_final: 0.6113 (p0)
REVERT: C  300 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: C  330 MET cc_start: 0.5229 (tmm) cc_final: 0.4957 (tmm)
  outliers start: 19
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1534
  time to fit residues: 26.6115
Evaluate side-chains
  122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  287 LYS
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.186972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.166095 restraints weight = 10045.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.170543 restraints weight = 6304.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.173651 restraints weight = 4332.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.6300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5223  Z= 0.172
  Angle     :  0.599  11.663   7021  Z= 0.320
  Chirality :  0.041   0.184    800
  Planarity :  0.004   0.053    823
  Dihedral  : 10.163  70.369    725
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.81 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.16 (0.35), residues: 580
  helix:  1.84 (0.26), residues: 373
  sheet: -0.90 (0.93), residues: 36
  loop : -1.28 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.025   0.001   PHE C 328 
 TYR   0.016   0.002   TYR B 127 
 ARG   0.007   0.001   ARG B  23 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  240 ASP cc_start: 0.8611 (m-30) cc_final: 0.8234 (t0)
REVERT: B  266 MET cc_start: 0.6891 (tpt) cc_final: 0.6651 (tpt)
REVERT: A  100 ASP cc_start: 0.4392 (m-30) cc_final: 0.3918 (t0)
REVERT: A  142 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7232 (mt-10)
REVERT: A  165 GLU cc_start: 0.6926 (pm20) cc_final: 0.6725 (pt0)
REVERT: A  246 ASP cc_start: 0.7237 (m-30) cc_final: 0.6952 (t0)
REVERT: A  271 ASN cc_start: 0.6361 (m-40) cc_final: 0.6127 (p0)
REVERT: C  300 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: C  330 MET cc_start: 0.5315 (tmm) cc_final: 0.5100 (tmm)
  outliers start: 24
  outliers final: 14
  residues processed: 134
  average time/residue: 0.1402
  time to fit residues: 25.1066
Evaluate side-chains
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain C residue  287 LYS
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 278 ASN
A 152 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.186707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.165452 restraints weight = 9807.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.169927 restraints weight = 6056.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.173172 restraints weight = 4143.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.6540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5223  Z= 0.190
  Angle     :  0.612  10.815   7021  Z= 0.326
  Chirality :  0.042   0.184    800
  Planarity :  0.004   0.052    823
  Dihedral  : 10.156  75.956    725
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 23.58 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.03 (0.35), residues: 580
  helix:  1.80 (0.26), residues: 372
  sheet: -1.04 (0.93), residues: 36
  loop : -1.44 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 174 
 HIS   0.005   0.001   HIS B 213 
 PHE   0.021   0.002   PHE C 328 
 TYR   0.025   0.002   TYR A 175 
 ARG   0.007   0.001   ARG A 194 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: B  240 ASP cc_start: 0.8649 (m-30) cc_final: 0.8277 (t0)
REVERT: B  285 ASN cc_start: 0.6431 (m110) cc_final: 0.6034 (m-40)
REVERT: A  100 ASP cc_start: 0.4377 (m-30) cc_final: 0.3777 (t0)
REVERT: A  142 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7336 (mt-10)
REVERT: A  246 ASP cc_start: 0.7273 (m-30) cc_final: 0.6963 (t0)
REVERT: A  271 ASN cc_start: 0.6317 (m-40) cc_final: 0.6112 (p0)
REVERT: C  300 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8318 (tm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1341
  time to fit residues: 23.1497
Evaluate side-chains
  129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.189050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.167567 restraints weight = 10129.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.172145 restraints weight = 6283.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.175527 restraints weight = 4287.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.6874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5223  Z= 0.162
  Angle     :  0.616  10.924   7021  Z= 0.319
  Chirality :  0.042   0.179    800
  Planarity :  0.004   0.050    823
  Dihedral  :  9.747  81.173    725
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.58 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.10 (0.35), residues: 580
  helix:  1.87 (0.26), residues: 374
  sheet: -0.99 (0.98), residues: 36
  loop : -1.51 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.026   0.001   PHE B 151 
 TYR   0.020   0.002   TYR A 175 
 ARG   0.005   0.001   ARG B  23 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7476 (mp)
REVERT: B  186 TYR cc_start: 0.7588 (m-80) cc_final: 0.7120 (m-80)
REVERT: B  240 ASP cc_start: 0.8638 (m-30) cc_final: 0.8321 (t0)
REVERT: B  255 LYS cc_start: 0.8560 (mttt) cc_final: 0.8019 (mmtt)
REVERT: B  266 MET cc_start: 0.6870 (tpt) cc_final: 0.6649 (tpt)
REVERT: B  325 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6628 (pm20)
REVERT: A  123 LYS cc_start: 0.7935 (tttt) cc_final: 0.7674 (pttm)
REVERT: A  165 GLU cc_start: 0.7280 (pm20) cc_final: 0.6658 (pt0)
REVERT: A  246 ASP cc_start: 0.7144 (m-30) cc_final: 0.6840 (t0)
REVERT: A  271 ASN cc_start: 0.6303 (m-40) cc_final: 0.6068 (p0)
REVERT: C  300 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8321 (tm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1475
  time to fit residues: 27.3547
Evaluate side-chains
  132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.185873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.163928 restraints weight = 10182.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.168060 restraints weight = 6298.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.171117 restraints weight = 4382.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.6999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5223  Z= 0.191
  Angle     :  0.644  11.117   7021  Z= 0.338
  Chirality :  0.043   0.175    800
  Planarity :  0.004   0.049    823
  Dihedral  :  9.907  86.921    725
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.82 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.85 (0.35), residues: 580
  helix:  1.71 (0.26), residues: 377
  sheet: -1.00 (0.96), residues: 36
  loop : -1.79 (0.45), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 174 
 HIS   0.005   0.001   HIS B 213 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.016   0.002   TYR B 175 
 ARG   0.004   0.000   ARG B  23 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7375 (mt)
REVERT: B  186 TYR cc_start: 0.7538 (m-80) cc_final: 0.7091 (m-80)
REVERT: B  240 ASP cc_start: 0.8589 (m-30) cc_final: 0.8318 (t0)
REVERT: B  255 LYS cc_start: 0.8570 (mttt) cc_final: 0.8008 (mmtt)
REVERT: B  285 ASN cc_start: 0.6436 (m110) cc_final: 0.6026 (m-40)
REVERT: B  300 GLU cc_start: 0.6598 (mm-30) cc_final: 0.5659 (tp30)
REVERT: B  325 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6585 (pm20)
REVERT: A  246 ASP cc_start: 0.7381 (m-30) cc_final: 0.7077 (t0)
REVERT: C  300 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8408 (tm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1468
  time to fit residues: 25.7761
Evaluate side-chains
  129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  317 PHE
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 53 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0570
   chunk 18 optimal weight:    6.9990
   chunk 23 optimal weight:    0.2980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
** A 168 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 = 0.4341 r_free = 0.4341 target = 0.191598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.170527 restraints weight = 9729.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.175137 restraints weight = 5850.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.178528 restraints weight = 3911.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.7423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5223  Z= 0.162
  Angle     :  0.626  12.245   7021  Z= 0.321
  Chirality :  0.042   0.171    800
  Planarity :  0.004   0.050    823
  Dihedral  :  9.425  88.917    725
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 25.53 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.98 (0.35), residues: 580
  helix:  1.84 (0.26), residues: 373
  sheet: -0.87 (1.01), residues: 36
  loop : -1.75 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.022   0.001   PHE B 151 
 TYR   0.013   0.001   TYR A 261 
 ARG   0.004   0.000   ARG B  23 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7283 (mp)
REVERT: B  240 ASP cc_start: 0.8619 (m-30) cc_final: 0.8344 (t0)
REVERT: B  266 MET cc_start: 0.6803 (tpt) cc_final: 0.6552 (tpt)
REVERT: B  300 GLU cc_start: 0.6502 (mm-30) cc_final: 0.6040 (pp20)
REVERT: B  325 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6522 (pm20)
REVERT: A  211 THR cc_start: 0.8315 (p) cc_final: 0.7990 (p)
REVERT: C  300 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8395 (tm-30)
REVERT: C  325 GLN cc_start: 0.8312 (pp30) cc_final: 0.7916 (pp30)
  outliers start: 14
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1579
  time to fit residues: 28.3123
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
** A 168 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 = 0.4287 r_free = 0.4287 target = 0.186309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.164351 restraints weight = 10334.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.168686 restraints weight = 6334.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.171722 restraints weight = 4346.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.7363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5223  Z= 0.196
  Angle     :  0.652  10.944   7021  Z= 0.341
  Chirality :  0.043   0.170    800
  Planarity :  0.004   0.049    823
  Dihedral  :  9.564  86.681    725
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 26.42 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.90 (0.35), residues: 580
  helix:  1.76 (0.26), residues: 375
  sheet: -0.92 (0.98), residues: 36
  loop : -1.76 (0.44), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 174 
 HIS   0.005   0.001   HIS B 213 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.018   0.002   TYR B 175 
 ARG   0.004   0.000   ARG B  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1838.72 seconds
wall clock time: 32 minutes 44.12 seconds (1964.12 seconds total)