Starting phenix.real_space_refine
on Thu Jul 31 02:14:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uml_26603/07_2025/7uml_26603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uml_26603/07_2025/7uml_26603.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2025/7uml_26603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2025/7uml_26603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2025/7uml_26603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uml_26603/07_2025/7uml_26603.cif"
  }
  resolution = 3.5
  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=   0.053 sd=   1.358
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
     P      13      5.49       5
     S      37      5.16       5
     C    4272      2.51       5
     N    1126      2.21       5
     O    1302      1.98       5
     H    6477      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13227
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 5980
          Classifications: {'peptide': 379}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 361}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 2741
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 10, 'TRANS': 160}
    Chain: "C"
      Number of atoms: 2770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2770
          Classifications: {'peptide': 172}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 161}
    Chain: "D"
      Number of atoms: 551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 551
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 4, 'TRANS': 29}
    Chain: "E"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 531
          Classifications: {'peptide': 39}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 34}
    Chain: "F"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 263
          Classifications: {'peptide': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
    Chain: "R"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 391
          Classifications: {'RNA': 13}
          Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 1, 'rna3p': 11}
  Time building chain proxies: 6.92, per 1000 atoms: 0.52
  Number of scatterers: 13227
  At special positions: 0
  Unit cell: (143.65, 100.3, 114.75, 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)
     S      37     16.00
     P      13     15.00
     O    1302      8.00
     N    1126      7.00
     C    4272      6.00
     H    6477      1.00
    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: 3.62
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1516

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      38.2% alpha, 13.5% beta
      0 base pairs and 6 stacking pairs defined.
    Time for finding SS restraints: 6.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 33
      removed outlier: 3.732A  pdb=" N   PHE A  32 " --> pdb=" O   PRO A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 62
      removed outlier: 3.636A  pdb=" N   LYS A  60 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 77
      removed outlier: 3.539A  pdb=" N   VAL A  69 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 133 through 145
    Processing helix  chain 'A' and resid 149 through 169
      removed outlier: 4.075A  pdb=" N   THR A 161 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 167 " --> pdb=" O   GLN A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 189 through 205
    Processing helix  chain 'A' and resid 210 through 221
      removed outlier: 4.623A  pdb=" N   ILE A 218 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   VAL A 219 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A 220 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A 221 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 239
    Processing helix  chain 'A' and resid 241 through 248
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 294 through 307
    Processing helix  chain 'A' and resid 323 through 341
      removed outlier: 4.412A  pdb=" N   LEU A 327 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR A 328 " --> pdb=" O   TYR A 324 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   THR A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 377
    Processing helix  chain 'A' and resid 378 through 385
    Processing helix  chain 'A' and resid 390 through 401
    Processing helix  chain 'A' and resid 411 through 420
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 101 through 115
      removed outlier: 3.718A  pdb=" N   ASN B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 125
      removed outlier: 3.755A  pdb=" N   LEU B 123 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 193
    Processing helix  chain 'B' and resid 201 through 208
      removed outlier: 3.571A  pdb=" N   PHE B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
      removed outlier: 3.733A  pdb=" N   VAL C  84 " --> pdb=" O   THR C  80 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   HIS C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 100
      No H-bonds generated for 'chain 'C' and resid 98 through 100'
    Processing helix  chain 'C' and resid 101 through 115
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.593A  pdb=" N   LEU C 123 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 193
      removed outlier: 3.550A  pdb=" N   HIS C 192 " --> pdb=" O   ILE C 189 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   PHE C 193 " --> pdb=" O   TRP C 190 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 189 through 193'
    Processing helix  chain 'C' and resid 200 through 209
    Processing helix  chain 'D' and resid 27 through 35
      removed outlier: 4.510A  pdb=" N   TYR D  31 " --> pdb=" O   TYR D  27 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   SER D  35 " --> pdb=" O   TYR D  31 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42
      removed outlier: 6.420A  pdb=" N   LEU A  40 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90
    Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118
    Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 213
      removed outlier: 6.959A  pdb=" N   ILE B 211 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 143
    Processing sheet with id=AA6, first strand: chain 'D' and resid 13 through 14
      removed outlier: 3.578A  pdb=" N   ILE D  14 " --> pdb=" O   VAL D   5 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL D   5 " --> pdb=" O   ILE D  14 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   CYS E 349 " --> pdb=" O   LYS D   6 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    678 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      6 stacking parallelities
  Total time for adding SS restraints: 5.74

  Time building geometry restraints manager: 4.41 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6470
        1.03 -     1.23: 22
        1.23 -     1.42: 3001
        1.42 -     1.62: 3863
        1.62 -     1.81: 67
  Bond restraints: 13423
  Sorted by residual:
  bond pdb=" CA  PHE B 198 "
       pdb=" CB  PHE B 198 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.020 1.69e-02 3.50e+03 1.46e+00
  bond pdb=" N   GLY C 146 "
       pdb=" CA  GLY C 146 "
    ideal  model  delta    sigma   weight residual
    1.449  1.461 -0.012 1.45e-02 4.76e+03 6.88e-01
  bond pdb=" CA  PHE A 182 "
       pdb=" CB  PHE A 182 "
    ideal  model  delta    sigma   weight residual
    1.533  1.547 -0.014 1.66e-02 3.63e+03 6.66e-01
  bond pdb=" C   ASN B  75 "
       pdb=" N   ARG B  76 "
    ideal  model  delta    sigma   weight residual
    1.331  1.348 -0.017 2.07e-02 2.33e+03 6.56e-01
  bond pdb=" CB  PHE B  78 "
       pdb=" CG  PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.502  1.484  0.018 2.30e-02 1.89e+03 6.44e-01
  ... (remaining 13418 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 23603
        1.51 -     3.02: 543
        3.02 -     4.53: 50
        4.53 -     6.04: 7
        6.04 -     7.55: 2
  Bond angle restraints: 24205
  Sorted by residual:
  angle pdb=" C   SER C 224 "
        pdb=" N   ILE C 225 "
        pdb=" CA  ILE C 225 "
      ideal   model   delta    sigma   weight residual
     121.97  129.52   -7.55 1.80e+00 3.09e-01 1.76e+01
  angle pdb=" N   ILE C 225 "
        pdb=" CA  ILE C 225 "
        pdb=" C   ILE C 225 "
      ideal   model   delta    sigma   weight residual
     109.34  102.84    6.50 2.08e+00 2.31e-01 9.78e+00
  angle pdb=" C   ASP A  85 "
        pdb=" N   LYS A  86 "
        pdb=" CA  LYS A  86 "
      ideal   model   delta    sigma   weight residual
     121.54  127.24   -5.70 1.91e+00 2.74e-01 8.91e+00
  angle pdb=" C   LYS B 197 "
        pdb=" N   PHE B 198 "
        pdb=" CA  PHE B 198 "
      ideal   model   delta    sigma   weight residual
     121.54  127.06   -5.52 1.91e+00 2.74e-01 8.37e+00
  angle pdb=" N   PHE B 198 "
        pdb=" CA  PHE B 198 "
        pdb=" CB  PHE B 198 "
      ideal   model   delta    sigma   weight residual
     110.49  115.35   -4.86 1.69e+00 3.50e-01 8.27e+00
  ... (remaining 24200 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 6170
       34.69 -    69.38: 237
       69.38 -   104.07: 6
      104.07 -   138.76: 1
      138.76 -   173.45: 1
  Dihedral angle restraints: 6415
    sinusoidal: 3523
      harmonic: 2892
  Sorted by residual:
  dihedral pdb=" CA  ILE C 225 "
           pdb=" C   ILE C 225 "
           pdb=" N   SER C 226 "
           pdb=" CA  SER C 226 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.49  -46.51     0      5.00e+00 4.00e-02 8.65e+01
  dihedral pdb=" O4'   U R  36 "
           pdb=" C1'   U R  36 "
           pdb=" N1    U R  36 "
           pdb=" C2    U R  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   13.45 -173.45     1      1.50e+01 4.44e-03 8.51e+01
  dihedral pdb=" O4'   U R  27 "
           pdb=" C1'   U R  27 "
           pdb=" N1    U R  27 "
           pdb=" C2    U R  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -26.98 -133.02     1      1.50e+01 4.44e-03 7.18e+01
  ... (remaining 6412 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 703
       0.034 -    0.068: 223
       0.068 -    0.102: 57
       0.102 -    0.135: 26
       0.135 -    0.169: 6
  Chirality restraints: 1015
  Sorted by residual:
  chirality pdb=" C1'   U R  36 "
            pdb=" O4'   U R  36 "
            pdb=" C2'   U R  36 "
            pdb=" N1    U R  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.30    0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CA  ILE C 225 "
            pdb=" N   ILE C 225 "
            pdb=" C   ILE C 225 "
            pdb=" CB  ILE C 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL B  68 "
            pdb=" N   VAL B  68 "
            pdb=" C   VAL B  68 "
            pdb=" CB  VAL B  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1012 not shown)

  Planarity restraints: 1933
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 197 "   -0.013 2.00e-02 2.50e+03   2.70e-02 7.27e+00
        pdb=" C   LYS B 197 "    0.047 2.00e-02 2.50e+03
        pdb=" O   LYS B 197 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PHE B 198 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 128 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.22e+00
        pdb=" N   PRO C 129 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 160 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO B 161 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 161 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 161 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1930 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1020
        2.21 -     2.81: 26688
        2.81 -     3.41: 33005
        3.41 -     4.00: 42734
        4.00 -     4.60: 65211
  Nonbonded interactions: 168658
  Sorted by model distance:
  nonbonded pdb=" HE1 TRP B 190 "
            pdb=" O   TRP B 220 "
     model   vdw
     1.616 2.450
  nonbonded pdb=" HH  TYR A 152 "
            pdb=" OP2   U R  35 "
     model   vdw
     1.618 2.450
  nonbonded pdb=" H   SER A 291 "
            pdb=" OP2   U R  31 "
     model   vdw
     1.644 2.450
  nonbonded pdb=" O   ARG D   7 "
            pdb=" H   ASN D  11 "
     model   vdw
     1.659 2.450
  nonbonded pdb=" OE1 GLN E 346 "
            pdb=" H   TYR E 355 "
     model   vdw
     1.682 2.450
  ... (remaining 168653 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ 
 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 59 through 227))
  selection = (chain 'C' and resid 58 through 227)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             0.700
  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:             0.230
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     36.910
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  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:4.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
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      :  0.003   0.024   6946  Z= 0.116
  Angle     :  0.579   7.548   9448  Z= 0.314
  Chirality :  0.040   0.169   1015
  Planarity :  0.005   0.051   1173
  Dihedral  : 16.391 173.453   2661
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  2.01 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.22 %
    Twisted General : 0.26 %

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: -2.75 (0.27), residues: 798
  helix: -0.80 (0.30), residues: 273
  sheet: -0.74 (0.49), residues: 99
  loop : -2.91 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A  88 
 HIS   0.003   0.001   HIS A 298 
 PHE   0.013   0.001   PHE C 208 
 TYR   0.014   0.001   TYR B 178 
 ARG   0.003   0.000   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16876 (  247)
  hydrogen bonds       : angle       6.84100 (  678)
  covalent geometry    : bond        0.00254 ( 6946)
  covalent geometry    : angle       0.57850 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 TYR cc_start: 0.7194 (m-10) cc_final: 0.6984 (m-10)
REVERT: C  188 MET cc_start: 0.6581 (mmp) cc_final: 0.6269 (mmt)
REVERT: D    4 THR cc_start: 0.8169 (p) cc_final: 0.7964 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.4373
  time to fit residues: 100.8443
Evaluate side-chains
  132 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
E 347 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.193989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.168190 restraints weight = 31111.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.172939 restraints weight = 13799.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.175932 restraints weight = 7905.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4074 r_free = 0.4074    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4074 r_free = 0.4074    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.4074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6946  Z= 0.170
  Angle     :  0.586   4.916   9448  Z= 0.313
  Chirality :  0.040   0.159   1015
  Planarity :  0.005   0.042   1173
  Dihedral  : 14.891 172.064   1096
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  7.39 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.92 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.28 (0.28), residues: 798
  helix: -0.20 (0.31), residues: 278
  sheet: -0.64 (0.46), residues: 119
  loop : -2.86 (0.27), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 381 
 HIS   0.004   0.001   HIS C  90 
 PHE   0.013   0.001   PHE B 198 
 TYR   0.011   0.001   TYR B 140 
 ARG   0.003   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04996 (  247)
  hydrogen bonds       : angle       5.49666 (  678)
  covalent geometry    : bond        0.00392 ( 6946)
  covalent geometry    : angle       0.58552 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.6683 (p0) cc_final: 0.6187 (p0)
REVERT: B   92 ASP cc_start: 0.8021 (p0) cc_final: 0.7731 (p0)
REVERT: C  175 MET cc_start: 0.4167 (mtt) cc_final: 0.3842 (mtt)
REVERT: C  188 MET cc_start: 0.6966 (mmp) cc_final: 0.6583 (mmt)
REVERT: D    4 THR cc_start: 0.8360 (p) cc_final: 0.8115 (t)
  outliers start: 12
  outliers final: 11
  residues processed: 147
  average time/residue: 0.4004
  time to fit residues: 78.1212
Evaluate side-chains
  142 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain D residue   12 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 134 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.190030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.163113 restraints weight = 31636.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.167547 restraints weight = 15154.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.170471 restraints weight = 9249.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4019 r_free = 0.4019    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4019 r_free = 0.4019    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.4019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6946  Z= 0.208
  Angle     :  0.607   5.025   9448  Z= 0.327
  Chirality :  0.041   0.177   1015
  Planarity :  0.005   0.040   1173
  Dihedral  : 14.740 172.551   1096
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  9.52 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 10.79 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.31 (0.28), residues: 798
  helix: -0.18 (0.31), residues: 280
  sheet: -0.86 (0.45), residues: 119
  loop : -2.85 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 248 
 HIS   0.004   0.001   HIS C  90 
 PHE   0.013   0.002   PHE B 110 
 TYR   0.013   0.002   TYR B 140 
 ARG   0.003   0.000   ARG C  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04936 (  247)
  hydrogen bonds       : angle       5.48592 (  678)
  covalent geometry    : bond        0.00480 ( 6946)
  covalent geometry    : angle       0.60728 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ASP cc_start: 0.8047 (p0) cc_final: 0.7732 (p0)
REVERT: C  188 MET cc_start: 0.7029 (mmp) cc_final: 0.6578 (mmt)
REVERT: D    4 THR cc_start: 0.8361 (p) cc_final: 0.8095 (t)
  outliers start: 22
  outliers final: 17
  residues processed: 142
  average time/residue: 0.4152
  time to fit residues: 78.1245
Evaluate side-chains
  143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0170
   chunk 52 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5822

-------------------------------------------------------------------------------
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 = 0.194863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.169303 restraints weight = 30943.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.173997 restraints weight = 13612.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176920 restraints weight = 7859.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4067 r_free = 0.4067    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4067 r_free = 0.4067    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6946  Z= 0.107
  Angle     :  0.530   4.607   9448  Z= 0.281
  Chirality :  0.039   0.188   1015
  Planarity :  0.004   0.035   1173
  Dihedral  : 14.546 175.655   1096
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.89 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.67 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.93 (0.29), residues: 798
  helix:  0.19 (0.32), residues: 281
  sheet: -0.80 (0.45), residues: 119
  loop : -2.63 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 190 
 HIS   0.003   0.001   HIS A 298 
 PHE   0.009   0.001   PHE B 198 
 TYR   0.009   0.001   TYR A  72 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  247)
  hydrogen bonds       : angle       4.92081 (  678)
  covalent geometry    : bond        0.00243 ( 6946)
  covalent geometry    : angle       0.53038 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ASP cc_start: 0.8020 (p0) cc_final: 0.7719 (p0)
REVERT: C  188 MET cc_start: 0.7038 (mmp) cc_final: 0.6506 (mmt)
REVERT: D    4 THR cc_start: 0.8421 (p) cc_final: 0.8169 (t)
  outliers start: 13
  outliers final: 12
  residues processed: 142
  average time/residue: 0.4193
  time to fit residues: 79.9871
Evaluate side-chains
  142 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 26 optimal weight:    0.4980
   chunk 67 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0770
   chunk 68 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    1.0942

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.193577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.167499 restraints weight = 31378.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.171972 restraints weight = 14598.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.174887 restraints weight = 8747.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6946  Z= 0.132
  Angle     :  0.541   5.232   9448  Z= 0.285
  Chirality :  0.039   0.177   1015
  Planarity :  0.004   0.037   1173
  Dihedral  : 14.482 173.192   1096
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  8.02 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.24 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.86 (0.29), residues: 798
  helix:  0.18 (0.32), residues: 287
  sheet: -0.73 (0.46), residues: 119
  loop : -2.58 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 248 
 HIS   0.002   0.001   HIS C  90 
 PHE   0.011   0.001   PHE B 110 
 TYR   0.011   0.001   TYR B 140 
 ARG   0.003   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  247)
  hydrogen bonds       : angle       4.86866 (  678)
  covalent geometry    : bond        0.00309 ( 6946)
  covalent geometry    : angle       0.54149 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ASP cc_start: 0.7998 (p0) cc_final: 0.7673 (p0)
REVERT: C  188 MET cc_start: 0.6978 (mmp) cc_final: 0.6350 (mmt)
REVERT: D    4 THR cc_start: 0.8323 (p) cc_final: 0.8075 (t)
  outliers start: 18
  outliers final: 16
  residues processed: 141
  average time/residue: 0.4070
  time to fit residues: 75.4397
Evaluate side-chains
  144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  115 ASN
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    1.1562

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.192017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.165755 restraints weight = 31580.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.170351 restraints weight = 14222.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.173275 restraints weight = 8399.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6946  Z= 0.132
  Angle     :  0.536   4.321   9448  Z= 0.282
  Chirality :  0.039   0.174   1015
  Planarity :  0.004   0.037   1173
  Dihedral  : 14.425 173.351   1096
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  8.52 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.25 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.78 (0.29), residues: 798
  helix:  0.25 (0.32), residues: 287
  sheet: -0.69 (0.47), residues: 119
  loop : -2.53 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 248 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.013   0.001   PHE B 110 
 TYR   0.011   0.001   TYR B 140 
 ARG   0.003   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  247)
  hydrogen bonds       : angle       4.80363 (  678)
  covalent geometry    : bond        0.00306 ( 6946)
  covalent geometry    : angle       0.53597 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6525 (tmm)
REVERT: B   92 ASP cc_start: 0.8038 (p0) cc_final: 0.7706 (p0)
REVERT: C  188 MET cc_start: 0.6995 (mmp) cc_final: 0.6374 (mmt)
REVERT: D    4 THR cc_start: 0.8331 (p) cc_final: 0.8086 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 138
  average time/residue: 0.4112
  time to fit residues: 76.7981
Evaluate side-chains
  143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.192840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.166855 restraints weight = 31468.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.171512 restraints weight = 14088.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.174499 restraints weight = 8274.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6946  Z= 0.114
  Angle     :  0.525   4.453   9448  Z= 0.275
  Chirality :  0.039   0.173   1015
  Planarity :  0.004   0.037   1173
  Dihedral  : 14.384 173.605   1096
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.52 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.97 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.64 (0.29), residues: 798
  helix:  0.34 (0.32), residues: 291
  sheet: -0.61 (0.47), residues: 119
  loop : -2.45 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 190 
 HIS   0.002   0.001   HIS A 298 
 PHE   0.011   0.001   PHE B 110 
 TYR   0.012   0.001   TYR C 167 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  247)
  hydrogen bonds       : angle       4.66812 (  678)
  covalent geometry    : bond        0.00264 ( 6946)
  covalent geometry    : angle       0.52466 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6418 (tmm)
REVERT: B   92 ASP cc_start: 0.8022 (p0) cc_final: 0.7691 (p0)
REVERT: C  188 MET cc_start: 0.6933 (mmp) cc_final: 0.6375 (mmt)
REVERT: D    4 THR cc_start: 0.8347 (p) cc_final: 0.8124 (t)
  outliers start: 17
  outliers final: 16
  residues processed: 142
  average time/residue: 0.3930
  time to fit residues: 75.0825
Evaluate side-chains
  146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  115 ASN
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.188404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.161723 restraints weight = 31624.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.166351 restraints weight = 14561.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.169207 restraints weight = 8582.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6946  Z= 0.210
  Angle     :  0.603   4.629   9448  Z= 0.323
  Chirality :  0.042   0.172   1015
  Planarity :  0.005   0.039   1173
  Dihedral  : 14.445 171.123   1096
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  : 11.40 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.26 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.29), residues: 798
  helix:  0.25 (0.31), residues: 282
  sheet: -0.55 (0.48), residues: 111
  loop : -2.60 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 248 
 HIS   0.004   0.001   HIS B 143 
 PHE   0.012   0.002   PHE A 105 
 TYR   0.015   0.002   TYR B 140 
 ARG   0.003   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04454 (  247)
  hydrogen bonds       : angle       5.12782 (  678)
  covalent geometry    : bond        0.00491 ( 6946)
  covalent geometry    : angle       0.60347 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6560 (tmm)
REVERT: B   92 ASP cc_start: 0.8148 (p0) cc_final: 0.7792 (p0)
REVERT: C  188 MET cc_start: 0.6974 (mmp) cc_final: 0.6457 (mmt)
REVERT: D    4 THR cc_start: 0.8361 (p) cc_final: 0.8101 (t)
  outliers start: 20
  outliers final: 19
  residues processed: 139
  average time/residue: 0.3843
  time to fit residues: 71.6084
Evaluate side-chains
  148 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  115 ASN
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.190957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.164546 restraints weight = 31515.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.169322 restraints weight = 14392.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.172266 restraints weight = 8362.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6946  Z= 0.128
  Angle     :  0.549   4.684   9448  Z= 0.289
  Chirality :  0.039   0.182   1015
  Planarity :  0.005   0.042   1173
  Dihedral  : 14.358 174.170   1096
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.77 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.98 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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: -1.62 (0.29), residues: 798
  helix:  0.47 (0.32), residues: 282
  sheet: -0.82 (0.46), residues: 121
  loop : -2.40 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 190 
 HIS   0.002   0.001   HIS A 298 
 PHE   0.012   0.001   PHE B 110 
 TYR   0.013   0.001   TYR A 277 
 ARG   0.003   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  247)
  hydrogen bonds       : angle       4.80360 (  678)
  covalent geometry    : bond        0.00296 ( 6946)
  covalent geometry    : angle       0.54863 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6426 (tmm)
REVERT: B   92 ASP cc_start: 0.8079 (p0) cc_final: 0.7705 (p0)
REVERT: C  188 MET cc_start: 0.6926 (mmp) cc_final: 0.6345 (mmt)
REVERT: D    4 THR cc_start: 0.8363 (p) cc_final: 0.8120 (t)
  outliers start: 17
  outliers final: 15
  residues processed: 141
  average time/residue: 0.3742
  time to fit residues: 71.0298
Evaluate side-chains
  144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   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 = 0.4251 r_free = 0.4251 target = 0.190373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.164317 restraints weight = 31297.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.168972 restraints weight = 14208.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.171947 restraints weight = 8292.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6946  Z= 0.143
  Angle     :  0.560   4.800   9448  Z= 0.295
  Chirality :  0.040   0.176   1015
  Planarity :  0.005   0.043   1173
  Dihedral  : 14.353 172.201   1096
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.78 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.41 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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: -1.55 (0.29), residues: 798
  helix:  0.50 (0.32), residues: 282
  sheet: -0.46 (0.48), residues: 111
  loop : -2.41 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 190 
 HIS   0.003   0.001   HIS A 298 
 PHE   0.011   0.001   PHE B 110 
 TYR   0.014   0.001   TYR B 140 
 ARG   0.004   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  247)
  hydrogen bonds       : angle       4.78671 (  678)
  covalent geometry    : bond        0.00334 ( 6946)
  covalent geometry    : angle       0.56040 ( 9448)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6538 (tmm)
REVERT: B   92 ASP cc_start: 0.8066 (p0) cc_final: 0.7678 (p0)
REVERT: C  188 MET cc_start: 0.6927 (mmp) cc_final: 0.6389 (mmt)
REVERT: D    4 THR cc_start: 0.8361 (p) cc_final: 0.8118 (t)
  outliers start: 16
  outliers final: 14
  residues processed: 138
  average time/residue: 0.3824
  time to fit residues: 72.7262
Evaluate side-chains
  143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   88 TRP
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   12 THR
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue   46 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.190950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.164885 restraints weight = 31412.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.169580 restraints weight = 14147.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.172546 restraints weight = 8238.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6946  Z= 0.129
  Angle     :  0.547   4.789   9448  Z= 0.287
  Chirality :  0.040   0.175   1015
  Planarity :  0.005   0.093   1173
  Dihedral  : 14.324 173.097   1096
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.78 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.41 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.13 %
    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: -1.49 (0.29), residues: 798
  helix:  0.58 (0.32), residues: 282
  sheet: -0.46 (0.49), residues: 109
  loop : -2.39 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 190 
 HIS   0.002   0.001   HIS A 298 
 PHE   0.011   0.001   PHE B 110 
 TYR   0.013   0.001   TYR B 140 
 ARG   0.003   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  247)
  hydrogen bonds       : angle       4.70118 (  678)
  covalent geometry    : bond        0.00302 ( 6946)
  covalent geometry    : angle       0.54709 ( 9448)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5060.69 seconds
wall clock time: 88 minutes 41.13 seconds (5321.13 seconds total)