Starting phenix.real_space_refine
on Tue Mar  3 16:03:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0p_23099/03_2026/7l0p_23099.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0p_23099/03_2026/7l0p_23099.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2026/7l0p_23099.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2026/7l0p_23099.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2026/7l0p_23099.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2026/7l0p_23099.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4442      2.51       5
     N    1173      2.21       5
     O    1286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6953
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 2409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2409
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 298}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1791
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2385
          Classifications: {'peptide': 311}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 305}
    Chain: "G"
      Number of atoms: 310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 310
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 3, 'TRANS': 35}
  Time building chain proxies: 1.41, per 1000 atoms: 0.20
  Number of scatterers: 6953
  At special positions: 0
  Unit cell: (75.075, 109.725, 124.575, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1286      8.00
     N    1173      7.00
     C    4442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 225 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 315.9 milliseconds
  

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 11 sheets defined
      42.8% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'C' and resid 60 through 90
    Processing helix  chain 'C' and resid 102 through 128
      Proline residue:  C 122  - end of helix
    Processing helix  chain 'C' and resid 138 through 172
    Processing helix  chain 'C' and resid 173 through 180
    Processing helix  chain 'C' and resid 182 through 206
      Proline residue:  C 203  - end of helix
    Processing helix  chain 'C' and resid 230 through 269
      Proline residue:  C 249  - end of helix
    Processing helix  chain 'C' and resid 298 through 334
      removed outlier: 3.791A  pdb=" N   VAL C 313 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      Proline residue:  C 323  - end of helix
      removed outlier: 3.602A  pdb=" N   ILE C 334 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 371
      Proline residue:  C 366  - end of helix
    Processing helix  chain 'C' and resid 373 through 385
    Processing helix  chain 'A' and resid 4 through 7
    Processing helix  chain 'A' and resid 8 through 33
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.572A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 4.064A  pdb=" N   GLY A 203 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.605A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 4.755A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 48
    Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222
      removed outlier: 6.222A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 222
      removed outlier: 6.222A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.631A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.597A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105
      removed outlier: 5.870A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 153
      removed outlier: 6.527A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.760A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 235
      removed outlier: 4.573A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.427A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.90

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1876
        1.33 -     1.46: 1678
        1.46 -     1.58: 3463
        1.58 -     1.70: 0
        1.70 -     1.83: 75
  Bond restraints: 7092
  Sorted by residual:
  bond pdb=" N   ILE B 232 "
       pdb=" CA  ILE B 232 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.08e-02 8.57e+03 1.16e+01
  bond pdb=" N   PRO B 236 "
       pdb=" CA  PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.469  1.508 -0.039 1.28e-02 6.10e+03 9.45e+00
  bond pdb=" N   CYS B 233 "
       pdb=" CA  CYS B 233 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.82e+00
  bond pdb=" N   PHE B 234 "
       pdb=" CA  PHE B 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.21e-02 6.83e+03 6.21e+00
  bond pdb=" N   TYR C 333 "
       pdb=" CA  TYR C 333 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.31e-02 5.83e+03 5.67e+00
  ... (remaining 7087 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 9052
        1.97 -     3.93: 464
        3.93 -     5.90: 57
        5.90 -     7.87: 19
        7.87 -     9.84: 19
  Bond angle restraints: 9611
  Sorted by residual:
  angle pdb=" N   PRO C 297 "
        pdb=" CA  PRO C 297 "
        pdb=" CB  PRO C 297 "
      ideal   model   delta    sigma   weight residual
     103.25  111.61   -8.36 1.05e+00 9.07e-01 6.34e+01
  angle pdb=" C   PHE B 235 "
        pdb=" N   PRO B 236 "
        pdb=" CA  PRO B 236 "
      ideal   model   delta    sigma   weight residual
     119.84  127.37   -7.53 1.25e+00 6.40e-01 3.63e+01
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     122.08  129.12   -7.04 1.47e+00 4.63e-01 2.29e+01
  angle pdb=" C   SER C 335 "
        pdb=" N   ASP C 336 "
        pdb=" CA  ASP C 336 "
      ideal   model   delta    sigma   weight residual
     121.54  130.63   -9.09 1.91e+00 2.74e-01 2.26e+01
  angle pdb=" CA  ASN B 268 "
        pdb=" CB  ASN B 268 "
        pdb=" CG  ASN B 268 "
      ideal   model   delta    sigma   weight residual
     112.60  117.29   -4.69 1.00e+00 1.00e+00 2.20e+01
  ... (remaining 9606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 3588
       16.04 -    32.07: 454
       32.07 -    48.10: 122
       48.10 -    64.14: 20
       64.14 -    80.17: 6
  Dihedral angle restraints: 4190
    sinusoidal: 1611
      harmonic: 2579
  Sorted by residual:
  dihedral pdb=" CA  SER B 160 "
           pdb=" C   SER B 160 "
           pdb=" N   SER B 161 "
           pdb=" CA  SER B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.17  -23.83     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  LEU B 192 "
           pdb=" C   LEU B 192 "
           pdb=" N   ALA B 193 "
           pdb=" CA  ALA B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.73   23.27     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  PHE C 248 "
           pdb=" C   PHE C 248 "
           pdb=" N   PRO C 249 "
           pdb=" CA  PRO C 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.92   23.08     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 4187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 813
       0.060 -    0.119: 241
       0.119 -    0.179: 42
       0.179 -    0.239: 13
       0.239 -    0.298: 3
  Chirality restraints: 1112
  Sorted by residual:
  chirality pdb=" CA  PRO C 297 "
            pdb=" N   PRO C 297 "
            pdb=" C   PRO C 297 "
            pdb=" CB  PRO C 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  HIS C 133 "
            pdb=" N   HIS C 133 "
            pdb=" C   HIS C 133 "
            pdb=" CB  HIS C 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  ASN B 268 "
            pdb=" N   ASN B 268 "
            pdb=" C   ASN B 268 "
            pdb=" CB  ASN B 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1109 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 248 "   -0.063 5.00e-02 4.00e+02   9.43e-02 1.42e+01
        pdb=" N   PRO C 249 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO C 249 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C 249 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A   4 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   THR A   4 "    0.057 2.00e-02 2.50e+03
        pdb=" O   THR A   4 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A   5 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 340 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   THR A 340 "    0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 340 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 341 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1280
        2.76 -     3.30: 6656
        3.30 -     3.83: 11898
        3.83 -     4.37: 13500
        4.37 -     4.90: 23341
  Nonbonded interactions: 56675
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR C 146 "
            pdb=" OXT LEU D  13 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SER B 277 "
            pdb=" O   LEU B 318 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.301 3.040
  ... (remaining 56670 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.120
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093   7093  Z= 0.310
  Angle     :  1.062   9.835   9613  Z= 0.605
  Chirality :  0.061   0.298   1112
  Planarity :  0.007   0.094   1206
  Dihedral  : 15.233  80.175   2519
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.78 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 13.98 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.23), residues: 870
  helix: -2.20 (0.20), residues: 368
  sheet: -2.14 (0.39), residues: 151
  loop : -2.90 (0.28), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 327 
 TYR   0.014   0.002   TYR C 146 
 PHE   0.022   0.003   PHE A 189 
 TRP   0.019   0.003   TRP C 135 
 HIS   0.005   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 7092)
  covalent geometry    : angle       1.06192 ( 9611)
  SS BOND              : bond        0.00792 (    1)
  SS BOND              : angle       1.36555 (    2)
  hydrogen bonds       : bond        0.13497 (  367)
  hydrogen bonds       : angle       7.38435 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 221
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  263 LYS cc_start: 0.6987 (mmmm) cc_final: 0.6619 (ttmt)
REVERT: A  248 LYS cc_start: 0.8836 (tppt) cc_final: 0.8597 (tppt)
REVERT: A  318 GLU cc_start: 0.8543 (pt0) cc_final: 0.8282 (pt0)
REVERT: B   42 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8250 (ttm170)
REVERT: B   82 TRP cc_start: 0.8327 (m100) cc_final: 0.7966 (m100)
REVERT: B  172 GLU cc_start: 0.6589 (mp0) cc_final: 0.6310 (mp0)
REVERT: B  234 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7953 (m-80)
REVERT: B  241 PHE cc_start: 0.8760 (p90) cc_final: 0.8351 (p90)
REVERT: B  289 TYR cc_start: 0.8566 (m-10) cc_final: 0.8261 (m-10)
REVERT: G   55 LYS cc_start: 0.8655 (tttp) cc_final: 0.8015 (mmtt)
  outliers start: 4
  outliers final: 1
  residues processed: 225
  average time/residue: 0.0997
  time to fit residues: 28.7713
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 175
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 132 HIS
C 159 ASN
C 348 HIS
A 188 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.173909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.147140 restraints weight = 8804.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.145483 restraints weight = 10789.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.146438 restraints weight = 9817.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146997 restraints weight = 7727.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.147163 restraints weight = 7192.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7093  Z= 0.138
  Angle     :  0.658   7.647   9613  Z= 0.346
  Chirality :  0.044   0.177   1112
  Planarity :  0.005   0.081   1206
  Dihedral  :  5.760  58.990    955
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.48 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.96 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.26), residues: 870
  helix: -0.61 (0.24), residues: 376
  sheet: -1.76 (0.37), residues: 162
  loop : -2.58 (0.29), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 327 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.020   0.002   PHE C 344 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.004   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7092)
  covalent geometry    : angle       0.65681 ( 9611)
  SS BOND              : bond        0.00078 (    1)
  SS BOND              : angle       2.38922 (    2)
  hydrogen bonds       : bond        0.04481 (  367)
  hydrogen bonds       : angle       5.70683 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8812 (t) cc_final: 0.8604 (t)
REVERT: C  327 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7501 (ttp80)
REVERT: A   24 ARG cc_start: 0.6140 (mtt180) cc_final: 0.5666 (mtp-110)
REVERT: A  248 LYS cc_start: 0.8529 (tppt) cc_final: 0.8296 (tppt)
REVERT: A  304 GLN cc_start: 0.8143 (tt0) cc_final: 0.7806 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0763
  time to fit residues: 21.4673
Evaluate side-chains
  164 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN
** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 301 GLN
C 365 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.174021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155456 restraints weight = 8834.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.153926 restraints weight = 14311.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.152075 restraints weight = 13641.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.150670 restraints weight = 10241.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.151153 restraints weight = 9566.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7093  Z= 0.141
  Angle     :  0.624   6.972   9613  Z= 0.328
  Chirality :  0.043   0.173   1112
  Planarity :  0.005   0.078   1206
  Dihedral  :  5.474  61.101    955
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.75 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.01 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.27), residues: 870
  helix:  0.05 (0.26), residues: 379
  sheet: -1.75 (0.36), residues: 169
  loop : -2.37 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 327 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.022   0.002   PHE B 234 
 TRP   0.040   0.002   TRP B 339 
 HIS   0.005   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7092)
  covalent geometry    : angle       0.62352 ( 9611)
  SS BOND              : bond        0.00474 (    1)
  SS BOND              : angle       1.75779 (    2)
  hydrogen bonds       : bond        0.04195 (  367)
  hydrogen bonds       : angle       5.41115 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8837 (t) cc_final: 0.8571 (t)
REVERT: C  350 PHE cc_start: 0.8036 (t80) cc_final: 0.7832 (t80)
REVERT: A   24 ARG cc_start: 0.6145 (mtt180) cc_final: 0.5832 (mtp-110)
REVERT: A  248 LYS cc_start: 0.8548 (tppt) cc_final: 0.8270 (tppt)
REVERT: A  287 TYR cc_start: 0.7323 (m-80) cc_final: 0.7045 (m-10)
REVERT: B  339 TRP cc_start: 0.7493 (m-10) cc_final: 0.6982 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0900
  time to fit residues: 23.6290
Evaluate side-chains
  166 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
C 127 ASN
A 188 HIS
A 269 ASN
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.175977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.158013 restraints weight = 8779.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.156906 restraints weight = 13529.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.157000 restraints weight = 13231.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156704 restraints weight = 10202.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156673 restraints weight = 9816.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7093  Z= 0.138
  Angle     :  0.624   6.716   9613  Z= 0.329
  Chirality :  0.043   0.172   1112
  Planarity :  0.005   0.077   1206
  Dihedral  :  5.304  60.178    955
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.63 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.03 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.27), residues: 870
  helix:  0.43 (0.26), residues: 377
  sheet: -1.67 (0.37), residues: 173
  loop : -2.31 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 327 
 TYR   0.012   0.001   TYR C 324 
 PHE   0.018   0.001   PHE B 234 
 TRP   0.019   0.001   TRP B 339 
 HIS   0.005   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7092)
  covalent geometry    : angle       0.62366 ( 9611)
  SS BOND              : bond        0.00507 (    1)
  SS BOND              : angle       1.88730 (    2)
  hydrogen bonds       : bond        0.04092 (  367)
  hydrogen bonds       : angle       5.16791 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8768 (t) cc_final: 0.8482 (t)
REVERT: A   24 ARG cc_start: 0.6324 (mtt180) cc_final: 0.5935 (mtp-110)
REVERT: A   53 MET cc_start: 0.7140 (mmt) cc_final: 0.6934 (mmt)
REVERT: A  248 LYS cc_start: 0.8437 (tppt) cc_final: 0.8173 (tppt)
REVERT: A  287 TYR cc_start: 0.7115 (m-80) cc_final: 0.6831 (m-10)
REVERT: A  304 GLN cc_start: 0.8007 (tt0) cc_final: 0.7791 (tt0)
REVERT: A  312 LYS cc_start: 0.8162 (mttt) cc_final: 0.7719 (mmtt)
REVERT: B  264 TYR cc_start: 0.7497 (m-80) cc_final: 0.7259 (m-80)
REVERT: B  339 TRP cc_start: 0.7450 (m-10) cc_final: 0.6973 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0951
  time to fit residues: 25.1935
Evaluate side-chains
  167 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0670
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
C 270 GLN
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.172658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.154175 restraints weight = 8872.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.152980 restraints weight = 15135.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150489 restraints weight = 13823.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.148320 restraints weight = 10025.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.148864 restraints weight = 9396.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7093  Z= 0.158
  Angle     :  0.644   8.025   9613  Z= 0.337
  Chirality :  0.044   0.173   1112
  Planarity :  0.004   0.077   1206
  Dihedral  :  5.292  57.576    955
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.63 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.27), residues: 870
  helix:  0.50 (0.26), residues: 378
  sheet: -1.45 (0.39), residues: 168
  loop : -2.25 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 242 
 TYR   0.021   0.001   TYR B 264 
 PHE   0.021   0.002   PHE B 199 
 TRP   0.017   0.002   TRP B 339 
 HIS   0.004   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7092)
  covalent geometry    : angle       0.64335 ( 9611)
  SS BOND              : bond        0.00546 (    1)
  SS BOND              : angle       2.32992 (    2)
  hydrogen bonds       : bond        0.04057 (  367)
  hydrogen bonds       : angle       5.11685 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8846 (t) cc_final: 0.8630 (t)
REVERT: C  208 MET cc_start: 0.4121 (tpp) cc_final: 0.3816 (tpp)
REVERT: A   24 ARG cc_start: 0.6115 (mtt180) cc_final: 0.5833 (mtp-110)
REVERT: A  248 LYS cc_start: 0.8550 (tppt) cc_final: 0.8229 (tppt)
REVERT: A  312 LYS cc_start: 0.8299 (mttt) cc_final: 0.7809 (mmtt)
REVERT: B  220 GLN cc_start: 0.6806 (mm110) cc_final: 0.6438 (mm110)
REVERT: B  339 TRP cc_start: 0.7667 (m-10) cc_final: 0.6789 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 193
  average time/residue: 0.0896
  time to fit residues: 22.6963
Evaluate side-chains
  163 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0870
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
C 262 ASN
C 365 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.174563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155368 restraints weight = 8839.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.153019 restraints weight = 15307.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.154047 restraints weight = 15745.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.154070 restraints weight = 10494.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.154238 restraints weight = 8918.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7093  Z= 0.128
  Angle     :  0.612   8.393   9613  Z= 0.318
  Chirality :  0.043   0.174   1112
  Planarity :  0.004   0.075   1206
  Dihedral  :  5.084  56.503    955
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.29 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.28), residues: 870
  helix:  0.72 (0.26), residues: 378
  sheet: -1.46 (0.38), residues: 172
  loop : -2.11 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 327 
 TYR   0.011   0.001   TYR B  85 
 PHE   0.023   0.001   PHE A 199 
 TRP   0.017   0.001   TRP B 297 
 HIS   0.004   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7092)
  covalent geometry    : angle       0.61211 ( 9611)
  SS BOND              : bond        0.00331 (    1)
  SS BOND              : angle       1.35987 (    2)
  hydrogen bonds       : bond        0.03908 (  367)
  hydrogen bonds       : angle       4.98817 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8719 (t) cc_final: 0.8479 (t)
REVERT: A   24 ARG cc_start: 0.6207 (mtt180) cc_final: 0.5861 (mtp-110)
REVERT: A  227 LEU cc_start: 0.8059 (mt) cc_final: 0.7850 (mt)
REVERT: A  248 LYS cc_start: 0.8413 (tppt) cc_final: 0.8095 (tppt)
REVERT: A  312 LYS cc_start: 0.8208 (mttt) cc_final: 0.7855 (mmtt)
REVERT: B  339 TRP cc_start: 0.7628 (m-10) cc_final: 0.6869 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0900
  time to fit residues: 23.0451
Evaluate side-chains
  153 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 52 optimal weight:    0.2980
   chunk 26 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0010
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.4390

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.170503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.152481 restraints weight = 8886.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.151492 restraints weight = 15054.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.151763 restraints weight = 13371.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.151039 restraints weight = 11042.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.151118 restraints weight = 10431.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7093  Z= 0.173
  Angle     :  0.667   8.265   9613  Z= 0.347
  Chirality :  0.045   0.175   1112
  Planarity :  0.005   0.075   1206
  Dihedral  :  5.487  73.938    955
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.21 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.58 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.28), residues: 870
  helix:  0.72 (0.26), residues: 379
  sheet: -1.44 (0.40), residues: 172
  loop : -2.14 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 327 
 TYR   0.016   0.002   TYR B 264 
 PHE   0.031   0.002   PHE B 234 
 TRP   0.035   0.002   TRP B 297 
 HIS   0.004   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7092)
  covalent geometry    : angle       0.66669 ( 9611)
  SS BOND              : bond        0.00608 (    1)
  SS BOND              : angle       1.62865 (    2)
  hydrogen bonds       : bond        0.04029 (  367)
  hydrogen bonds       : angle       5.00579 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  310 LEU cc_start: 0.7355 (mp) cc_final: 0.7086 (mp)
REVERT: C  327 ARG cc_start: 0.7443 (ttp80) cc_final: 0.6603 (ttp80)
REVERT: A  227 LEU cc_start: 0.8101 (mt) cc_final: 0.7832 (mt)
REVERT: A  248 LYS cc_start: 0.8367 (tppt) cc_final: 0.8077 (tppt)
REVERT: A  312 LYS cc_start: 0.8239 (mttt) cc_final: 0.7931 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0887
  time to fit residues: 22.3164
Evaluate side-chains
  157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 365 ASN
A  52 GLN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.173154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.155759 restraints weight = 9002.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.154749 restraints weight = 15362.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.154225 restraints weight = 13575.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.152905 restraints weight = 12979.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.153403 restraints weight = 10515.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7093  Z= 0.142
  Angle     :  0.641   8.657   9613  Z= 0.335
  Chirality :  0.045   0.227   1112
  Planarity :  0.005   0.075   1206
  Dihedral  :  5.394  77.002    955
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.63 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.28), residues: 870
  helix:  0.79 (0.26), residues: 379
  sheet: -1.48 (0.39), residues: 175
  loop : -2.03 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 314 
 TYR   0.017   0.001   TYR B 124 
 PHE   0.018   0.002   PHE A 199 
 TRP   0.029   0.002   TRP B 297 
 HIS   0.009   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7092)
  covalent geometry    : angle       0.64130 ( 9611)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       1.27542 (    2)
  hydrogen bonds       : bond        0.03897 (  367)
  hydrogen bonds       : angle       4.92756 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8737 (t) cc_final: 0.8471 (t)
REVERT: C  327 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7062 (ttp80)
REVERT: A  227 LEU cc_start: 0.8075 (mt) cc_final: 0.7800 (mt)
REVERT: A  248 LYS cc_start: 0.8410 (tppt) cc_final: 0.8091 (tppt)
REVERT: A  312 LYS cc_start: 0.8220 (mttt) cc_final: 0.7929 (mmtt)
REVERT: B  264 TYR cc_start: 0.7390 (m-80) cc_final: 0.7097 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0822
  time to fit residues: 20.4372
Evaluate side-chains
  157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 72 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 73 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
A 213 HIS
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.180484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.158802 restraints weight = 8863.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.156268 restraints weight = 15905.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.156690 restraints weight = 14842.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.157227 restraints weight = 11918.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157130 restraints weight = 11199.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7093  Z= 0.132
  Angle     :  0.645   8.979   9613  Z= 0.338
  Chirality :  0.044   0.172   1112
  Planarity :  0.004   0.072   1206
  Dihedral  :  5.377  83.015    955
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.86 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.28), residues: 870
  helix:  0.83 (0.26), residues: 378
  sheet: -1.42 (0.40), residues: 172
  loop : -1.94 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 314 
 TYR   0.018   0.001   TYR C 154 
 PHE   0.024   0.002   PHE C 344 
 TRP   0.026   0.002   TRP B 297 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7092)
  covalent geometry    : angle       0.64491 ( 9611)
  SS BOND              : bond        0.00297 (    1)
  SS BOND              : angle       1.27343 (    2)
  hydrogen bonds       : bond        0.03948 (  367)
  hydrogen bonds       : angle       4.87319 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8683 (t) cc_final: 0.8445 (t)
REVERT: C  310 LEU cc_start: 0.7092 (mp) cc_final: 0.6841 (mp)
REVERT: C  327 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7009 (ttp80)
REVERT: A  214 CYS cc_start: 0.8008 (m) cc_final: 0.7629 (t)
REVERT: A  248 LYS cc_start: 0.8431 (tppt) cc_final: 0.8159 (tppt)
REVERT: A  312 LYS cc_start: 0.8204 (mttt) cc_final: 0.7948 (mmtt)
REVERT: B  264 TYR cc_start: 0.7320 (m-80) cc_final: 0.7042 (m-80)
REVERT: B  289 TYR cc_start: 0.8600 (m-10) cc_final: 0.8389 (m-10)
REVERT: G   67 LEU cc_start: 0.8214 (mm) cc_final: 0.8013 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0840
  time to fit residues: 20.4316
Evaluate side-chains
  160 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 60 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0020
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.180877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.161609 restraints weight = 9020.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.159817 restraints weight = 15885.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.156444 restraints weight = 14683.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.153863 restraints weight = 12798.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.154415 restraints weight = 10550.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7093  Z= 0.127
  Angle     :  0.634   9.097   9613  Z= 0.333
  Chirality :  0.045   0.263   1112
  Planarity :  0.004   0.072   1206
  Dihedral  :  5.377  85.972    955
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.86 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.28), residues: 870
  helix:  0.84 (0.26), residues: 379
  sheet: -1.39 (0.40), residues: 168
  loop : -1.79 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 314 
 TYR   0.014   0.001   TYR C 146 
 PHE   0.015   0.002   PHE A 199 
 TRP   0.028   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7092)
  covalent geometry    : angle       0.63394 ( 9611)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       0.94893 (    2)
  hydrogen bonds       : bond        0.03823 (  367)
  hydrogen bonds       : angle       4.81303 ( 1050)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: C  164 SER cc_start: 0.8772 (t) cc_final: 0.8521 (t)
REVERT: C  327 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7550 (ttp80)
REVERT: D    8 ARG cc_start: 0.5841 (mpt180) cc_final: 0.5622 (mpt180)
REVERT: A  248 LYS cc_start: 0.8450 (tppt) cc_final: 0.8193 (tppt)
REVERT: A  312 LYS cc_start: 0.8207 (mttt) cc_final: 0.7952 (mmtt)
REVERT: B  255 LEU cc_start: 0.8180 (mm) cc_final: 0.7901 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0796
  time to fit residues: 19.1488
Evaluate side-chains
  157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0270
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.180546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.161189 restraints weight = 8925.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.159262 restraints weight = 14956.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.159076 restraints weight = 14668.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.157778 restraints weight = 13218.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.158417 restraints weight = 11575.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7093  Z= 0.131
  Angle     :  0.639   8.904   9613  Z= 0.337
  Chirality :  0.044   0.242   1112
  Planarity :  0.004   0.072   1206
  Dihedral  :  5.177  75.513    955
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.86 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.28), residues: 870
  helix:  1.01 (0.26), residues: 373
  sheet: -1.16 (0.40), residues: 168
  loop : -1.73 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 314 
 TYR   0.018   0.001   TYR B 124 
 PHE   0.020   0.002   PHE A 199 
 TRP   0.028   0.002   TRP B 297 
 HIS   0.006   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7092)
  covalent geometry    : angle       0.63886 ( 9611)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.84280 (    2)
  hydrogen bonds       : bond        0.03801 (  367)
  hydrogen bonds       : angle       4.75223 ( 1050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1226.73 seconds
wall clock time: 21 minutes 59.20 seconds (1319.20 seconds total)