Starting phenix.real_space_refine
on Tue Feb 11 10:13:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9q_35280/02_2025/8i9q_35280_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9q_35280/02_2025/8i9q_35280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9q_35280/02_2025/8i9q_35280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9q_35280/02_2025/8i9q_35280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9q_35280/02_2025/8i9q_35280_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9q_35280/02_2025/8i9q_35280_neut.cif"
  }
  resolution = 4.22
  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=   0.003 sd=   0.059
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      29      5.16       5
     C    3264      2.51       5
     N     897      2.21       5
     O     989      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5179
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 3832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 3832
          Classifications: {'peptide': 508}
          Link IDs: {'PTRANS': 14, 'TRANS': 493}
    Chain: "Q"
      Number of atoms: 1347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 1347
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 8, 'TRANS': 158}
  Time building chain proxies: 3.97, per 1000 atoms: 0.77
  Number of scatterers: 5179
  At special positions: 0
  Unit cell: (117.52, 118.65, 110.74, 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      29     16.00
     O     989      8.00
     N     897      7.00
     C    3264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 647.1 milliseconds
  

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1264

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      51.4% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'D' and resid 27 through 49
      removed outlier: 4.035A  pdb=" N   ILE D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 52
      No H-bonds generated for 'chain 'D' and resid 50 through 52'
    Processing helix  chain 'D' and resid 73 through 81
      removed outlier: 3.784A  pdb=" N   ILE D  77 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   MET D  81 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 102
      removed outlier: 3.543A  pdb=" N   LEU D  91 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 126
      removed outlier: 3.674A  pdb=" N   ILE D 111 " --> pdb=" O   THR D 107 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS D 122 " --> pdb=" O   ASP D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 152
      removed outlier: 3.572A  pdb=" N   GLU D 146 " --> pdb=" O   GLU D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 173
    Processing helix  chain 'D' and resid 188 through 194
    Processing helix  chain 'D' and resid 204 through 209
      removed outlier: 4.009A  pdb=" N   LYS D 209 " --> pdb=" O   ARG D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 291
      removed outlier: 4.332A  pdb=" N   MET D 272 " --> pdb=" O   ASP D 268 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   ASP D 273 " --> pdb=" O   TYR D 269 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG D 274 " --> pdb=" O   ALA D 270 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU D 276 " --> pdb=" O   MET D 272 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ARG D 277 " --> pdb=" O   ASP D 273 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU D 278 " --> pdb=" O   ARG D 274 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU D 284 " --> pdb=" O   ARG D 280 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU D 286 " --> pdb=" O   TYR D 282 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   VAL D 287 " --> pdb=" O   ILE D 283 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 320
    Processing helix  chain 'D' and resid 329 through 340
      removed outlier: 3.888A  pdb=" N   CYS D 337 " --> pdb=" O   ILE D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 401
      removed outlier: 3.581A  pdb=" N   ILE D 398 " --> pdb=" O   ASN D 394 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 419
      removed outlier: 3.640A  pdb=" N   LEU D 415 " --> pdb=" O   VAL D 411 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL D 416 " --> pdb=" O   ILE D 412 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   LYS D 417 " --> pdb=" O   ARG D 413 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS D 418 " --> pdb=" O   CYS D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 443
    Processing helix  chain 'D' and resid 445 through 459
      removed outlier: 4.454A  pdb=" N   TYR D 449 " --> pdb=" O   GLY D 445 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   CYS D 450 " --> pdb=" O   MET D 446 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU D 459 " --> pdb=" O   ALA D 455 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 460 through 470
      removed outlier: 3.598A  pdb=" N   THR D 464 " --> pdb=" O   VAL D 460 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 472 through 487
      removed outlier: 3.809A  pdb=" N   THR D 476 " --> pdb=" O   ASN D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 512 through 532
      removed outlier: 4.101A  pdb=" N   ALA D 518 " --> pdb=" O   VAL D 514 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 67 through 78
      removed outlier: 4.581A  pdb=" N   TYR Q  74 " --> pdb=" O   ALA Q  70 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ARG Q  75 " --> pdb=" O   ILE Q  71 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG Q  76 " --> pdb=" O   GLU Q  72 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 81 through 85
    Processing helix  chain 'Q' and resid 104 through 109
    Processing helix  chain 'Q' and resid 124 through 141
      removed outlier: 3.637A  pdb=" N   ALA Q 128 " --> pdb=" O   ILE Q 124 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU Q 129 " --> pdb=" O   PRO Q 125 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN Q 131 " --> pdb=" O   CYS Q 127 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN Q 132 " --> pdb=" O   ALA Q 128 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   HIS Q 133 " --> pdb=" O   LEU Q 129 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   SER Q 135 " --> pdb=" O   ASN Q 131 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG Q 139 " --> pdb=" O   SER Q 135 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS Q 140 " --> pdb=" O   GLY Q 136 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 181 through 185
    Processing helix  chain 'Q' and resid 190 through 196
    Processing helix  chain 'Q' and resid 204 through 208
    Processing helix  chain 'Q' and resid 220 through 231
      removed outlier: 4.348A  pdb=" N   VAL Q 224 " --> pdb=" O   LEU Q 220 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG Q 225 " --> pdb=" O   LEU Q 221 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER Q 227 " --> pdb=" O   SER Q 223 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 59 through 62
      removed outlier: 3.606A  pdb=" N   LYS D  59 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 153 through 154
      removed outlier: 3.590A  pdb=" N   ARG D 153 " --> pdb=" O   LEU D 421 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 299 through 301
      removed outlier: 7.077A  pdb=" N   ILE D 300 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'Q' and resid 95 through 96
      removed outlier: 7.682A  pdb=" N   LEU Q  95 " --> pdb=" O   LYS Q 148 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    207 hydrogen bonds defined for protein.
    597 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1640
        1.34 -     1.46: 540
        1.46 -     1.57: 3009
        1.57 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 5236
  Sorted by residual:
  bond pdb=" C   ILE Q 155 "
       pdb=" N   PRO Q 156 "
    ideal  model  delta    sigma   weight residual
    1.335  1.498 -0.162 1.36e-02 5.41e+03 1.43e+02
  bond pdb=" C   TYR Q 158 "
       pdb=" N   PRO Q 159 "
    ideal  model  delta    sigma   weight residual
    1.333  1.497 -0.164 1.44e-02 4.82e+03 1.29e+02
  bond pdb=" N   ARG Q 161 "
       pdb=" CA  ARG Q 161 "
    ideal  model  delta    sigma   weight residual
    1.457  1.518 -0.061 1.33e-02 5.65e+03 2.09e+01
  bond pdb=" N   CYS Q 154 "
       pdb=" CA  CYS Q 154 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.041 1.17e-02 7.31e+03 1.21e+01
  bond pdb=" N   ILE Q 155 "
       pdb=" CA  ILE Q 155 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.23e-02 6.61e+03 1.04e+01
  ... (remaining 5231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.12: 7018
        4.12 -     8.25: 38
        8.25 -    12.37: 4
       12.37 -    16.50: 2
       16.50 -    20.62: 2
  Bond angle restraints: 7064
  Sorted by residual:
  angle pdb=" C   TYR Q 158 "
        pdb=" N   PRO Q 159 "
        pdb=" CA  PRO Q 159 "
      ideal   model   delta    sigma   weight residual
     119.47  140.09  -20.62 1.16e+00 7.43e-01 3.16e+02
  angle pdb=" C   ILE Q 155 "
        pdb=" N   PRO Q 156 "
        pdb=" CA  PRO Q 156 "
      ideal   model   delta    sigma   weight residual
     119.05  137.20  -18.15 1.11e+00 8.12e-01 2.67e+02
  angle pdb=" C   PRO Q 159 "
        pdb=" CA  PRO Q 159 "
        pdb=" CB  PRO Q 159 "
      ideal   model   delta    sigma   weight residual
     112.26  102.02   10.24 1.67e+00 3.59e-01 3.76e+01
  angle pdb=" N   PRO Q 159 "
        pdb=" CD  PRO Q 159 "
        pdb=" CG  PRO Q 159 "
      ideal   model   delta    sigma   weight residual
     103.20   94.78    8.42 1.50e+00 4.44e-01 3.15e+01
  angle pdb=" N   PRO Q 156 "
        pdb=" CA  PRO Q 156 "
        pdb=" C   PRO Q 156 "
      ideal   model   delta    sigma   weight residual
     113.53  121.08   -7.55 1.39e+00 5.18e-01 2.95e+01
  ... (remaining 7059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 2925
       17.46 -    34.92: 281
       34.92 -    52.38: 52
       52.38 -    69.84: 11
       69.84 -    87.30: 6
  Dihedral angle restraints: 3275
    sinusoidal: 1328
      harmonic: 1947
  Sorted by residual:
  dihedral pdb=" CA  CYS D 221 "
           pdb=" C   CYS D 221 "
           pdb=" N   GLU D 222 "
           pdb=" CA  GLU D 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.79  -27.21     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  ILE Q 216 "
           pdb=" C   ILE Q 216 "
           pdb=" N   GLU Q 217 "
           pdb=" CA  GLU Q 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.70  -23.30     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" C   PRO Q 159 "
           pdb=" N   PRO Q 159 "
           pdb=" CA  PRO Q 159 "
           pdb=" CB  PRO Q 159 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.29  -11.41     0      2.50e+00 1.60e-01 2.08e+01
  ... (remaining 3272 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 620
       0.048 -    0.095: 173
       0.095 -    0.143: 53
       0.143 -    0.190: 9
       0.190 -    0.238: 6
  Chirality restraints: 861
  Sorted by residual:
  chirality pdb=" CA  PRO Q 156 "
            pdb=" N   PRO Q 156 "
            pdb=" C   PRO Q 156 "
            pdb=" CB  PRO Q 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  ILE Q 155 "
            pdb=" N   ILE Q 155 "
            pdb=" C   ILE Q 155 "
            pdb=" CB  ILE Q 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  VAL Q  94 "
            pdb=" N   VAL Q  94 "
            pdb=" C   VAL Q  94 "
            pdb=" CB  VAL Q  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 858 not shown)

  Planarity restraints: 894
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE Q 147 "    0.019 2.00e-02 2.50e+03   3.79e-02 1.43e+01
        pdb=" C   ILE Q 147 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   ILE Q 147 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LYS Q 148 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS Q 214 "   -0.058 5.00e-02 4.00e+02   8.92e-02 1.27e+01
        pdb=" N   PRO Q 215 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 215 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 215 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  64 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.35e+00
        pdb=" C   GLY D  64 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   GLY D  64 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LYS D  65 "    0.018 2.00e-02 2.50e+03
  ... (remaining 891 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.34: 17
        2.34 -     2.98: 2777
        2.98 -     3.62: 7797
        3.62 -     4.26: 10534
        4.26 -     4.90: 16543
  Nonbonded interactions: 37668
  Sorted by model distance:
  nonbonded pdb=" CE  LYS Q 121 "
            pdb=" O   PRO Q 159 "
     model   vdw
     1.697 3.440
  nonbonded pdb=" CG1 VAL Q  94 "
            pdb=" NZ  LYS Q 148 "
     model   vdw
     1.954 3.540
  nonbonded pdb=" CE1 TYR Q 158 "
            pdb=" OD1 ASN Q 162 "
     model   vdw
     1.969 3.340
  nonbonded pdb=" OG1 THR Q 190 "
            pdb=" OD1 ASP Q 192 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   ASN Q 157 "
            pdb=" ND2 ASN Q 157 "
     model   vdw
     2.161 3.120
  ... (remaining 37663 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.020
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
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      :  0.007   0.164   5236  Z= 0.465
  Angle     :  0.984  20.623   7064  Z= 0.599
  Chirality :  0.052   0.238    861
  Planarity :  0.005   0.089    894
  Dihedral  : 14.664  87.297   2011
  Min Nonbonded Distance : 1.697

Molprobity Statistics.
  All-atom Clashscore : 22.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.17 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.28), residues: 671
  helix: -1.30 (0.28), residues: 275
  sheet: -3.77 (0.58), residues: 49
  loop : -3.68 (0.27), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.003   0.001   HIS D 315 
 PHE   0.011   0.001   PHE D 335 
 TYR   0.017   0.002   TYR D 269 
 ARG   0.009   0.000   ARG D 413 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  272 MET cc_start: 0.7996 (tmm) cc_final: 0.7286 (tmm)
REVERT: D  279 GLU cc_start: 0.7575 (pt0) cc_final: 0.6811 (mm-30)
REVERT: D  391 ARG cc_start: 0.6703 (ptm-80) cc_final: 0.6404 (ptm-80)
REVERT: Q   69 ARG cc_start: 0.9642 (mtm180) cc_final: 0.9107 (ptp90)
REVERT: Q  160 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6019 (p0)
  outliers start: 5
  outliers final: 1
  residues processed: 74
  average time/residue: 0.2642
  time to fit residues: 23.5457
Evaluate side-chains
  57 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 27 optimal weight:    0.2980
   chunk 17 optimal weight:    0.0670
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0060
   overall best weight:    0.3934

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

Flipped N/Q/H residues before XYZ refinement:
D  98 GLN
D 231 GLN
D 296 ASN
D 318 ASN
D 350 GLN
D 484 HIS
** D 494 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 = 0.4610 r_free = 0.4610 target = 0.190197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.171218 restraints weight = 13595.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.172960 restraints weight = 25013.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.171310 restraints weight = 15970.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5812
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5236  Z= 0.170
  Angle     :  0.681   9.018   7064  Z= 0.344
  Chirality :  0.046   0.189    861
  Planarity :  0.004   0.055    894
  Dihedral  :  5.514  19.403    718
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  7.41 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.31), residues: 671
  helix:  0.11 (0.32), residues: 286
  sheet: -3.06 (0.66), residues: 45
  loop : -3.36 (0.29), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP Q  82 
 HIS   0.004   0.001   HIS D 484 
 PHE   0.011   0.001   PHE D 137 
 TYR   0.011   0.001   TYR Q 169 
 ARG   0.004   0.000   ARG D 419 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.652 
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: Q  165 THR cc_start: 0.8214 (p) cc_final: 0.7977 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2212
  time to fit residues: 23.2903
Evaluate side-chains
  59 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 3 optimal weight:   30.0000
   chunk 2 optimal weight:    0.0870
   chunk 13 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 122 GLN
Q 133 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.184650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.166269 restraints weight = 13015.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.165111 restraints weight = 19815.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.164784 restraints weight = 19035.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6002
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5236  Z= 0.237
  Angle     :  0.707   9.003   7064  Z= 0.358
  Chirality :  0.045   0.175    861
  Planarity :  0.004   0.058    894
  Dihedral  :  5.662  20.351    718
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.32), residues: 671
  helix:  0.35 (0.31), residues: 294
  sheet: -2.65 (0.66), residues: 53
  loop : -3.25 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.002   0.001   HIS D 347 
 PHE   0.016   0.002   PHE D 137 
 TYR   0.022   0.002   TYR Q 169 
 ARG   0.005   0.000   ARG D 391 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  210 GLU cc_start: 0.5537 (mp0) cc_final: 0.5173 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.2119
  time to fit residues: 18.2484
Evaluate side-chains
  51 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0870
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0070
   chunk 5 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
D  85 HIS
** D 494 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 = 0.4562 r_free = 0.4562 target = 0.185564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.167275 restraints weight = 13905.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.164419 restraints weight = 20433.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.163398 restraints weight = 22524.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6044
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5236  Z= 0.194
  Angle     :  0.673   8.730   7064  Z= 0.338
  Chirality :  0.044   0.182    861
  Planarity :  0.004   0.052    894
  Dihedral  :  5.398  18.453    718
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.32), residues: 671
  helix:  0.51 (0.32), residues: 295
  sheet: -2.25 (0.77), residues: 45
  loop : -3.13 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP Q 196 
 HIS   0.001   0.000   HIS D 347 
 PHE   0.013   0.001   PHE Q  91 
 TYR   0.008   0.001   TYR D 269 
 ARG   0.003   0.000   ARG D 391 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  210 GLU cc_start: 0.5508 (mp0) cc_final: 0.5133 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.2342
  time to fit residues: 19.4800
Evaluate side-chains
  50 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8988

-------------------------------------------------------------------------------
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 = 0.4579 r_free = 0.4579 target = 0.187137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.168757 restraints weight = 13527.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.167143 restraints weight = 20373.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.165789 restraints weight = 19149.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5994
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5236  Z= 0.172
  Angle     :  0.656   8.634   7064  Z= 0.328
  Chirality :  0.043   0.155    861
  Planarity :  0.004   0.041    894
  Dihedral  :  5.281  22.427    718
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.32), residues: 671
  helix:  0.47 (0.31), residues: 302
  sheet: -1.72 (0.82), residues: 43
  loop : -3.17 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP Q 114 
 HIS   0.001   0.000   HIS D 315 
 PHE   0.023   0.002   PHE D 137 
 TYR   0.013   0.001   TYR Q 169 
 ARG   0.009   0.000   ARG Q 225 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.2271
  time to fit residues: 19.2280
Evaluate side-chains
  52 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0370
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.5862

-------------------------------------------------------------------------------
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 = 0.4555 r_free = 0.4555 target = 0.185975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.171640 restraints weight = 14932.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.169082 restraints weight = 26572.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.166773 restraints weight = 22402.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5901
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5236  Z= 0.152
  Angle     :  0.651   9.963   7064  Z= 0.318
  Chirality :  0.044   0.217    861
  Planarity :  0.003   0.036    894
  Dihedral  :  5.077  22.179    718
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.32), residues: 671
  helix:  0.54 (0.31), residues: 303
  sheet: -1.37 (0.73), residues: 52
  loop : -2.96 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP Q 196 
 HIS   0.001   0.000   HIS Q 118 
 PHE   0.024   0.002   PHE D 137 
 TYR   0.008   0.001   TYR Q 169 
 ARG   0.004   0.000   ARG D 391 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7586 (tpt) cc_final: 0.7226 (mmm)
REVERT: Q  210 GLU cc_start: 0.5736 (mp0) cc_final: 0.5365 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1971
  time to fit residues: 16.2849
Evaluate side-chains
  53 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:   30.0000
   chunk 58 optimal weight:    0.4980
   chunk 14 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** D 394 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 = 0.4542 r_free = 0.4542 target = 0.184555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.171146 restraints weight = 14464.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.169162 restraints weight = 29014.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.166526 restraints weight = 24077.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5884
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5236  Z= 0.165
  Angle     :  0.680   9.306   7064  Z= 0.330
  Chirality :  0.044   0.209    861
  Planarity :  0.003   0.033    894
  Dihedral  :  5.008  20.164    718
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.33), residues: 671
  helix:  0.68 (0.31), residues: 298
  sheet: -0.96 (0.83), residues: 41
  loop : -2.78 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP Q 196 
 HIS   0.002   0.000   HIS D 347 
 PHE   0.015   0.001   PHE Q  91 
 TYR   0.014   0.001   TYR Q 169 
 ARG   0.005   0.000   ARG D 413 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7358 (tpt) cc_final: 0.7089 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2029
  time to fit residues: 16.3512
Evaluate side-chains
  53 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 13 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0770
   chunk 33 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 65 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.4716

-------------------------------------------------------------------------------
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 = 0.4560 r_free = 0.4560 target = 0.186314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.170371 restraints weight = 14523.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.170117 restraints weight = 26765.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.168004 restraints weight = 20785.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5863
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5236  Z= 0.152
  Angle     :  0.664   9.221   7064  Z= 0.323
  Chirality :  0.044   0.224    861
  Planarity :  0.003   0.033    894
  Dihedral  :  4.901  21.142    718
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.33), residues: 671
  helix:  0.70 (0.31), residues: 297
  sheet: -1.04 (0.76), residues: 52
  loop : -2.58 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP Q 196 
 HIS   0.001   0.000   HIS D 347 
 PHE   0.016   0.001   PHE Q  91 
 TYR   0.004   0.001   TYR D 269 
 ARG   0.003   0.000   ARG D 413 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7415 (tpt) cc_final: 0.7151 (mmm)
REVERT: Q  117 LEU cc_start: 0.9026 (mm) cc_final: 0.8747 (mm)
REVERT: Q  137 LEU cc_start: 0.7898 (mp) cc_final: 0.7671 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1896
  time to fit residues: 15.8274
Evaluate side-chains
  50 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:   40.0000
   chunk 43 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 60 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 51 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0470
   overall best weight:    1.3680

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

Flipped N/Q/H residues before XYZ refinement:
Q 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.183023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.169805 restraints weight = 13819.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.167313 restraints weight = 27130.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.164822 restraints weight = 22915.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5937
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5236  Z= 0.214
  Angle     :  0.713   8.982   7064  Z= 0.350
  Chirality :  0.045   0.221    861
  Planarity :  0.004   0.033    894
  Dihedral  :  5.169  20.982    718
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.33), residues: 671
  helix:  0.59 (0.31), residues: 305
  sheet: -0.65 (0.89), residues: 42
  loop : -2.81 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Q  82 
 HIS   0.004   0.001   HIS D 347 
 PHE   0.021   0.002   PHE Q  91 
 TYR   0.010   0.001   TYR Q 158 
 ARG   0.005   0.000   ARG D 413 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7394 (tpt) cc_final: 0.7187 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1847
  time to fit residues: 14.9442
Evaluate side-chains
  51 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0170
   chunk 31 optimal weight:    0.0030
   chunk 0 optimal weight:   30.0000
   chunk 5 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0970
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.2026

-------------------------------------------------------------------------------
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 = 0.4578 r_free = 0.4578 target = 0.188062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.172325 restraints weight = 14593.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.173470 restraints weight = 27916.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.171908 restraints weight = 16800.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.4814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5236  Z= 0.149
  Angle     :  0.671   9.054   7064  Z= 0.324
  Chirality :  0.045   0.236    861
  Planarity :  0.003   0.031    894
  Dihedral  :  4.773  22.048    718
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.33), residues: 671
  helix:  0.62 (0.31), residues: 306
  sheet: -1.02 (0.88), residues: 40
  loop : -2.51 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q 114 
 HIS   0.002   0.000   HIS D 406 
 PHE   0.014   0.001   PHE Q  91 
 TYR   0.005   0.001   TYR Q 169 
 ARG   0.002   0.000   ARG D 391 

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7392 (tpt) cc_final: 0.7165 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1878
  time to fit residues: 16.2131
Evaluate side-chains
  51 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0070
   chunk 43 optimal weight:    0.0170
   chunk 48 optimal weight:   30.0000
   chunk 10 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    0.9440

-------------------------------------------------------------------------------
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 = 0.4540 r_free = 0.4540 target = 0.184560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.169611 restraints weight = 14350.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.169338 restraints weight = 29184.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.167328 restraints weight = 19841.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5861
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5236  Z= 0.185
  Angle     :  0.702   8.896   7064  Z= 0.343
  Chirality :  0.045   0.222    861
  Planarity :  0.004   0.031    894
  Dihedral  :  4.854  23.917    718
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.26 (0.33), residues: 671
  helix:  0.70 (0.31), residues: 305
  sheet: -1.10 (0.87), residues: 40
  loop : -2.42 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.001   0.000   HIS D 129 
 PHE   0.024   0.002   PHE D 137 
 TYR   0.007   0.001   TYR D 269 
 ARG   0.004   0.000   ARG D 413 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1760.34 seconds
wall clock time: 32 minutes 45.62 seconds (1965.62 seconds total)