Starting phenix.real_space_refine
on Thu Mar  6 06:48:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9q_35280/03_2025/8i9q_35280_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9q_35280/03_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_35280/03_2025/8i9q_35280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9q_35280/03_2025/8i9q_35280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9q_35280/03_2025/8i9q_35280_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9q_35280/03_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-5624/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: 3.99, 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: 1.32
  Conformation dependent library (CDL) restraints added in 673.1 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: 0.57
  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: 1.27

  Time building geometry restraints manager: 1.56 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:             1.950
  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:                     16.560
  Find NCS groups from input model:        0.050
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.050
-------------------------------------------------------------------------------
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  : 0.641 
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: 0.2686
  time to fit residues: 23.9947
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  : 0.638 
-------------------------------------------------------------------------------
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:    5.9990
   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 = 0.190193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.171235 restraints weight = 13597.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.172982 restraints weight = 24968.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.171309 restraints weight = 15946.702|
|-----------------------------------------------------------------------------|
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  : 0.531 
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: 0.8213 (p) cc_final: 0.7976 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2227
  time to fit residues: 23.2710
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  : 0.530 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:   30.0000
   chunk 2 optimal weight:    0.2980
   chunk 13 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0770
   chunk 5 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.4744

-------------------------------------------------------------------------------
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 133 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.185247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.165617 restraints weight = 13489.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.165617 restraints weight = 19836.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.165617 restraints weight = 19836.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5991
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5236  Z= 0.228
  Angle     :  0.698   8.910   7064  Z= 0.353
  Chirality :  0.045   0.166    861
  Planarity :  0.004   0.056    894
  Dihedral  :  5.608  20.149    718
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  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: -2.29 (0.32), residues: 671
  helix:  0.33 (0.31), residues: 295
  sheet: -2.68 (0.66), residues: 53
  loop : -3.23 (0.30), residues: 323

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   0.014   0.002   PHE D 137 
 TYR   0.021   0.002   TYR Q 169 
 ARG   0.003   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  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  210 GLU cc_start: 0.5674 (mp0) cc_final: 0.5292 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.2556
  time to fit residues: 22.1986
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  : 0.779 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 65 optimal weight:    0.4980
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 50 optimal weight:    0.4980
   chunk 5 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
D  85 HIS
D 347 HIS
** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 122 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.180175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.161317 restraints weight = 13934.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.159623 restraints weight = 20896.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.158957 restraints weight = 20479.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6148
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5236  Z= 0.305
  Angle     :  0.766   8.686   7064  Z= 0.389
  Chirality :  0.047   0.193    861
  Planarity :  0.004   0.065    894
  Dihedral  :  5.899  19.437    718
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.73 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  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: -2.09 (0.32), residues: 671
  helix:  0.52 (0.32), residues: 289
  sheet: -2.44 (0.79), residues: 45
  loop : -3.13 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Q  82 
 HIS   0.003   0.001   HIS D 347 
 PHE   0.012   0.002   PHE Q  91 
 TYR   0.019   0.002   TYR Q 169 
 ARG   0.004   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
  60 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.3704
  time to fit residues: 27.6753
Evaluate side-chains
  45 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0060
   chunk 59 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.4154

-------------------------------------------------------------------------------
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 = 0.4593 r_free = 0.4593 target = 0.188316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.169066 restraints weight = 13602.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.166548 restraints weight = 19902.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.164322 restraints weight = 18993.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6032
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5236  Z= 0.155
  Angle     :  0.664   8.750   7064  Z= 0.331
  Chirality :  0.044   0.166    861
  Planarity :  0.004   0.043    894
  Dihedral  :  5.279  18.302    718
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  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: -1.94 (0.32), residues: 671
  helix:  0.53 (0.31), residues: 293
  sheet: -1.84 (0.81), residues: 43
  loop : -3.05 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.001   0.000   HIS D 406 
 PHE   0.027   0.002   PHE D 137 
 TYR   0.008   0.001   TYR Q  74 
 ARG   0.010   0.001   ARG D  49 

*********************** 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
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  260 MET cc_start: 0.3792 (ptt) cc_final: 0.3402 (ptt)
REVERT: Q  117 LEU cc_start: 0.8966 (mm) cc_final: 0.8758 (mm)
REVERT: Q  124 ILE cc_start: 0.8550 (mm) cc_final: 0.8330 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2742
  time to fit residues: 24.1997
Evaluate side-chains
  54 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0770
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0970
   chunk 26 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7738

-------------------------------------------------------------------------------
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 = 0.4543 r_free = 0.4543 target = 0.184074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.163333 restraints weight = 14912.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.162504 restraints weight = 21012.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.161831 restraints weight = 19040.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6077
moved from start:          0.3881

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= 0.162
  Angle     :  0.668   9.856   7064  Z= 0.326
  Chirality :  0.044   0.205    861
  Planarity :  0.004   0.038    894
  Dihedral  :  5.138  18.781    718
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  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: -1.83 (0.32), residues: 671
  helix:  0.50 (0.31), residues: 302
  sheet: -1.62 (0.75), residues: 51
  loop : -3.00 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP Q 196 
 HIS   0.001   0.000   HIS D 315 
 PHE   0.024   0.002   PHE D 137 
 TYR   0.011   0.001   TYR Q 169 
 ARG   0.005   0.000   ARG Q 225 

*********************** 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  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7386 (tpt) cc_final: 0.7032 (mmm)
REVERT: D  260 MET cc_start: 0.3945 (ptt) cc_final: 0.3698 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2760
  time to fit residues: 22.7772
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  : 0.594 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 52 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 14 optimal weight:   30.0000
   chunk 50 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0170
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7858

-------------------------------------------------------------------------------
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 = 0.4542 r_free = 0.4542 target = 0.184460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.171918 restraints weight = 14750.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.168394 restraints weight = 27307.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.166235 restraints weight = 25035.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5917
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5236  Z= 0.166
  Angle     :  0.682   9.252   7064  Z= 0.332
  Chirality :  0.044   0.173    861
  Planarity :  0.003   0.034    894
  Dihedral  :  5.016  19.008    718
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  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: -1.68 (0.33), residues: 671
  helix:  0.49 (0.31), residues: 304
  sheet: -0.74 (0.88), residues: 42
  loop : -2.89 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP Q 196 
 HIS   0.001   0.000   HIS D 129 
 PHE   0.027   0.002   PHE D 137 
 TYR   0.009   0.001   TYR Q  74 
 ARG   0.005   0.000   ARG Q  69 

*********************** 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
  68 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7531 (tpt) cc_final: 0.7287 (mmm)
REVERT: Q   69 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7158 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1833
  time to fit residues: 16.2606
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  : 0.623 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 55 optimal weight:    0.2980
   chunk 43 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.2184

-------------------------------------------------------------------------------
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 = 0.4500 r_free = 0.4500 target = 0.180116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.161125 restraints weight = 13811.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.160017 restraints weight = 21662.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.158826 restraints weight = 20518.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6128
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5236  Z= 0.293
  Angle     :  0.787   9.740   7064  Z= 0.389
  Chirality :  0.047   0.205    861
  Planarity :  0.004   0.043    894
  Dihedral  :  5.538  19.770    718
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.73 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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: -1.64 (0.33), residues: 671
  helix:  0.61 (0.32), residues: 297
  sheet: -1.27 (0.86), residues: 44
  loop : -2.82 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP Q  82 
 HIS   0.003   0.001   HIS D 315 
 PHE   0.025   0.002   PHE D 137 
 TYR   0.025   0.003   TYR Q 169 
 ARG   0.006   0.001   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
  60 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: D  260 MET cc_start: 0.3883 (ptt) cc_final: 0.3309 (ptt)
REVERT: Q  210 GLU cc_start: 0.5657 (mp0) cc_final: 0.5208 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1955
  time to fit residues: 15.2247
Evaluate side-chains
  48 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 46 optimal weight:   50.0000
   chunk 43 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 60 optimal weight:    0.4980
   chunk 4 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.8988

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

Flipped N/Q/H residues before XYZ refinement:
** D 494 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 = 0.4478 r_free = 0.4478 target = 0.178677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.159576 restraints weight = 13837.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.158863 restraints weight = 20436.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.158593 restraints weight = 17972.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6164
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   5236  Z= 0.362
  Angle     :  0.844  10.200   7064  Z= 0.422
  Chirality :  0.049   0.241    861
  Planarity :  0.004   0.052    894
  Dihedral  :  5.939  20.295    718
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.77 %
    Favored  : 88.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  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: -1.84 (0.33), residues: 671
  helix:  0.43 (0.31), residues: 305
  sheet: -1.54 (0.87), residues: 44
  loop : -2.95 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP Q  82 
 HIS   0.003   0.001   HIS D 315 
 PHE   0.016   0.002   PHE Q  91 
 TYR   0.019   0.003   TYR Q 169 
 ARG   0.005   0.001   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
  56 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2134
  time to fit residues: 15.4059
Evaluate side-chains
  45 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 58 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0970
   chunk 0 optimal weight:   30.0000
   chunk 5 optimal weight:   30.0000
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    0.2980
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4548 r_free = 0.4548 target = 0.184996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.167929 restraints weight = 13979.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.168722 restraints weight = 26825.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.167153 restraints weight = 15310.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5900
moved from start:          0.4555

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= 0.173
  Angle     :  0.732  10.561   7064  Z= 0.357
  Chirality :  0.046   0.212    861
  Planarity :  0.004   0.037    894
  Dihedral  :  5.246  22.439    718
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  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: -1.72 (0.33), residues: 671
  helix:  0.34 (0.31), residues: 312
  sheet: -0.68 (0.88), residues: 40
  loop : -2.85 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Q  82 
 HIS   0.002   0.000   HIS D 406 
 PHE   0.051   0.003   PHE D 137 
 TYR   0.008   0.001   TYR Q 169 
 ARG   0.005   0.000   ARG Q  69 

********************** 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
  65 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  248 LEU cc_start: 0.6510 (tp) cc_final: 0.5903 (tt)
REVERT: D  260 MET cc_start: 0.3487 (ptt) cc_final: 0.3214 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1864
  time to fit residues: 16.0668
Evaluate side-chains
  49 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.2980
   chunk 43 optimal weight:    6.9990
   chunk 48 optimal weight:   20.0000
   chunk 10 optimal weight:    0.0670
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   chunk 6 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.8520

-------------------------------------------------------------------------------
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 = 0.4539 r_free = 0.4539 target = 0.183958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.169543 restraints weight = 13980.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.168686 restraints weight = 29380.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.166873 restraints weight = 20320.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5236  Z= 0.179
  Angle     :  0.723   9.407   7064  Z= 0.349
  Chirality :  0.045   0.222    861
  Planarity :  0.004   0.041    894
  Dihedral  :  5.195  23.491    718
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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: -1.51 (0.33), residues: 671
  helix:  0.58 (0.31), residues: 302
  sheet: -0.47 (0.87), residues: 40
  loop : -2.74 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.001   0.000   HIS D 406 
 PHE   0.019   0.001   PHE Q  91 
 TYR   0.023   0.002   TYR Q  74 
 ARG   0.008   0.000   ARG Q  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1961.05 seconds
wall clock time: 36 minutes 8.87 seconds (2168.87 seconds total)