Starting phenix.real_space_refine
on Thu Jul 24 05:21:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yi9_33854/07_2025/7yi9_33854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yi9_33854/07_2025/7yi9_33854.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2025/7yi9_33854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2025/7yi9_33854.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2025/7yi9_33854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2025/7yi9_33854.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.076
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      27      5.16       5
     C    3335      2.51       5
     N     892      2.21       5
     O     972      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5226
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2117
          Classifications: {'peptide': 257}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 249}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1819
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 215}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 269
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
    Chain: "D"
      Number of atoms: 994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 994
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Time building chain proxies: 4.01, per 1000 atoms: 0.77
  Number of scatterers: 5226
  At special positions: 0
  Unit cell: (80.75, 68, 122.4, 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      27     16.00
     O     972      8.00
     N     892      7.00
     C    3335      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: 1.19
  Conformation dependent library (CDL) restraints added in 556.6 milliseconds
  

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1206

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      39.9% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 106 through 109
    Processing helix  chain 'A' and resid 165 through 170
      removed outlier: 3.707A  pdb=" N   SER A 170 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
    Processing helix  chain 'A' and resid 218 through 227
    Processing helix  chain 'A' and resid 320 through 334
    Processing helix  chain 'A' and resid 337 through 341
      removed outlier: 4.321A  pdb=" N   SER A 340 " --> pdb=" O   ILE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 346
    Processing helix  chain 'A' and resid 402 through 414
    Processing helix  chain 'B' and resid 141 through 167
    Processing helix  chain 'B' and resid 187 through 199
    Processing helix  chain 'B' and resid 231 through 237
    Processing helix  chain 'B' and resid 239 through 244
      removed outlier: 3.655A  pdb=" N   GLN B 244 " --> pdb=" O   ILE B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 256
      No H-bonds generated for 'chain 'B' and resid 254 through 256'
    Processing helix  chain 'B' and resid 257 through 268
    Processing helix  chain 'B' and resid 336 through 346
      removed outlier: 3.701A  pdb=" N   GLN B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 3.614A  pdb=" N   LEU B 361 " --> pdb=" O   ARG B 358 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 159
      removed outlier: 3.743A  pdb=" N   ASN C 158 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   GLU C 159 " --> pdb=" O   ASP C 155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 154 through 159'
    Processing helix  chain 'C' and resid 169 through 183
      removed outlier: 4.420A  pdb=" N   ALA C 175 " --> pdb=" O   TYR C 171 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   VAL C 178 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 26
    Processing helix  chain 'D' and resid 38 through 43
      removed outlier: 3.750A  pdb=" N   PHE D  42 " --> pdb=" O   ASN D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 66
    Processing helix  chain 'D' and resid 70 through 76
    Processing helix  chain 'D' and resid 83 through 96
      removed outlier: 4.639A  pdb=" N   CYS D  92 " --> pdb=" O   GLU D  88 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET D  93 " --> pdb=" O   LEU D  89 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE D  94 " --> pdb=" O   ARG D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 104
      removed outlier: 3.744A  pdb=" N   TYR D 104 " --> pdb=" O   THR D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 118
    Processing helix  chain 'D' and resid 125 through 129
      removed outlier: 4.037A  pdb=" N   ASN D 128 " --> pdb=" O   LYS D 125 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129
      removed outlier: 6.227A  pdb=" N   ALA A 146 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   LEU A 432 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   PHE A 148 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   TRP A 187 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY A 182 " --> pdb=" O   ARG A 367 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   THR A 361 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET A 364 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A 209 " --> pdb=" O   MET A 364 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ARG A 366 " --> pdb=" O   TYR A 207 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   TYR A 207 " --> pdb=" O   ARG A 366 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 177 through 180
      removed outlier: 6.520A  pdb=" N   TYR B 351 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   ILE B 368 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLU B 353 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   ILE B 354 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   MET B 207 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER B 301 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL B 306 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   LEU B 272 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)

    188 hydrogen bonds defined for protein.
    528 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 1.44 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: 1686
        1.34 -     1.46: 761
        1.46 -     1.57: 2824
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 5319
  Sorted by residual:
  bond pdb=" C2  SAM B 401 "
       pdb=" N3  SAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.378 -0.056 2.00e-02 2.50e+03 7.88e+00
  bond pdb=" C8  SAM B 401 "
       pdb=" N7  SAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.298  1.351 -0.053 2.00e-02 2.50e+03 7.10e+00
  bond pdb=" C2  SAM B 401 "
       pdb=" N1  SAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.329  1.378 -0.049 2.00e-02 2.50e+03 5.98e+00
  bond pdb=" C6  SAM B 401 "
       pdb=" N1  SAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.337  1.377 -0.040 2.00e-02 2.50e+03 4.06e+00
  bond pdb=" C1' SAM B 401 "
       pdb=" N9  SAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.452  1.478 -0.026 2.00e-02 2.50e+03 1.67e+00
  ... (remaining 5314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 6987
        1.78 -     3.56: 133
        3.56 -     5.34: 17
        5.34 -     7.12: 9
        7.12 -     8.90: 3
  Bond angle restraints: 7149
  Sorted by residual:
  angle pdb=" N   ILE A 337 "
        pdb=" CA  ILE A 337 "
        pdb=" C   ILE A 337 "
      ideal   model   delta    sigma   weight residual
     111.90  107.94    3.96 8.10e-01 1.52e+00 2.38e+01
  angle pdb=" C   LEU D  87 "
        pdb=" N   GLU D  88 "
        pdb=" CA  GLU D  88 "
      ideal   model   delta    sigma   weight residual
     122.38  115.48    6.90 1.81e+00 3.05e-01 1.45e+01
  angle pdb=" CA  GLU D  88 "
        pdb=" CB  GLU D  88 "
        pdb=" CG  GLU D  88 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.30e+00
  angle pdb=" O   SAM B 401 "
        pdb=" C   SAM B 401 "
        pdb=" OXT SAM B 401 "
      ideal   model   delta    sigma   weight residual
     126.77  117.87    8.90 3.00e+00 1.11e-01 8.79e+00
  angle pdb=" N1  SAM B 401 "
        pdb=" C2  SAM B 401 "
        pdb=" N3  SAM B 401 "
      ideal   model   delta    sigma   weight residual
     128.51  120.01    8.50 3.00e+00 1.11e-01 8.02e+00
  ... (remaining 7144 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 2898
       17.48 -    34.95: 294
       34.95 -    52.43: 61
       52.43 -    69.90: 7
       69.90 -    87.38: 8
  Dihedral angle restraints: 3268
    sinusoidal: 1413
      harmonic: 1855
  Sorted by residual:
  dihedral pdb=" CA  LEU A 178 "
           pdb=" C   LEU A 178 "
           pdb=" N   MET A 179 "
           pdb=" CA  MET A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.46  -20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  MET A 402 "
           pdb=" C   MET A 402 "
           pdb=" N   LYS A 403 "
           pdb=" CA  LYS A 403 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  HIS A 379 "
           pdb=" C   HIS A 379 "
           pdb=" N   GLN A 380 "
           pdb=" CA  GLN A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.47  -16.53     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 3265 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    2.218: 780
       2.218 -    4.436: 0
       4.436 -    6.654: 0
       6.654 -    8.872: 0
       8.872 -   11.090: 1
  Chirality restraints: 781
  Sorted by residual:
  chirality pdb=" SD  SAM B 401 "
            pdb=" CG  SAM B 401 "
            pdb=" CE  SAM B 401 "
            pdb=" C5' SAM B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      5.50   -5.59   11.09 2.00e-01 2.50e+01 3.07e+03
  chirality pdb=" CA  GLN B 161 "
            pdb=" N   GLN B 161 "
            pdb=" C   GLN B 161 "
            pdb=" CB  GLN B 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" C2' SAM B 401 "
            pdb=" C1' SAM B 401 "
            pdb=" C3' SAM B 401 "
            pdb=" O2' SAM B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.59   -0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 778 not shown)

  Planarity restraints: 909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 112 "    0.036 5.00e-02 4.00e+02   5.39e-02 4.64e+00
        pdb=" N   PRO A 113 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 113 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 113 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 352 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.54e+00
        pdb=" N   PRO A 353 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 353 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 353 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 174 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO A 175 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 175 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 175 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 906 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 67
        2.67 -     3.23: 4830
        3.23 -     3.79: 7715
        3.79 -     4.34: 11199
        4.34 -     4.90: 17983
  Nonbonded interactions: 41794
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 164 "
            pdb=" OH  TYR C 171 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" NE2 GLN A 380 "
            pdb=" O   GLY B 292 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OD1 ASN A 210 "
            pdb=" OG1 THR A 361 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" NE1 TRP A 153 "
            pdb=" O   TRP A 187 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" OD2 ASP B 204 "
            pdb=" NH1 ARG B 314 "
     model   vdw
     2.260 3.120
  ... (remaining 41789 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 individual isotropic
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:             1.070
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.010
  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:15.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
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      :  0.004   0.056   5319  Z= 0.168
  Angle     :  0.651   8.895   7149  Z= 0.340
  Chirality :  0.399  11.090    781
  Planarity :  0.004   0.054    909
  Dihedral  : 14.607  87.381   2062
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -0.81 (0.33), residues: 620
  helix: -0.03 (0.36), residues: 204
  sheet:  0.53 (0.52), residues: 102
  loop : -1.23 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  50 
 HIS   0.002   0.001   HIS C 169 
 PHE   0.014   0.002   PHE B 158 
 TYR   0.008   0.001   TYR B 258 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17991 (  188)
  hydrogen bonds       : angle       7.02784 (  528)
  covalent geometry    : bond        0.00362 ( 5319)
  covalent geometry    : angle       0.65079 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.488 
Fit side-chains
REVERT: B  371 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7383 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 1.2900
  time to fit residues: 135.4308
Evaluate side-chains
  79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 334 ASN
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
D 128 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.193158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.150003 restraints weight = 5911.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.42
r_work: 0.3728 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5319  Z= 0.197
  Angle     :  0.642   6.173   7149  Z= 0.343
  Chirality :  0.044   0.152    781
  Planarity :  0.005   0.062    909
  Dihedral  :  7.114  53.882    707
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.13 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.33), residues: 620
  helix:  0.06 (0.36), residues: 212
  sheet:  0.50 (0.50), residues: 103
  loop : -1.40 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.016   0.002   PHE B 250 
 TYR   0.009   0.002   TYR A 407 
 ARG   0.004   0.001   ARG A 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05116 (  188)
  hydrogen bonds       : angle       5.75204 (  528)
  covalent geometry    : bond        0.00458 ( 5319)
  covalent geometry    : angle       0.64177 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7790 (tp)
REVERT: A  326 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6117 (pt0)
REVERT: A  381 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7668 (mmt-90)
REVERT: B  289 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7644 (mppt)
REVERT: D   63 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6650 (pp20)
REVERT: D  110 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6175 (mp0)
REVERT: D  114 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.4877 (tt0)
  outliers start: 15
  outliers final: 3
  residues processed: 83
  average time/residue: 1.2277
  time to fit residues: 106.3684
Evaluate side-chains
  83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
D 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.195898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.146488 restraints weight = 5952.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 2.33
r_work: 0.3764 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5319  Z= 0.110
  Angle     :  0.524   5.235   7149  Z= 0.283
  Chirality :  0.040   0.136    781
  Planarity :  0.004   0.053    909
  Dihedral  :  6.581  57.919    707
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.38 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.33), residues: 620
  helix:  0.23 (0.36), residues: 219
  sheet:  0.76 (0.50), residues: 103
  loop : -1.42 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.015   0.001   PHE B 158 
 TYR   0.007   0.001   TYR B 258 
 ARG   0.001   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  188)
  hydrogen bonds       : angle       5.32280 (  528)
  covalent geometry    : bond        0.00245 ( 5319)
  covalent geometry    : angle       0.52381 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A  223 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6357 (mt0)
REVERT: A  381 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7720 (mmt-90)
REVERT: B  171 MET cc_start: 0.5633 (pmm) cc_final: 0.5084 (pp-130)
REVERT: B  289 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7552 (mppt)
REVERT: B  371 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7095 (pp20)
REVERT: B  372 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7092 (tp)
REVERT: D   88 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6085 (pm20)
REVERT: D  110 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6176 (mp0)
REVERT: D  114 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4856 (tt0)
  outliers start: 19
  outliers final: 6
  residues processed: 83
  average time/residue: 1.2960
  time to fit residues: 111.9999
Evaluate side-chains
  82 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
D 128 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.193205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.143586 restraints weight = 6019.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 2.35
r_work: 0.3718 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3595 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5319  Z= 0.159
  Angle     :  0.566   5.351   7149  Z= 0.307
  Chirality :  0.042   0.146    781
  Planarity :  0.004   0.054    909
  Dihedral  :  6.571  56.452    707
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 16.12 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.33), residues: 620
  helix:  0.33 (0.36), residues: 213
  sheet:  0.69 (0.50), residues: 103
  loop : -1.26 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.014   0.002   PHE B 250 
 TYR   0.010   0.001   TYR B 153 
 ARG   0.002   0.000   ARG A 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  188)
  hydrogen bonds       : angle       5.30338 (  528)
  covalent geometry    : bond        0.00370 ( 5319)
  covalent geometry    : angle       0.56627 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7783 (tp)
REVERT: A  223 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6406 (mt0)
REVERT: A  381 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7921 (mmt-90)
REVERT: B  289 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7594 (mppt)
REVERT: B  372 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7343 (tp)
REVERT: D   63 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6740 (pp20)
REVERT: D   88 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6077 (pm20)
REVERT: D  110 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6215 (mp0)
REVERT: D  114 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.4884 (tt0)
  outliers start: 24
  outliers final: 9
  residues processed: 82
  average time/residue: 1.2720
  time to fit residues: 108.6970
Evaluate side-chains
  86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 15 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   overall best weight:    1.0922

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 GLN
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
D 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.192952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.145264 restraints weight = 6081.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.32
r_work: 0.3729 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5319  Z= 0.138
  Angle     :  0.543   6.182   7149  Z= 0.294
  Chirality :  0.041   0.140    781
  Planarity :  0.004   0.053    909
  Dihedral  :  6.390  51.563    707
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.68 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.33), residues: 620
  helix:  0.55 (0.37), residues: 207
  sheet:  0.73 (0.52), residues: 99
  loop : -1.19 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.013   0.002   PHE B 250 
 TYR   0.011   0.001   TYR B 153 
 ARG   0.003   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  188)
  hydrogen bonds       : angle       5.21765 (  528)
  covalent geometry    : bond        0.00322 ( 5319)
  covalent geometry    : angle       0.54295 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7807 (tp)
REVERT: A  223 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6391 (mt0)
REVERT: A  381 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7732 (mmt-90)
REVERT: B  171 MET cc_start: 0.5747 (pmm) cc_final: 0.5129 (pp-130)
REVERT: B  289 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7574 (mppt)
REVERT: B  372 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7333 (tp)
REVERT: D   84 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5578 (tp)
REVERT: D   88 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6126 (pm20)
REVERT: D  110 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6186 (mp0)
REVERT: D  114 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.4890 (tt0)
  outliers start: 22
  outliers final: 9
  residues processed: 81
  average time/residue: 1.1764
  time to fit residues: 99.4945
Evaluate side-chains
  88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
A 360 HIS
B 161 GLN
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
D 128 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.191011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.143029 restraints weight = 6099.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.31
r_work: 0.3701 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5319  Z= 0.183
  Angle     :  0.596   5.521   7149  Z= 0.322
  Chirality :  0.043   0.148    781
  Planarity :  0.005   0.055    909
  Dihedral  :  6.516  49.221    707
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 17.50 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.33), residues: 620
  helix:  0.23 (0.36), residues: 213
  sheet:  0.64 (0.50), residues: 103
  loop : -1.36 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.012   0.002   PHE B 250 
 TYR   0.009   0.001   TYR B 153 
 ARG   0.002   0.000   ARG A 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  188)
  hydrogen bonds       : angle       5.32154 (  528)
  covalent geometry    : bond        0.00432 ( 5319)
  covalent geometry    : angle       0.59579 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7857 (tp)
REVERT: A  223 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6346 (mt0)
REVERT: A  381 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7870 (mmt-90)
REVERT: A  429 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7611 (mtp)
REVERT: B  207 MET cc_start: 0.8497 (mtp) cc_final: 0.8222 (mmm)
REVERT: B  372 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7403 (tp)
REVERT: D   84 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5699 (tp)
REVERT: D   88 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6093 (pm20)
REVERT: D  110 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.6058 (mp0)
REVERT: D  114 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4866 (tt0)
  outliers start: 25
  outliers final: 11
  residues processed: 80
  average time/residue: 1.2305
  time to fit residues: 103.0897
Evaluate side-chains
  88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0670
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7924

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

Flipped N/Q/H residues before XYZ refinement:
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.192985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.145052 restraints weight = 6051.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 2.30
r_work: 0.3731 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5319  Z= 0.119
  Angle     :  0.534   7.923   7149  Z= 0.288
  Chirality :  0.040   0.136    781
  Planarity :  0.004   0.053    909
  Dihedral  :  6.109  45.155    707
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.85 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.33), residues: 620
  helix:  0.39 (0.37), residues: 213
  sheet:  0.87 (0.51), residues: 97
  loop : -1.25 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.014   0.001   PHE A 330 
 TYR   0.007   0.001   TYR B 153 
 ARG   0.001   0.000   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03667 (  188)
  hydrogen bonds       : angle       5.12155 (  528)
  covalent geometry    : bond        0.00276 ( 5319)
  covalent geometry    : angle       0.53391 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7793 (tp)
REVERT: A  180 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (mmmm)
REVERT: A  223 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6401 (mt0)
REVERT: A  429 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7491 (mtp)
REVERT: B  171 MET cc_start: 0.5794 (pmm) cc_final: 0.5150 (pp-130)
REVERT: B  372 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7315 (tp)
REVERT: D   84 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5639 (tp)
REVERT: D   88 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.6036 (pm20)
REVERT: D  114 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4830 (tt0)
  outliers start: 23
  outliers final: 9
  residues processed: 81
  average time/residue: 1.2488
  time to fit residues: 105.6384
Evaluate side-chains
  84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  180 LYS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.193716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.145939 restraints weight = 6102.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.32
r_work: 0.3744 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5319  Z= 0.116
  Angle     :  0.538   7.507   7149  Z= 0.288
  Chirality :  0.040   0.136    781
  Planarity :  0.004   0.051    909
  Dihedral  :  5.916  45.391    707
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 18.37 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.33), residues: 620
  helix:  0.53 (0.37), residues: 213
  sheet:  0.84 (0.49), residues: 101
  loop : -1.24 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 212 
 HIS   0.002   0.001   HIS B 291 
 PHE   0.013   0.001   PHE A 330 
 TYR   0.006   0.001   TYR B 258 
 ARG   0.001   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  188)
  hydrogen bonds       : angle       5.04196 (  528)
  covalent geometry    : bond        0.00270 ( 5319)
  covalent geometry    : angle       0.53850 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.599 
Fit side-chains
REVERT: A  180 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7198 (mmmm)
REVERT: A  223 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6408 (mt0)
REVERT: B  171 MET cc_start: 0.5706 (pmm) cc_final: 0.5078 (pp-130)
REVERT: B  372 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7290 (tp)
REVERT: D   84 ILE cc_start: 0.5906 (OUTLIER) cc_final: 0.5640 (tp)
REVERT: D   88 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5938 (pm20)
REVERT: D  114 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.4935 (tt0)
  outliers start: 22
  outliers final: 11
  residues processed: 77
  average time/residue: 1.2957
  time to fit residues: 104.0115
Evaluate side-chains
  84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  180 LYS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  264 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.193497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.145789 restraints weight = 6028.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.29
r_work: 0.3737 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5319  Z= 0.125
  Angle     :  0.548   6.951   7149  Z= 0.293
  Chirality :  0.041   0.137    781
  Planarity :  0.004   0.051    909
  Dihedral  :  5.874  45.401    707
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.24 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.33), residues: 620
  helix:  0.35 (0.36), residues: 219
  sheet:  0.86 (0.49), residues: 101
  loop : -1.35 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 250 
 TYR   0.006   0.001   TYR B 258 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  188)
  hydrogen bonds       : angle       5.02459 (  528)
  covalent geometry    : bond        0.00292 ( 5319)
  covalent geometry    : angle       0.54798 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7796 (tp)
REVERT: A  180 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7191 (mmmm)
REVERT: A  223 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6389 (mt0)
REVERT: A  381 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7850 (mmt-90)
REVERT: B  171 MET cc_start: 0.5673 (pmm) cc_final: 0.5078 (pp-130)
REVERT: B  372 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7292 (tp)
REVERT: D   63 GLU cc_start: 0.6172 (pp20) cc_final: 0.5925 (tm-30)
REVERT: D   84 ILE cc_start: 0.6002 (OUTLIER) cc_final: 0.5755 (tp)
REVERT: D   88 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.6009 (pm20)
REVERT: D  102 GLU cc_start: 0.6937 (mp0) cc_final: 0.6724 (mm-30)
REVERT: D  114 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.4956 (tt0)
  outliers start: 20
  outliers final: 11
  residues processed: 77
  average time/residue: 1.3258
  time to fit residues: 106.4642
Evaluate side-chains
  83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  180 LYS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  208 MET
Chi-restraints excluded: chain B residue  264 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0770
   chunk 52 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.194769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.147229 restraints weight = 6051.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 2.32
r_work: 0.3761 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5319  Z= 0.110
  Angle     :  0.534   6.966   7149  Z= 0.287
  Chirality :  0.040   0.133    781
  Planarity :  0.004   0.051    909
  Dihedral  :  5.689  44.774    707
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.10 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.33), residues: 620
  helix:  0.45 (0.37), residues: 219
  sheet:  0.84 (0.50), residues: 102
  loop : -1.32 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.011   0.001   PHE B 250 
 TYR   0.006   0.001   TYR B 258 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03436 (  188)
  hydrogen bonds       : angle       4.93708 (  528)
  covalent geometry    : bond        0.00254 ( 5319)
  covalent geometry    : angle       0.53394 ( 7149)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A  223 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6362 (mt0)
REVERT: B  171 MET cc_start: 0.5619 (pmm) cc_final: 0.5053 (pp-130)
REVERT: B  372 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7255 (tp)
REVERT: D   63 GLU cc_start: 0.6333 (pp20) cc_final: 0.5949 (tm-30)
REVERT: D   84 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.5674 (tp)
REVERT: D   88 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6060 (pm20)
REVERT: D  114 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.4976 (tt0)
  outliers start: 18
  outliers final: 10
  residues processed: 73
  average time/residue: 1.1624
  time to fit residues: 88.8930
Evaluate side-chains
  78 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  264 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain D residue   27 ASN
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  114 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    0.1980
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 61 optimal weight:    0.2980
   chunk 2 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.194989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.147668 restraints weight = 6074.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.30
r_work: 0.3764 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5319  Z= 0.110
  Angle     :  0.535   6.846   7149  Z= 0.290
  Chirality :  0.040   0.133    781
  Planarity :  0.004   0.051    909
  Dihedral  :  5.613  44.233    707
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.97 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.33), residues: 620
  helix:  0.51 (0.37), residues: 219
  sheet:  0.89 (0.50), residues: 102
  loop : -1.28 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 212 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.017   0.001   PHE A 330 
 TYR   0.006   0.001   TYR B 258 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  188)
  hydrogen bonds       : angle       4.90471 (  528)
  covalent geometry    : bond        0.00253 ( 5319)
  covalent geometry    : angle       0.53461 ( 7149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5125.60 seconds
wall clock time: 87 minutes 41.73 seconds (5261.73 seconds total)