Starting phenix.real_space_refine
on Sun Apr 27 02:45:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f3u_31441/04_2025/7f3u_31441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f3u_31441/04_2025/7f3u_31441.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f3u_31441/04_2025/7f3u_31441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f3u_31441/04_2025/7f3u_31441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f3u_31441/04_2025/7f3u_31441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f3u_31441/04_2025/7f3u_31441.cif"
  }
  resolution = 4.0
  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=   1.000
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      18      5.16       5
     C    2716      2.51       5
     N     740      2.21       5
     O     800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4274
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2137
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 153}
          Link IDs: {'PTRANS': 8, 'TRANS': 319}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 653
          Unresolved non-hydrogen angles: 828
          Unresolved non-hydrogen dihedrals: 568
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 18, 'GLU:plan': 12, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 397
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.85, per 1000 atoms: 0.90
  Number of scatterers: 4274
  At special positions: 0
  Unit cell: (71.34, 113.98, 88.56, 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      18     16.00
     O     800      8.00
     N     740      7.00
     C    2716      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: 1.35
  Conformation dependent library (CDL) restraints added in 654.3 milliseconds
  

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1244

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      85.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 72
      Proline residue:  A  70  - end of helix
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 4.186A  pdb=" N   ALA A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 122 through 154
    Processing helix  chain 'A' and resid 157 through 186
      removed outlier: 3.623A  pdb=" N   ASP A 161 " --> pdb=" O   SER A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 209
    Processing helix  chain 'A' and resid 213 through 252
      removed outlier: 4.526A  pdb=" N   ASN A 221 " --> pdb=" O   GLN A 217 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   GLN A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 297
      Proline residue:  A 277  - end of helix
    Processing helix  chain 'A' and resid 306 through 334
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'B' and resid 8 through 72
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 73 through 99
      removed outlier: 4.185A  pdb=" N   ALA B  79 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 122 through 154
    Processing helix  chain 'B' and resid 157 through 186
      removed outlier: 3.623A  pdb=" N   ASP B 161 " --> pdb=" O   SER B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 209
    Processing helix  chain 'B' and resid 213 through 252
      removed outlier: 4.527A  pdb=" N   ASN B 221 " --> pdb=" O   GLN B 217 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   GLN B 222 " --> pdb=" O   LYS B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 297
      Proline residue:  B 277  - end of helix
    Processing helix  chain 'B' and resid 306 through 334
      Proline residue:  B 313  - end of helix

    461 hydrogen bonds defined for protein.
    1383 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.56 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: 1428
        1.34 -     1.45: 646
        1.45 -     1.57: 2258
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 4356
  Sorted by residual:
  bond pdb=" CG  ARG A 178 "
       pdb=" CD  ARG A 178 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.80e+00
  bond pdb=" CG  ARG B 178 "
       pdb=" CD  ARG B 178 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.79e+00
  bond pdb=" CA  VAL A 233 "
       pdb=" CB  VAL A 233 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.25e-02 6.40e+03 1.51e+00
  bond pdb=" CB  TRP A 170 "
       pdb=" CG  TRP A 170 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.49e+00
  bond pdb=" CA  ILE B 145 "
       pdb=" CB  ILE B 145 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.014 1.17e-02 7.31e+03 1.49e+00
  ... (remaining 4351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 5828
        2.26 -     4.51: 126
        4.51 -     6.77: 32
        6.77 -     9.02: 6
        9.02 -    11.28: 2
  Bond angle restraints: 5994
  Sorted by residual:
  angle pdb=" N   PRO B   8 "
        pdb=" CA  PRO B   8 "
        pdb=" CB  PRO B   8 "
      ideal   model   delta    sigma   weight residual
     103.39  110.08   -6.69 1.08e+00 8.57e-01 3.84e+01
  angle pdb=" N   PRO A   8 "
        pdb=" CA  PRO A   8 "
        pdb=" CB  PRO A   8 "
      ideal   model   delta    sigma   weight residual
     103.39  110.07   -6.68 1.08e+00 8.57e-01 3.83e+01
  angle pdb=" NE  ARG B 178 "
        pdb=" CZ  ARG B 178 "
        pdb=" NH1 ARG B 178 "
      ideal   model   delta    sigma   weight residual
     121.50  117.42    4.08 1.00e+00 1.00e+00 1.66e+01
  angle pdb=" NE  ARG A 178 "
        pdb=" CZ  ARG A 178 "
        pdb=" NH1 ARG A 178 "
      ideal   model   delta    sigma   weight residual
     121.50  117.52    3.98 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" CB  MET A  87 "
        pdb=" CG  MET A  87 "
        pdb=" SD  MET A  87 "
      ideal   model   delta    sigma   weight residual
     112.70  123.98  -11.28 3.00e+00 1.11e-01 1.41e+01
  ... (remaining 5989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.29: 2272
       12.29 -    24.58: 152
       24.58 -    36.86: 74
       36.86 -    49.15: 6
       49.15 -    61.44: 6
  Dihedral angle restraints: 2510
    sinusoidal: 586
      harmonic: 1924
  Sorted by residual:
  dihedral pdb=" CA  LEU B 154 "
           pdb=" C   LEU B 154 "
           pdb=" N   LEU B 155 "
           pdb=" CA  LEU B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.52  -26.48     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  LEU A 154 "
           pdb=" C   LEU A 154 "
           pdb=" N   LEU A 155 "
           pdb=" CA  LEU A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.53  -26.47     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  GLY A 106 "
           pdb=" C   GLY A 106 "
           pdb=" N   LEU A 107 "
           pdb=" CA  LEU A 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.77   25.23     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 2507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 524
       0.046 -    0.093: 174
       0.093 -    0.139: 17
       0.139 -    0.185: 7
       0.185 -    0.231: 2
  Chirality restraints: 724
  Sorted by residual:
  chirality pdb=" CA  PRO A   8 "
            pdb=" N   PRO A   8 "
            pdb=" C   PRO A   8 "
            pdb=" CB  PRO A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  PRO B   8 "
            pdb=" N   PRO B   8 "
            pdb=" C   PRO B   8 "
            pdb=" CB  PRO B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CG  LEU B 140 "
            pdb=" CB  LEU B 140 "
            pdb=" CD1 LEU B 140 "
            pdb=" CD2 LEU B 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 721 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 139 "    0.016 2.00e-02 2.50e+03   1.39e-02 3.84e+00
        pdb=" CG  TYR B 139 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 139 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 139 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 139 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 139 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 139 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 139 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 139 "   -0.016 2.00e-02 2.50e+03   1.38e-02 3.79e+00
        pdb=" CG  TYR A 139 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 139 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 139 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 139 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 139 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 139 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 139 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 238 "    0.016 2.00e-02 2.50e+03   9.75e-03 1.90e+00
        pdb=" CG  TYR A 238 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 238 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 238 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 238 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A 238 "    0.000 2.00e-02 2.50e+03
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1454
        2.82 -     3.34: 5127
        3.34 -     3.86: 7295
        3.86 -     4.38: 7293
        4.38 -     4.90: 11642
  Nonbonded interactions: 32811
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 105 "
            pdb=" O   ASN A 115 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND2 ASN B 105 "
            pdb=" O   ASN B 115 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND2 ASN B 165 "
            pdb=" OG  SER B 204 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" ND2 ASN A 165 "
            pdb=" OG  SER A 204 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   MET A 228 "
            pdb=" OG  SER A 231 "
     model   vdw
     2.324 3.040
  ... (remaining 32806 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.230
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.280
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   4356  Z= 0.307
  Angle     :  0.885  11.280   5994  Z= 0.512
  Chirality :  0.045   0.231    724
  Planarity :  0.004   0.029    790
  Dihedral  : 11.591  61.439   1266
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 21.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  2.22 (0.33), residues: 652
  helix:  2.47 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -3.11 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 210 
 HIS   0.009   0.003   HIS A 197 
 PHE   0.021   0.002   PHE A 153 
 TYR   0.034   0.003   TYR B 139 
 ARG   0.009   0.001   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09859 (  461)
  hydrogen bonds       : angle       4.75288 ( 1383)
  covalent geometry    : bond        0.00590 ( 4356)
  covalent geometry    : angle       0.88521 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.8931 (mmmm) cc_final: 0.7947 (mmmm)
REVERT: A  139 TYR cc_start: 0.7886 (m-80) cc_final: 0.7335 (m-80)
REVERT: B  135 LYS cc_start: 0.8908 (mmmm) cc_final: 0.7930 (mmmm)
REVERT: B  136 PHE cc_start: 0.8159 (t80) cc_final: 0.7954 (t80)
REVERT: B  139 TYR cc_start: 0.7900 (m-80) cc_final: 0.7287 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1458
  time to fit residues: 30.8605
Evaluate side-chains
  120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:   30.0000
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:   20.0000
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.101218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.082575 restraints weight = 15439.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.084742 restraints weight = 9452.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.086282 restraints weight = 6610.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4356  Z= 0.149
  Angle     :  0.726  10.899   5994  Z= 0.371
  Chirality :  0.040   0.143    724
  Planarity :  0.003   0.024    790
  Dihedral  :  4.712  21.899    690
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 19.79 %
    Favored  : 74.65 %
  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:  3.45 (0.34), residues: 652
  helix:  3.37 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.91 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 210 
 HIS   0.002   0.001   HIS A 197 
 PHE   0.018   0.001   PHE A 153 
 TYR   0.021   0.002   TYR B 139 
 ARG   0.004   0.001   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  461)
  hydrogen bonds       : angle       3.66558 ( 1383)
  covalent geometry    : bond        0.00282 ( 4356)
  covalent geometry    : angle       0.72570 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8207 (mmmm)
REVERT: A  139 TYR cc_start: 0.8105 (m-80) cc_final: 0.7487 (m-80)
REVERT: A  153 PHE cc_start: 0.8445 (m-80) cc_final: 0.8119 (m-80)
REVERT: B  129 TYR cc_start: 0.8360 (t80) cc_final: 0.8116 (t80)
REVERT: B  135 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8260 (mmmm)
REVERT: B  139 TYR cc_start: 0.8009 (m-80) cc_final: 0.7429 (m-80)
REVERT: B  153 PHE cc_start: 0.8400 (m-80) cc_final: 0.8102 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 169
  average time/residue: 0.1475
  time to fit residues: 31.6002
Evaluate side-chains
  155 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  232 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 47 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
A 185 ASN
B 165 ASN
B 185 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.098598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.079424 restraints weight = 15804.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.081539 restraints weight = 9636.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.082949 restraints weight = 6821.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4356  Z= 0.168
  Angle     :  0.739   8.653   5994  Z= 0.391
  Chirality :  0.041   0.159    724
  Planarity :  0.003   0.020    790
  Dihedral  :  4.621  22.216    690
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 28.12 %
    Favored  : 63.89 %
  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:  3.49 (0.34), residues: 652
  helix:  3.30 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -3.03 (0.55), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 210 
 HIS   0.004   0.002   HIS A 196 
 PHE   0.011   0.001   PHE A 153 
 TYR   0.016   0.002   TYR B 171 
 ARG   0.002   0.001   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  461)
  hydrogen bonds       : angle       3.75166 ( 1383)
  covalent geometry    : bond        0.00339 ( 4356)
  covalent geometry    : angle       0.73939 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.8030 (m-80) cc_final: 0.7774 (m-80)
REVERT: A  153 PHE cc_start: 0.8551 (m-10) cc_final: 0.8099 (m-80)
REVERT: A  175 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9074 (tt)
REVERT: A  314 PHE cc_start: 0.9081 (m-80) cc_final: 0.8715 (m-80)
REVERT: B  153 PHE cc_start: 0.8515 (m-10) cc_final: 0.8040 (m-80)
REVERT: B  314 PHE cc_start: 0.9089 (m-80) cc_final: 0.8722 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1499
  time to fit residues: 29.1509
Evaluate side-chains
  159 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 24 optimal weight:   30.0000
   chunk 25 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0170
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    1.7824

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
A 237 GLN
B 185 ASN
B 237 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.099295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.080526 restraints weight = 15684.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.082569 restraints weight = 9693.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.084043 restraints weight = 6888.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4356  Z= 0.147
  Angle     :  0.724   8.321   5994  Z= 0.371
  Chirality :  0.040   0.150    724
  Planarity :  0.003   0.019    790
  Dihedral  :  4.493  20.912    690
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 28.47 %
    Favored  : 63.19 %
  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:  3.57 (0.34), residues: 652
  helix:  3.34 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.93 (0.56), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 210 
 HIS   0.003   0.001   HIS A 196 
 PHE   0.015   0.001   PHE B 219 
 TYR   0.015   0.002   TYR B 238 
 ARG   0.003   0.001   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04428 (  461)
  hydrogen bonds       : angle       3.57247 ( 1383)
  covalent geometry    : bond        0.00290 ( 4356)
  covalent geometry    : angle       0.72352 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A  153 PHE cc_start: 0.8558 (m-10) cc_final: 0.8112 (m-80)
REVERT: A  175 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9017 (tt)
REVERT: A  314 PHE cc_start: 0.9048 (m-80) cc_final: 0.8686 (m-80)
REVERT: B  153 PHE cc_start: 0.8514 (m-10) cc_final: 0.8066 (m-80)
  outliers start: 24
  outliers final: 21
  residues processed: 160
  average time/residue: 0.1640
  time to fit residues: 32.9865
Evaluate side-chains
  163 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 41 optimal weight:    0.7980
   chunk 6 optimal weight:   20.0000
   chunk 36 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0870
   chunk 46 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   overall best weight:    2.1764

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.099456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.080400 restraints weight = 15777.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.082471 restraints weight = 9765.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.083890 restraints weight = 6990.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4356  Z= 0.155
  Angle     :  0.731   8.221   5994  Z= 0.378
  Chirality :  0.041   0.220    724
  Planarity :  0.003   0.017    790
  Dihedral  :  4.461  20.546    690
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 32.64 %
    Favored  : 59.38 %
  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:  3.61 (0.34), residues: 652
  helix:  3.32 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.78 (0.56), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 210 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.014   0.001   PHE B 219 
 TYR   0.021   0.002   TYR B 171 
 ARG   0.004   0.001   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04426 (  461)
  hydrogen bonds       : angle       3.63299 ( 1383)
  covalent geometry    : bond        0.00311 ( 4356)
  covalent geometry    : angle       0.73065 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  153 PHE cc_start: 0.8590 (m-10) cc_final: 0.8191 (m-80)
REVERT: A  165 ASN cc_start: 0.8535 (t0) cc_final: 0.8236 (t0)
REVERT: B  153 PHE cc_start: 0.8565 (m-10) cc_final: 0.8158 (m-80)
REVERT: B  165 ASN cc_start: 0.8462 (t0) cc_final: 0.8141 (t0)
  outliers start: 23
  outliers final: 22
  residues processed: 154
  average time/residue: 0.1475
  time to fit residues: 28.6958
Evaluate side-chains
  165 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:   30.0000
   chunk 44 optimal weight:    0.9980
   chunk 56 optimal weight:   30.0000
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 58 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0070
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.101118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.082270 restraints weight = 15536.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.084314 restraints weight = 9716.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.085769 restraints weight = 6928.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4356  Z= 0.138
  Angle     :  0.745   8.930   5994  Z= 0.371
  Chirality :  0.041   0.194    724
  Planarity :  0.003   0.018    790
  Dihedral  :  4.361  18.977    690
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 31.94 %
    Favored  : 59.72 %
  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:  3.62 (0.34), residues: 652
  helix:  3.33 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.77 (0.56), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 210 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.011   0.001   PHE B 219 
 TYR   0.015   0.001   TYR B 238 
 ARG   0.003   0.001   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  461)
  hydrogen bonds       : angle       3.45683 ( 1383)
  covalent geometry    : bond        0.00271 ( 4356)
  covalent geometry    : angle       0.74455 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A  153 PHE cc_start: 0.8446 (m-10) cc_final: 0.8189 (m-80)
REVERT: A  314 PHE cc_start: 0.9017 (m-80) cc_final: 0.8708 (m-80)
REVERT: B  153 PHE cc_start: 0.8454 (m-10) cc_final: 0.8227 (m-80)
  outliers start: 24
  outliers final: 20
  residues processed: 162
  average time/residue: 0.2058
  time to fit residues: 41.4953
Evaluate side-chains
  162 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.101194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.082148 restraints weight = 15402.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.084258 restraints weight = 9604.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.085756 restraints weight = 6865.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4356  Z= 0.147
  Angle     :  0.775   9.053   5994  Z= 0.395
  Chirality :  0.043   0.222    724
  Planarity :  0.005   0.075    790
  Dihedral  :  4.353  18.962    690
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 33.68 %
    Favored  : 57.99 %
  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:  3.43 (0.34), residues: 652
  helix:  3.18 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.73 (0.57), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 210 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.024   0.001   PHE A 136 
 TYR   0.014   0.001   TYR B 238 
 ARG   0.016   0.002   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 (  461)
  hydrogen bonds       : angle       3.68928 ( 1383)
  covalent geometry    : bond        0.00291 ( 4356)
  covalent geometry    : angle       0.77456 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  314 PHE cc_start: 0.8997 (m-80) cc_final: 0.8673 (m-80)
REVERT: B  175 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8720 (tt)
  outliers start: 24
  outliers final: 20
  residues processed: 156
  average time/residue: 0.1499
  time to fit residues: 29.4355
Evaluate side-chains
  159 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 57 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.096513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.077769 restraints weight = 15797.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.079742 restraints weight = 9741.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.081091 restraints weight = 6950.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4356  Z= 0.236
  Angle     :  0.850   9.742   5994  Z= 0.453
  Chirality :  0.045   0.196    724
  Planarity :  0.005   0.063    790
  Dihedral  :  4.810  24.032    690
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 36.46 %
    Favored  : 55.90 %
  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:  3.14 (0.33), residues: 652
  helix:  2.92 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.47 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.029   0.002   PHE A 153 
 TYR   0.020   0.002   TYR A 133 
 ARG   0.012   0.003   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05015 (  461)
  hydrogen bonds       : angle       4.20010 ( 1383)
  covalent geometry    : bond        0.00479 ( 4356)
  covalent geometry    : angle       0.85045 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 21
  residues processed: 150
  average time/residue: 0.1617
  time to fit residues: 30.4601
Evaluate side-chains
  158 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   chunk 57 optimal weight:   30.0000
   chunk 32 optimal weight:   30.0000
   chunk 20 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 39 optimal weight:   30.0000
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.097832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.079241 restraints weight = 16012.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.081227 restraints weight = 9829.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.082669 restraints weight = 7004.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4356  Z= 0.184
  Angle     :  0.823  10.260   5994  Z= 0.430
  Chirality :  0.045   0.316    724
  Planarity :  0.004   0.056    790
  Dihedral  :  4.726  23.572    690
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  8.68 %
    Allowed  : 35.76 %
    Favored  : 55.56 %
  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:  3.28 (0.34), residues: 652
  helix:  3.05 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.63 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 210 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.027   0.002   PHE B 153 
 TYR   0.015   0.002   TYR B 238 
 ARG   0.012   0.002   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04677 (  461)
  hydrogen bonds       : angle       4.00941 ( 1383)
  covalent geometry    : bond        0.00376 ( 4356)
  covalent geometry    : angle       0.82262 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
REVERT: B  175 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8973 (tt)
  outliers start: 25
  outliers final: 22
  residues processed: 152
  average time/residue: 0.1573
  time to fit residues: 30.2970
Evaluate side-chains
  162 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.098257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.079747 restraints weight = 15549.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.081701 restraints weight = 9669.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.083115 restraints weight = 6919.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4356  Z= 0.183
  Angle     :  0.836  10.935   5994  Z= 0.436
  Chirality :  0.046   0.333    724
  Planarity :  0.004   0.052    790
  Dihedral  :  4.716  23.504    690
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 36.46 %
    Favored  : 55.90 %
  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:  3.27 (0.34), residues: 652
  helix:  3.05 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.64 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 210 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.027   0.002   PHE B 153 
 TYR   0.015   0.002   TYR B 238 
 ARG   0.011   0.002   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 (  461)
  hydrogen bonds       : angle       4.00745 ( 1383)
  covalent geometry    : bond        0.00376 ( 4356)
  covalent geometry    : angle       0.83647 ( 5994)

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8961 (tt)
  outliers start: 22
  outliers final: 21
  residues processed: 150
  average time/residue: 0.1449
  time to fit residues: 27.4995
Evaluate side-chains
  162 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  235 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 37 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.097954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.079358 restraints weight = 15760.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.081187 restraints weight = 9725.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.082670 restraints weight = 7118.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4356  Z= 0.190
  Angle     :  0.835  10.912   5994  Z= 0.437
  Chirality :  0.046   0.338    724
  Planarity :  0.004   0.048    790
  Dihedral  :  4.714  23.442    690
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 37.85 %
    Favored  : 54.51 %
  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:  3.25 (0.34), residues: 652
  helix:  3.04 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.65 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 210 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.026   0.002   PHE B 153 
 TYR   0.014   0.002   TYR B 238 
 ARG   0.011   0.002   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04658 (  461)
  hydrogen bonds       : angle       4.02242 ( 1383)
  covalent geometry    : bond        0.00391 ( 4356)
  covalent geometry    : angle       0.83505 ( 5994)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1792.15 seconds
wall clock time: 32 minutes 23.09 seconds (1943.09 seconds total)