Starting phenix.real_space_refine
on Tue Feb 11 14:29:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vq7_32087/02_2025/7vq7_32087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vq7_32087/02_2025/7vq7_32087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vq7_32087/02_2025/7vq7_32087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vq7_32087/02_2025/7vq7_32087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vq7_32087/02_2025/7vq7_32087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vq7_32087/02_2025/7vq7_32087.cif"
  }
  resolution = 3.6
  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=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     S      34      5.16       5
     C    3942      2.51       5
     N    1030      2.21       5
     O    1120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6127
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3063
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 10, 'TRANS': 378}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AL': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.48, per 1000 atoms: 0.89
  Number of scatterers: 6127
  At special positions: 0
  Unit cell: (86.19, 84.162, 111.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     Al      1     13.00
     O    1120      8.00
     N    1030      7.00
     C    3942      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: 1.46
  Conformation dependent library (CDL) restraints added in 820.7 milliseconds
  

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
      removed outlier: 3.743A  pdb=" N   ARG A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 39
      removed outlier: 3.728A  pdb=" N   GLY A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 66
      removed outlier: 3.518A  pdb=" N   PHE A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 102
      removed outlier: 3.966A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 125
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.876A  pdb=" N   LYS A 133 " --> pdb=" O   TRP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 150
    Processing helix  chain 'A' and resid 154 through 183
      removed outlier: 3.766A  pdb=" N   ILE A 158 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   MET A 159 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A 183 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 214
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 5.001A  pdb=" N   ARG A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   TYR A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 267 through 293
      removed outlier: 3.611A  pdb=" N   TYR A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 304
      removed outlier: 3.638A  pdb=" N   LYS A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 331
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 4.058A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 399
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 3.811A  pdb=" N   ASP B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 39
      removed outlier: 3.728A  pdb=" N   GLY B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 66
      removed outlier: 3.518A  pdb=" N   PHE B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 102
      removed outlier: 3.967A  pdb=" N   GLY B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 125
    Processing helix  chain 'B' and resid 127 through 133
      removed outlier: 3.876A  pdb=" N   LYS B 133 " --> pdb=" O   TRP B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 150
    Processing helix  chain 'B' and resid 154 through 183
      removed outlier: 3.766A  pdb=" N   ILE B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   MET B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 183 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 214
    Processing helix  chain 'B' and resid 223 through 240
      removed outlier: 5.000A  pdb=" N   ARG B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   TYR B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
    Processing helix  chain 'B' and resid 267 through 293
      removed outlier: 3.610A  pdb=" N   TYR B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.638A  pdb=" N   LYS B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 331
    Processing helix  chain 'B' and resid 335 through 356
      removed outlier: 4.058A  pdb=" N   ILE B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 399

    514 hydrogen bonds defined for protein.
    1542 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: 1.74

  Time building geometry restraints manager: 1.70 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: 1960
        1.34 -     1.46: 1387
        1.46 -     1.58: 2833
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 6240
  Sorted by residual:
  bond pdb=" N   HIS A 266 "
       pdb=" CA  HIS A 266 "
    ideal  model  delta    sigma   weight residual
    1.458  1.437  0.022 1.25e-02 6.40e+03 2.97e+00
  bond pdb=" N   HIS B 266 "
       pdb=" CA  HIS B 266 "
    ideal  model  delta    sigma   weight residual
    1.458  1.438  0.021 1.25e-02 6.40e+03 2.71e+00
  bond pdb=" C   TRP A 255 "
       pdb=" N   GLU A 256 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.023 1.60e-02 3.91e+03 2.11e+00
  bond pdb=" C   TRP B 255 "
       pdb=" N   GLU B 256 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.60e-02 3.91e+03 2.03e+00
  bond pdb=" CB  THR A  73 "
       pdb=" CG2 THR A  73 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.90e+00
  ... (remaining 6235 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 7745
        1.30 -     2.60: 589
        2.60 -     3.90: 65
        3.90 -     5.20: 13
        5.20 -     6.50: 10
  Bond angle restraints: 8422
  Sorted by residual:
  angle pdb=" N   HIS A 266 "
        pdb=" CA  HIS A 266 "
        pdb=" C   HIS A 266 "
      ideal   model   delta    sigma   weight residual
     109.10  102.60    6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" N   HIS B 266 "
        pdb=" CA  HIS B 266 "
        pdb=" C   HIS B 266 "
      ideal   model   delta    sigma   weight residual
     109.10  102.63    6.47 1.91e+00 2.74e-01 1.15e+01
  angle pdb=" CA  LYS B   3 "
        pdb=" CB  LYS B   3 "
        pdb=" CG  LYS B   3 "
      ideal   model   delta    sigma   weight residual
     114.10  120.24   -6.14 2.00e+00 2.50e-01 9.41e+00
  angle pdb=" CA  LYS A   3 "
        pdb=" CB  LYS A   3 "
        pdb=" CG  LYS A   3 "
      ideal   model   delta    sigma   weight residual
     114.10  120.23   -6.13 2.00e+00 2.50e-01 9.38e+00
  angle pdb=" C   PHE B 134 "
        pdb=" CA  PHE B 134 "
        pdb=" CB  PHE B 134 "
      ideal   model   delta    sigma   weight residual
     111.13  107.09    4.04 1.61e+00 3.86e-01 6.29e+00
  ... (remaining 8417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 3200
       16.55 -    33.10: 396
       33.10 -    49.65: 112
       49.65 -    66.21: 38
       66.21 -    82.76: 10
  Dihedral angle restraints: 3756
    sinusoidal: 1494
      harmonic: 2262
  Sorted by residual:
  dihedral pdb=" CA  LEU B 233 "
           pdb=" C   LEU B 233 "
           pdb=" N   GLU B 234 "
           pdb=" CA  GLU B 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.86  -21.14     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  LEU A 233 "
           pdb=" C   LEU A 233 "
           pdb=" N   GLU A 234 "
           pdb=" CA  GLU A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ILE B 181 "
           pdb=" C   ILE B 181 "
           pdb=" N   PHE B 182 "
           pdb=" CA  PHE B 182 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.63  -18.37     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 3753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 412
       0.027 -    0.055: 411
       0.055 -    0.082: 98
       0.082 -    0.109: 40
       0.109 -    0.136: 13
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CA  PRO B 365 "
            pdb=" N   PRO B 365 "
            pdb=" C   PRO B 365 "
            pdb=" CB  PRO B 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  PRO A 365 "
            pdb=" N   PRO A 365 "
            pdb=" C   PRO A 365 "
            pdb=" CB  PRO A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE B 298 "
            pdb=" N   ILE B 298 "
            pdb=" C   ILE B 298 "
            pdb=" CB  ILE B 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 184 "   -0.023 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 185 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 185 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 185 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 184 "   -0.023 5.00e-02 4.00e+02   3.54e-02 2.01e+00
        pdb=" N   PRO A 185 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 364 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 365 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 365 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 365 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1049 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 68
        2.64 -     3.20: 5998
        3.20 -     3.77: 9393
        3.77 -     4.33: 12175
        4.33 -     4.90: 20108
  Nonbonded interactions: 47742
  Sorted by model distance:
  nonbonded pdb=" SD  MET B  60 "
            pdb="AL    AL A 601 "
     model   vdw
     2.070 2.380
  nonbonded pdb=" O   CYS A 176 "
            pdb=" OG  SER A 180 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   SER A 294 "
            pdb=" NE2 GLN A 297 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   SER B 294 "
            pdb=" NE2 GLN B 297 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   LYS B 228 "
            pdb=" ND2 ASN B 232 "
     model   vdw
     2.255 3.120
  ... (remaining 47737 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 405)
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.480
  Find NCS groups from input model:        0.220
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   6240  Z= 0.480
  Angle     :  0.755   6.503   8422  Z= 0.452
  Chirality :  0.042   0.136    974
  Planarity :  0.004   0.036   1052
  Dihedral  : 16.807  82.757   2288
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  :  7.82 %
    Favored  : 87.32 %
  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: -1.30 (0.27), residues: 766
  helix: -0.48 (0.18), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.07 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 255 
 HIS   0.004   0.002   HIS A 259 
 PHE   0.017   0.002   PHE B 206 
 TYR   0.011   0.002   TYR B 291 
 ARG   0.004   0.000   ARG B   9 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6086 (ttm110)
REVERT: A  230 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7110 (tptp)
REVERT: A  265 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6633 (tpp-160)
REVERT: A  304 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6693 (ttpt)
REVERT: A  321 MET cc_start: 0.8308 (mtt) cc_final: 0.8093 (mtt)
REVERT: A  331 MET cc_start: 0.5936 (mtm) cc_final: 0.5244 (mpp)
REVERT: B  265 ARG cc_start: 0.6818 (mmt180) cc_final: 0.6558 (tpp-160)
REVERT: B  321 MET cc_start: 0.8252 (mtt) cc_final: 0.8001 (mtt)
REVERT: B  331 MET cc_start: 0.6491 (mtm) cc_final: 0.5717 (mpp)
  outliers start: 33
  outliers final: 6
  residues processed: 167
  average time/residue: 0.2023
  time to fit residues: 43.1550
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 193 HIS
A 261 GLN
A 289 ASN
B 193 HIS
B 232 ASN
B 261 GLN
B 289 ASN
B 293 ASN
B 330 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.174150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.126700 restraints weight = 8511.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.130416 restraints weight = 5530.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.132847 restraints weight = 4366.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6240  Z= 0.182
  Angle     :  0.485   5.241   8422  Z= 0.264
  Chirality :  0.037   0.146    974
  Planarity :  0.004   0.034   1052
  Dihedral  :  5.625  52.654    842
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.67 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.30), residues: 766
  helix:  1.45 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.37 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.024   0.001   PHE B  38 
 TYR   0.016   0.001   TYR B  40 
 ARG   0.004   0.000   ARG A 311 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.6038 (pptt) cc_final: 0.5294 (pptt)
REVERT: A    5 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.6189 (ttm110)
REVERT: A  230 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6965 (tptp)
REVERT: A  331 MET cc_start: 0.5553 (mtm) cc_final: 0.4860 (mpp)
REVERT: B   79 ASN cc_start: 0.8645 (m-40) cc_final: 0.8422 (m110)
REVERT: B  265 ARG cc_start: 0.6876 (mmt180) cc_final: 0.6662 (tpp-160)
REVERT: B  331 MET cc_start: 0.6203 (mtm) cc_final: 0.5399 (mpp)
REVERT: B  377 MET cc_start: 0.7211 (mmt) cc_final: 0.6874 (mtt)
  outliers start: 22
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1980
  time to fit residues: 38.2508
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
A 261 GLN
B 261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.171131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.122931 restraints weight = 8581.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.126519 restraints weight = 5629.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.128772 restraints weight = 4459.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6240  Z= 0.240
  Angle     :  0.495   5.377   8422  Z= 0.268
  Chirality :  0.038   0.148    974
  Planarity :  0.003   0.038   1052
  Dihedral  :  4.633  42.488    836
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 18.73 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.31), residues: 766
  helix:  2.19 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.25 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.024   0.001   PHE B  38 
 TYR   0.020   0.002   TYR B  40 
 ARG   0.002   0.000   ARG B 284 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.6386 (ttm110)
REVERT: A   56 MET cc_start: 0.7560 (ptp) cc_final: 0.7247 (ptp)
REVERT: A  230 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6730 (tptp)
REVERT: A  321 MET cc_start: 0.8135 (mtt) cc_final: 0.7647 (mtt)
REVERT: A  331 MET cc_start: 0.5368 (mtm) cc_final: 0.4851 (mpp)
REVERT: B  244 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.7977 (t)
REVERT: B  265 ARG cc_start: 0.7090 (mmt180) cc_final: 0.6698 (tpp-160)
REVERT: B  270 GLN cc_start: 0.7916 (mt0) cc_final: 0.7595 (mp10)
REVERT: B  321 MET cc_start: 0.7873 (mtt) cc_final: 0.7376 (mtt)
REVERT: B  331 MET cc_start: 0.6163 (mtm) cc_final: 0.5279 (mpp)
REVERT: B  405 MET cc_start: 0.3629 (ttm) cc_final: 0.2347 (mpp)
  outliers start: 28
  outliers final: 16
  residues processed: 140
  average time/residue: 0.1791
  time to fit residues: 32.7149
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 68 optimal weight:    9.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B  96 GLN
B 261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.172525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.124230 restraints weight = 8704.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.128011 restraints weight = 5611.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.130267 restraints weight = 4416.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6240  Z= 0.219
  Angle     :  0.484   5.495   8422  Z= 0.261
  Chirality :  0.037   0.147    974
  Planarity :  0.003   0.036   1052
  Dihedral  :  4.315  37.895    835
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.24 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.31), residues: 766
  helix:  2.43 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.89 (0.62), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.016   0.001   PHE A 206 
 TYR   0.020   0.002   TYR B  40 
 ARG   0.002   0.000   ARG B  20 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7407 (mtt-85) cc_final: 0.6256 (ttm110)
REVERT: A   56 MET cc_start: 0.7613 (ptp) cc_final: 0.7325 (ptp)
REVERT: A  208 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7908 (mt0)
REVERT: A  230 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6698 (tptp)
REVERT: A  265 ARG cc_start: 0.7085 (tpp-160) cc_final: 0.6776 (tpp-160)
REVERT: A  321 MET cc_start: 0.8110 (mtt) cc_final: 0.7582 (mtt)
REVERT: A  331 MET cc_start: 0.5436 (mtm) cc_final: 0.4903 (mpp)
REVERT: A  377 MET cc_start: 0.7213 (mmt) cc_final: 0.6944 (mtt)
REVERT: B  244 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8015 (t)
REVERT: B  265 ARG cc_start: 0.7075 (mmt180) cc_final: 0.6706 (tpp-160)
REVERT: B  321 MET cc_start: 0.7846 (mtt) cc_final: 0.7331 (mtt)
REVERT: B  331 MET cc_start: 0.6104 (mtm) cc_final: 0.5258 (mpp)
  outliers start: 25
  outliers final: 18
  residues processed: 135
  average time/residue: 0.1939
  time to fit residues: 34.1088
Evaluate side-chains
  134 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.170072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.121840 restraints weight = 8574.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.125466 restraints weight = 5567.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127651 restraints weight = 4413.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6240  Z= 0.291
  Angle     :  0.529   7.760   8422  Z= 0.281
  Chirality :  0.038   0.162    974
  Planarity :  0.003   0.035   1052
  Dihedral  :  4.332  36.492    835
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.12 %
    Favored  : 74.04 %
  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:  3.00 (0.31), residues: 766
  helix:  2.45 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.75 (0.65), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.023   0.002   PHE B  38 
 TYR   0.021   0.002   TYR B  40 
 ARG   0.003   0.000   ARG A  20 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7610 (mtt-85) cc_final: 0.6331 (ttm110)
REVERT: A   56 MET cc_start: 0.7697 (ptp) cc_final: 0.7482 (ptp)
REVERT: A  230 LYS cc_start: 0.6939 (mmtt) cc_final: 0.6676 (tptp)
REVERT: A  265 ARG cc_start: 0.7037 (tpp-160) cc_final: 0.6748 (tpp-160)
REVERT: A  321 MET cc_start: 0.8085 (mtt) cc_final: 0.7553 (mtt)
REVERT: A  331 MET cc_start: 0.5545 (mtm) cc_final: 0.4991 (mpp)
REVERT: A  377 MET cc_start: 0.7261 (mmt) cc_final: 0.6905 (mtt)
REVERT: B  244 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8056 (t)
REVERT: B  265 ARG cc_start: 0.7113 (mmt180) cc_final: 0.6704 (tpp-160)
REVERT: B  270 GLN cc_start: 0.7976 (mt0) cc_final: 0.7629 (mp10)
REVERT: B  321 MET cc_start: 0.7939 (mtt) cc_final: 0.7438 (mtt)
REVERT: B  331 MET cc_start: 0.5938 (mtm) cc_final: 0.5163 (mpp)
  outliers start: 26
  outliers final: 18
  residues processed: 130
  average time/residue: 0.1905
  time to fit residues: 32.3538
Evaluate side-chains
  125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ARG
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0170
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 330 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.173262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.127475 restraints weight = 8078.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.130906 restraints weight = 5239.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.133150 restraints weight = 4123.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6240  Z= 0.156
  Angle     :  0.459   8.025   8422  Z= 0.243
  Chirality :  0.037   0.152    974
  Planarity :  0.003   0.034   1052
  Dihedral  :  3.900  25.576    834
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.75 %
    Favored  : 73.75 %
  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:  3.52 (0.31), residues: 766
  helix:  2.77 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.36 (0.66), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.011   0.001   PHE B 215 
 TYR   0.021   0.001   TYR B  40 
 ARG   0.002   0.000   ARG A  20 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.6474 (ttm110)
REVERT: A   56 MET cc_start: 0.7617 (ptp) cc_final: 0.7375 (ptp)
REVERT: A  321 MET cc_start: 0.7945 (mtt) cc_final: 0.7389 (mtt)
REVERT: A  331 MET cc_start: 0.5659 (mtm) cc_final: 0.4968 (mpp)
REVERT: A  377 MET cc_start: 0.7158 (mmt) cc_final: 0.6945 (mtt)
REVERT: B  244 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8044 (t)
REVERT: B  265 ARG cc_start: 0.7135 (mmt180) cc_final: 0.6647 (tpp-160)
REVERT: B  321 MET cc_start: 0.7881 (mtt) cc_final: 0.7333 (mtt)
REVERT: B  331 MET cc_start: 0.6080 (mtm) cc_final: 0.5341 (mpp)
REVERT: B  405 MET cc_start: 0.4032 (ttm) cc_final: 0.3647 (mpp)
  outliers start: 17
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1863
  time to fit residues: 33.9305
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ARG
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 261 GLN
B  79 ASN
B 261 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.169029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.123354 restraints weight = 8244.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.126755 restraints weight = 5379.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.128844 restraints weight = 4233.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6240  Z= 0.213
  Angle     :  0.495   6.415   8422  Z= 0.266
  Chirality :  0.037   0.156    974
  Planarity :  0.003   0.034   1052
  Dihedral  :  3.932  19.308    833
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 24.78 %
    Favored  : 73.16 %
  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:  3.57 (0.31), residues: 766
  helix:  2.87 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.41 (0.62), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.012   0.001   PHE B 206 
 TYR   0.023   0.002   TYR B  40 
 ARG   0.003   0.000   ARG B 284 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.6539 (ttm110)
REVERT: A   56 MET cc_start: 0.7641 (ptp) cc_final: 0.7385 (ptp)
REVERT: A  321 MET cc_start: 0.7888 (mtt) cc_final: 0.7343 (mtt)
REVERT: A  331 MET cc_start: 0.5586 (mtm) cc_final: 0.4873 (mpp)
REVERT: A  377 MET cc_start: 0.7090 (mmt) cc_final: 0.6828 (mtt)
REVERT: B    3 LYS cc_start: 0.6331 (pptt) cc_final: 0.5971 (pptt)
REVERT: B  244 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8002 (t)
REVERT: B  265 ARG cc_start: 0.7075 (mmt180) cc_final: 0.6617 (tpp-160)
REVERT: B  321 MET cc_start: 0.7780 (mtt) cc_final: 0.7265 (mtt)
REVERT: B  331 MET cc_start: 0.5981 (mtm) cc_final: 0.5234 (mpp)
  outliers start: 14
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1877
  time to fit residues: 29.8333
Evaluate side-chains
  117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0370
   chunk 10 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.172334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.125811 restraints weight = 8104.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.129589 restraints weight = 5142.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.131838 restraints weight = 3980.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6240  Z= 0.179
  Angle     :  0.496   9.206   8422  Z= 0.263
  Chirality :  0.037   0.151    974
  Planarity :  0.003   0.034   1052
  Dihedral  :  3.781  17.339    832
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 25.37 %
    Favored  : 72.12 %
  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:  3.56 (0.31), residues: 766
  helix:  2.81 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.34 (0.65), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.011   0.001   PHE B 206 
 TYR   0.028   0.001   TYR B 291 
 ARG   0.002   0.000   ARG B 284 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7641 (mtt-85) cc_final: 0.6350 (ttm110)
REVERT: A   56 MET cc_start: 0.7541 (ptp) cc_final: 0.7287 (ptp)
REVERT: A  321 MET cc_start: 0.7664 (mtt) cc_final: 0.7099 (mtt)
REVERT: A  331 MET cc_start: 0.5670 (mtm) cc_final: 0.4863 (mpp)
REVERT: B    3 LYS cc_start: 0.6198 (pptt) cc_final: 0.5818 (pptt)
REVERT: B  244 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.7920 (t)
REVERT: B  265 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6737 (ttm170)
REVERT: B  293 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8191 (t0)
REVERT: B  321 MET cc_start: 0.7538 (mtt) cc_final: 0.6986 (mtt)
REVERT: B  331 MET cc_start: 0.5925 (mtm) cc_final: 0.5027 (mpp)
  outliers start: 17
  outliers final: 11
  residues processed: 126
  average time/residue: 0.2016
  time to fit residues: 32.7323
Evaluate side-chains
  123 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.3980
   chunk 73 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.172650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.126649 restraints weight = 8180.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.130213 restraints weight = 5299.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.132438 restraints weight = 4149.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6240  Z= 0.174
  Angle     :  0.507  11.111   8422  Z= 0.264
  Chirality :  0.037   0.158    974
  Planarity :  0.003   0.036   1052
  Dihedral  :  3.741  17.708    832
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 25.96 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.67 (0.31), residues: 766
  helix:  2.88 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.28 (0.64), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.011   0.001   PHE A 206 
 TYR   0.030   0.002   TYR B 291 
 ARG   0.002   0.000   ARG B  20 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.6990 (ttm170)
REVERT: A   56 MET cc_start: 0.7513 (ptp) cc_final: 0.7291 (ptp)
REVERT: A  321 MET cc_start: 0.7668 (mtt) cc_final: 0.7088 (mtt)
REVERT: A  331 MET cc_start: 0.5802 (mtm) cc_final: 0.4802 (mpp)
REVERT: B    3 LYS cc_start: 0.6206 (pptt) cc_final: 0.5812 (pptt)
REVERT: B  244 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.7941 (t)
REVERT: B  265 ARG cc_start: 0.7091 (mmt180) cc_final: 0.6753 (ttm170)
REVERT: B  293 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7814 (t0)
REVERT: B  321 MET cc_start: 0.7644 (mtt) cc_final: 0.7089 (mtt)
REVERT: B  331 MET cc_start: 0.6041 (mtm) cc_final: 0.5049 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1885
  time to fit residues: 29.9301
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.167197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.122559 restraints weight = 8360.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.125893 restraints weight = 5359.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.127962 restraints weight = 4170.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6240  Z= 0.253
  Angle     :  0.549  10.996   8422  Z= 0.289
  Chirality :  0.038   0.196    974
  Planarity :  0.003   0.030   1052
  Dihedral  :  3.936  17.796    832
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 26.25 %
    Favored  : 71.39 %
  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 (0.31), residues: 766
  helix:  2.89 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.34 (0.62), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.016   0.001   PHE A 206 
 TYR   0.023   0.002   TYR B  40 
 ARG   0.003   0.000   ARG A 312 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.6530 (ttm110)
REVERT: A   56 MET cc_start: 0.7603 (ptp) cc_final: 0.7346 (ptp)
REVERT: A  321 MET cc_start: 0.7788 (mtt) cc_final: 0.7229 (mtt)
REVERT: A  331 MET cc_start: 0.5909 (mtm) cc_final: 0.4956 (mpp)
REVERT: B    3 LYS cc_start: 0.6306 (pptt) cc_final: 0.5787 (pptt)
REVERT: B  244 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8095 (t)
REVERT: B  265 ARG cc_start: 0.7181 (mmt180) cc_final: 0.6852 (ttm170)
REVERT: B  293 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7858 (t0)
REVERT: B  321 MET cc_start: 0.7782 (mtt) cc_final: 0.7239 (mtt)
REVERT: B  331 MET cc_start: 0.6063 (mtm) cc_final: 0.5254 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1766
  time to fit residues: 28.4395
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0060
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0070
   chunk 43 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.172478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.127303 restraints weight = 8336.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.130911 restraints weight = 5233.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.133144 restraints weight = 4039.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6240  Z= 0.174
  Angle     :  0.501   8.566   8422  Z= 0.264
  Chirality :  0.037   0.188    974
  Planarity :  0.003   0.029   1052
  Dihedral  :  3.723  17.364    832
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 26.99 %
    Favored  : 70.80 %
  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:  3.79 (0.31), residues: 766
  helix:  2.96 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.26 (0.66), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.010   0.001   PHE B 206 
 TYR   0.023   0.001   TYR B  40 
 ARG   0.002   0.000   ARG A 312 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2020.59 seconds
wall clock time: 36 minutes 59.68 seconds (2219.68 seconds total)