Starting phenix.real_space_refine
on Tue Mar 11 14:28:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vq7_32087/03_2025/7vq7_32087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vq7_32087/03_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_32087/03_2025/7vq7_32087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_2025/7vq7_32087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_2025/7vq7_32087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_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-5624/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: 4.31, per 1000 atoms: 0.70
  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: 1.60
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 0.42
  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: 1.58

  Time building geometry restraints manager: 1.76 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:             0.220
  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:          0.280
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     16.760
  Find NCS groups from input model:        0.270
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.470
-------------------------------------------------------------------------------
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  : 0.686 
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: 0.1964
  time to fit residues: 42.0267
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  : 0.817 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.126699 restraints weight = 8511.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.130476 restraints weight = 5530.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.132847 restraints weight = 4347.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
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  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.6056 (pptt) cc_final: 0.5304 (pptt)
REVERT: A    5 ARG cc_start: 0.7055 (mtt-85) cc_final: 0.6200 (ttm110)
REVERT: A  230 LYS cc_start: 0.7240 (mmtt) cc_final: 0.6983 (tptp)
REVERT: A  331 MET cc_start: 0.5582 (mtm) cc_final: 0.4898 (mpp)
REVERT: B   79 ASN cc_start: 0.8651 (m-40) cc_final: 0.8428 (m110)
REVERT: B  265 ARG cc_start: 0.6875 (mmt180) cc_final: 0.6664 (tpp-160)
REVERT: B  331 MET cc_start: 0.6225 (mtm) cc_final: 0.5431 (mpp)
REVERT: B  377 MET cc_start: 0.7205 (mmt) cc_final: 0.6879 (mtt)
  outliers start: 22
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1928
  time to fit residues: 37.2287
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  : 0.697 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.178180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.131157 restraints weight = 8544.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.135144 restraints weight = 5457.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.137515 restraints weight = 4273.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6240  Z= 0.157
  Angle     :  0.442   5.473   8422  Z= 0.239
  Chirality :  0.036   0.151    974
  Planarity :  0.003   0.039   1052
  Dihedral  :  4.263  34.571    836
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.85 %
    Favored  : 78.47 %
  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:  2.72 (0.31), residues: 766
  helix:  2.22 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.99 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.022   0.001   PHE B  38 
 TYR   0.019   0.001   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
  157 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7018 (mtt-85) cc_final: 0.6216 (ttm110)
REVERT: A  230 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6724 (tptp)
REVERT: A  321 MET cc_start: 0.8113 (mtt) cc_final: 0.7648 (mtt)
REVERT: A  331 MET cc_start: 0.5473 (mtm) cc_final: 0.4904 (mpp)
REVERT: B  159 MET cc_start: 0.7793 (tpt) cc_final: 0.7569 (tpt)
REVERT: B  265 ARG cc_start: 0.6999 (mmt180) cc_final: 0.6660 (tpp-160)
REVERT: B  321 MET cc_start: 0.7808 (mtt) cc_final: 0.7306 (mtt)
REVERT: B  331 MET cc_start: 0.6142 (mtm) cc_final: 0.5201 (mpp)
  outliers start: 25
  outliers final: 13
  residues processed: 146
  average time/residue: 0.1785
  time to fit residues: 34.2268
Evaluate side-chains
  130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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  315 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  147 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0770
   chunk 48 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.4146

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 232 ASN
A 261 GLN
B  79 ASN
B 261 GLN
B 393 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.173935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.124916 restraints weight = 8649.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.128768 restraints weight = 5512.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.131161 restraints weight = 4311.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6240  Z= 0.208
  Angle     :  0.473   5.344   8422  Z= 0.254
  Chirality :  0.037   0.152    974
  Planarity :  0.003   0.037   1052
  Dihedral  :  4.092  28.615    835
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.06 %
    Favored  : 76.11 %
  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:  2.38 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -0.73 (0.69), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.016   0.001   PHE B  38 
 TYR   0.020   0.002   TYR B  40 
 ARG   0.003   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
  144 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6278 (ttm110)
REVERT: A  208 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8021 (mt0)
REVERT: A  230 LYS cc_start: 0.6917 (mmtt) cc_final: 0.6700 (tptp)
REVERT: A  321 MET cc_start: 0.8013 (mtt) cc_final: 0.7458 (mtt)
REVERT: A  331 MET cc_start: 0.5413 (mtm) cc_final: 0.4843 (mpp)
REVERT: A  377 MET cc_start: 0.7141 (mmt) cc_final: 0.6890 (mtt)
REVERT: B  265 ARG cc_start: 0.7089 (mmt180) cc_final: 0.6675 (tpp-160)
REVERT: B  321 MET cc_start: 0.7763 (mtt) cc_final: 0.7190 (mtt)
REVERT: B  331 MET cc_start: 0.5905 (mtm) cc_final: 0.5076 (mpp)
  outliers start: 26
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1742
  time to fit residues: 30.7904
Evaluate side-chains
  128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
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  208 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  315 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  168 THR
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  261 GLN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 393 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.174322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.126112 restraints weight = 8462.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.129888 restraints weight = 5425.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.132144 restraints weight = 4280.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6240  Z= 0.231
  Angle     :  0.490   6.588   8422  Z= 0.261
  Chirality :  0.037   0.160    974
  Planarity :  0.003   0.035   1052
  Dihedral  :  4.012  23.745    834
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 20.65 %
    Favored  : 75.96 %
  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:  3.32 (0.31), residues: 766
  helix:  2.71 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.60 (0.64), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.014   0.001   PHE B  38 
 TYR   0.021   0.002   TYR B  40 
 ARG   0.002   0.000   ARG B  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
  143 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7355 (mtt-85) cc_final: 0.6232 (ttm110)
REVERT: A  208 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7908 (mt0)
REVERT: A  230 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6604 (tptp)
REVERT: A  321 MET cc_start: 0.7992 (mtt) cc_final: 0.7434 (mtt)
REVERT: A  331 MET cc_start: 0.5428 (mtm) cc_final: 0.4905 (mpp)
REVERT: A  377 MET cc_start: 0.7115 (mmt) cc_final: 0.6832 (mtt)
REVERT: B  244 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.7945 (t)
REVERT: B  265 ARG cc_start: 0.7123 (mmt180) cc_final: 0.6644 (tpp-160)
REVERT: B  321 MET cc_start: 0.7809 (mtt) cc_final: 0.7262 (mtt)
REVERT: B  331 MET cc_start: 0.6002 (mtm) cc_final: 0.5223 (mpp)
  outliers start: 23
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1887
  time to fit residues: 32.8046
Evaluate side-chains
  131 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   56 MET
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  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  168 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  288 LEU
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:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.170417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.124953 restraints weight = 8185.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.128313 restraints weight = 5294.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.130443 restraints weight = 4151.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6240  Z= 0.172
  Angle     :  0.461   5.934   8422  Z= 0.248
  Chirality :  0.036   0.154    974
  Planarity :  0.003   0.035   1052
  Dihedral  :  3.826  16.505    833
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.71 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.60 (0.31), residues: 766
  helix:  2.79 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.11 (0.70), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.012   0.001   PHE B 215 
 TYR   0.021   0.001   TYR B  40 
 ARG   0.001   0.000   ARG A   9 

*********************** 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
  141 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.6327 (ttm110)
REVERT: A  321 MET cc_start: 0.7762 (mtt) cc_final: 0.7218 (mtt)
REVERT: A  331 MET cc_start: 0.5417 (mtm) cc_final: 0.4642 (mpp)
REVERT: B  244 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8038 (t)
REVERT: B  265 ARG cc_start: 0.7061 (mmt180) cc_final: 0.6753 (ttm170)
REVERT: B  321 MET cc_start: 0.7727 (mtt) cc_final: 0.7220 (mtt)
REVERT: B  331 MET cc_start: 0.6038 (mtm) cc_final: 0.5280 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 133
  average time/residue: 0.1763
  time to fit residues: 31.1271
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   56 MET
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  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   56 MET
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:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.9588

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.170517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.125764 restraints weight = 8257.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129195 restraints weight = 5327.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.131232 restraints weight = 4153.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6240  Z= 0.187
  Angle     :  0.480   8.637   8422  Z= 0.259
  Chirality :  0.037   0.153    974
  Planarity :  0.003   0.036   1052
  Dihedral  :  3.762  17.002    832
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.86 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.58 (0.31), residues: 766
  helix:  2.77 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.07 (0.68), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.012   0.001   PHE B 206 
 TYR   0.036   0.002   TYR B 291 
 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
  139 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7484 (mtt-85) cc_final: 0.6392 (ttm110)
REVERT: A  321 MET cc_start: 0.7780 (mtt) cc_final: 0.7205 (mtt)
REVERT: A  331 MET cc_start: 0.5552 (mtm) cc_final: 0.4886 (mpp)
REVERT: B  244 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8013 (t)
REVERT: B  265 ARG cc_start: 0.7034 (mmt180) cc_final: 0.6745 (ttm170)
REVERT: B  293 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8180 (t0)
REVERT: B  321 MET cc_start: 0.7820 (mtt) cc_final: 0.7271 (mtt)
REVERT: B  331 MET cc_start: 0.6179 (mtm) cc_final: 0.5288 (mpp)
  outliers start: 19
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1768
  time to fit residues: 30.0435
Evaluate side-chains
  127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   56 MET
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  315 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   56 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 71 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 17 optimal weight:    0.3980
   chunk 10 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.173165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.126778 restraints weight = 8082.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.130314 restraints weight = 5283.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.132301 restraints weight = 4165.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6240  Z= 0.178
  Angle     :  0.487   9.976   8422  Z= 0.257
  Chirality :  0.037   0.176    974
  Planarity :  0.003   0.038   1052
  Dihedral  :  3.732  16.786    832
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.60 %
    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:  3.67 (0.31), residues: 766
  helix:  2.86 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.16 (0.66), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.013   0.001   PHE B 206 
 TYR   0.023   0.002   TYR B 291 
 ARG   0.002   0.000   ARG A 312 

*********************** 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
  135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.6379 (ttm110)
REVERT: A  291 TYR cc_start: 0.7486 (t80) cc_final: 0.7281 (t80)
REVERT: A  319 ASN cc_start: 0.7947 (m-40) cc_final: 0.7197 (t0)
REVERT: A  321 MET cc_start: 0.7583 (mtt) cc_final: 0.6991 (mtt)
REVERT: A  331 MET cc_start: 0.5747 (mtm) cc_final: 0.4842 (mpp)
REVERT: B  244 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8037 (t)
REVERT: B  265 ARG cc_start: 0.7045 (mmt180) cc_final: 0.6739 (ttm170)
REVERT: B  293 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7838 (t0)
REVERT: B  321 MET cc_start: 0.7695 (mtt) cc_final: 0.7125 (mtt)
REVERT: B  331 MET cc_start: 0.6138 (mtm) cc_final: 0.5187 (mpp)
  outliers start: 18
  outliers final: 12
  residues processed: 126
  average time/residue: 0.1749
  time to fit residues: 29.0733
Evaluate side-chains
  130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   56 MET
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  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   56 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.171742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.125225 restraints weight = 8152.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.128924 restraints weight = 5188.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.131200 restraints weight = 4013.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6240  Z= 0.194
  Angle     :  0.501  10.932   8422  Z= 0.261
  Chirality :  0.037   0.155    974
  Planarity :  0.003   0.037   1052
  Dihedral  :  3.739  16.870    832
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.45 %
    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:  3.75 (0.31), residues: 766
  helix:  2.92 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.19 (0.66), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.011   0.001   PHE B 206 
 TYR   0.013   0.001   TYR B 291 
 ARG   0.002   0.000   ARG A 312 

*********************** 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
  135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7504 (mtt-85) cc_final: 0.6375 (ttm110)
REVERT: A  319 ASN cc_start: 0.7961 (m-40) cc_final: 0.7138 (t0)
REVERT: A  321 MET cc_start: 0.7474 (mtt) cc_final: 0.6867 (mtt)
REVERT: A  331 MET cc_start: 0.5680 (mtm) cc_final: 0.4730 (mpp)
REVERT: B    3 LYS cc_start: 0.6321 (pptt) cc_final: 0.6046 (pptt)
REVERT: B  244 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.7990 (t)
REVERT: B  265 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6742 (ttm170)
REVERT: B  293 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7962 (t0)
REVERT: B  321 MET cc_start: 0.7618 (mtt) cc_final: 0.7056 (mtt)
REVERT: B  331 MET cc_start: 0.6120 (mtm) cc_final: 0.5086 (mpp)
  outliers start: 19
  outliers final: 13
  residues processed: 125
  average time/residue: 0.1754
  time to fit residues: 28.7992
Evaluate side-chains
  129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   56 MET
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  315 SER
Chi-restraints excluded: chain A residue  316 GLU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   56 MET
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:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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
B 393 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.166996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.122353 restraints weight = 8307.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.125645 restraints weight = 5349.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.127738 restraints weight = 4189.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6240  Z= 0.252
  Angle     :  0.539  10.869   8422  Z= 0.283
  Chirality :  0.038   0.183    974
  Planarity :  0.003   0.029   1052
  Dihedral  :  3.920  17.384    832
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.60 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.31), residues: 766
  helix:  2.91 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.35 (0.63), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.012   0.001   PHE B 206 
 TYR   0.027   0.002   TYR A 291 
 ARG   0.002   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
  136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.6414 (ttm110)
REVERT: A  319 ASN cc_start: 0.8043 (m-40) cc_final: 0.7219 (t0)
REVERT: A  321 MET cc_start: 0.7693 (mtt) cc_final: 0.7103 (mtt)
REVERT: A  331 MET cc_start: 0.5785 (mtm) cc_final: 0.4895 (mpp)
REVERT: B    3 LYS cc_start: 0.6436 (pptt) cc_final: 0.6065 (pptt)
REVERT: B   74 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8688 (tt)
REVERT: B  244 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8064 (t)
REVERT: B  265 ARG cc_start: 0.7061 (mmt180) cc_final: 0.6752 (ttm170)
REVERT: B  293 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7914 (t0)
REVERT: B  321 MET cc_start: 0.7802 (mtt) cc_final: 0.7257 (mtt)
REVERT: B  331 MET cc_start: 0.6157 (mtm) cc_final: 0.5372 (mpp)
  outliers start: 20
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1725
  time to fit residues: 29.2622
Evaluate side-chains
  124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    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   56 MET
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  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue   74 LEU
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 53 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0870
   chunk 43 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3865 r_free = 0.3865 target = 0.171316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.126221 restraints weight = 8325.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.129689 restraints weight = 5317.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.131906 restraints weight = 4135.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6240  Z= 0.184
  Angle     :  0.525  11.977   8422  Z= 0.271
  Chirality :  0.037   0.176    974
  Planarity :  0.003   0.029   1052
  Dihedral  :  3.799  17.886    832
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 24.93 %
    Favored  : 72.57 %
  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:  3.81 (0.31), residues: 766
  helix:  2.98 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.24 (0.66), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 
 PHE   0.011   0.001   PHE A 206 
 TYR   0.023   0.001   TYR B  40 
 ARG   0.003   0.000   ARG A 312 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2038.59 seconds
wall clock time: 36 minutes 42.24 seconds (2202.24 seconds total)