Starting phenix.real_space_refine
on Thu Feb 13 03:55:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s82_24889/02_2025/7s82_24889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s82_24889/02_2025/7s82_24889.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s82_24889/02_2025/7s82_24889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s82_24889/02_2025/7s82_24889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s82_24889/02_2025/7s82_24889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s82_24889/02_2025/7s82_24889.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4806 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    3104      2.51       5
     N     836      2.21       5
     O     920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4904
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2368
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
    Chain: "C"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "B"
      Number of atoms: 2368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2368
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
  Time building chain proxies: 3.59, per 1000 atoms: 0.73
  Number of scatterers: 4904
  At special positions: 0
  Unit cell: (73.789, 88.808, 73.789, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O     920      8.00
     N     836      7.00
     C    3104      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: 1.27
  Conformation dependent library (CDL) restraints added in 557.2 milliseconds
  

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 9 sheets defined
      28.4% alpha, 15.9% 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 10 through 15
      removed outlier: 4.306A  pdb=" N   GLY A  15 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 43
    Processing helix  chain 'A' and resid 53 through 61
      removed outlier: 3.725A  pdb=" N   ILE A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
    Processing helix  chain 'A' and resid 226 through 236
      removed outlier: 4.239A  pdb=" N   LYS A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 250
    Processing helix  chain 'A' and resid 250 through 258
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 292 through 301
    Processing helix  chain 'B' and resid 10 through 15
      removed outlier: 4.113A  pdb=" N   GLY B  15 " --> pdb=" O   GLY B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 43
      No H-bonds generated for 'chain 'B' and resid 41 through 43'
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.698A  pdb=" N   MET B  49 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 61
      removed outlier: 3.780A  pdb=" N   ILE B  59 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 214
    Processing helix  chain 'B' and resid 226 through 236
    Processing helix  chain 'B' and resid 243 through 250
    Processing helix  chain 'B' and resid 250 through 258
    Processing helix  chain 'B' and resid 260 through 275
    Processing helix  chain 'B' and resid 292 through 300
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75
      removed outlier: 4.165A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A  25 " --> pdb=" O   CYS A  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36
      removed outlier: 4.192A  pdb=" N   GLY A  79 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 129
      removed outlier: 3.616A  pdb=" N   TYR A 126 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118
    Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166
      removed outlier: 7.006A  pdb=" N   ALA A 173 " --> pdb=" O   HIS A 164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 75
      removed outlier: 4.256A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   ASN B  28 " --> pdb=" O   PRO B  39 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   CYS B  38 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 75
      removed outlier: 4.256A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118
      removed outlier: 5.681A  pdb=" N   TYR B 118 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166
      removed outlier: 6.853A  pdb=" N   ALA B 173 " --> pdb=" O   HIS B 164 " (cutoff:3.500A)

    170 hydrogen bonds defined for protein.
    462 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: 1.25

  Time building geometry restraints manager: 1.41 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: 1603
        1.34 -     1.45: 759
        1.45 -     1.57: 2582
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 5010
  Sorted by residual:
  bond pdb=" CA  MET B  82 "
       pdb=" C   MET B  82 "
    ideal  model  delta    sigma   weight residual
    1.533  1.513  0.020 9.60e-03 1.09e+04 4.17e+00
  bond pdb=" CB  THR A 175 "
       pdb=" CG2 THR A 175 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.18e+00
  bond pdb=" CG  MET B 264 "
       pdb=" SD  MET B 264 "
    ideal  model  delta    sigma   weight residual
    1.803  1.768  0.035 2.50e-02 1.60e+03 1.94e+00
  bond pdb=" C   PRO A 122 "
       pdb=" N   SER A 123 "
    ideal  model  delta    sigma   weight residual
    1.331  1.307  0.024 1.73e-02 3.34e+03 1.90e+00
  bond pdb=" CG  LEU B  87 "
       pdb=" CD1 LEU B  87 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.85e+00
  ... (remaining 5005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 6465
        1.47 -     2.94: 261
        2.94 -     4.41: 60
        4.41 -     5.87: 10
        5.87 -     7.34: 4
  Bond angle restraints: 6800
  Sorted by residual:
  angle pdb=" CA  MET B   6 "
        pdb=" CB  MET B   6 "
        pdb=" CG  MET B   6 "
      ideal   model   delta    sigma   weight residual
     114.10  121.44   -7.34 2.00e+00 2.50e-01 1.35e+01
  angle pdb=" CG  MET B 264 "
        pdb=" SD  MET B 264 "
        pdb=" CE  MET B 264 "
      ideal   model   delta    sigma   weight residual
     100.90   94.43    6.47 2.20e+00 2.07e-01 8.65e+00
  angle pdb=" N   ILE A  78 "
        pdb=" CA  ILE A  78 "
        pdb=" C   ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.88  108.85    3.03 1.06e+00 8.90e-01 8.20e+00
  angle pdb=" CA  GLN B  83 "
        pdb=" CB  GLN B  83 "
        pdb=" CG  GLN B  83 "
      ideal   model   delta    sigma   weight residual
     114.10  119.76   -5.66 2.00e+00 2.50e-01 8.00e+00
  angle pdb=" N   GLN B  83 "
        pdb=" CA  GLN B  83 "
        pdb=" C   GLN B  83 "
      ideal   model   delta    sigma   weight residual
     110.36  106.14    4.22 1.55e+00 4.16e-01 7.40e+00
  ... (remaining 6795 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2694
       17.98 -    35.95: 223
       35.95 -    53.93: 30
       53.93 -    71.90: 4
       71.90 -    89.88: 3
  Dihedral angle restraints: 2954
    sinusoidal: 1142
      harmonic: 1812
  Sorted by residual:
  dihedral pdb=" CA  GLN B  83 "
           pdb=" C   GLN B  83 "
           pdb=" N   ASN B  84 "
           pdb=" CA  ASN B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.04  -24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  THR A 175 "
           pdb=" C   THR A 175 "
           pdb=" N   ASP A 176 "
           pdb=" CA  ASP A 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.13   21.87     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  PRO A   9 "
           pdb=" C   PRO A   9 "
           pdb=" N   SER A  10 "
           pdb=" CA  SER A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.54  -17.46     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 2951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 380
       0.027 -    0.053: 233
       0.053 -    0.080: 92
       0.080 -    0.106: 50
       0.106 -    0.133: 11
  Chirality restraints: 766
  Sorted by residual:
  chirality pdb=" CA  ILE A 281 "
            pdb=" N   ILE A 281 "
            pdb=" C   ILE A 281 "
            pdb=" CB  ILE A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  ASP B 155 "
            pdb=" N   ASP B 155 "
            pdb=" C   ASP B 155 "
            pdb=" CB  ASP B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  ILE B 281 "
            pdb=" N   ILE B 281 "
            pdb=" C   ILE B 281 "
            pdb=" CB  ILE B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 763 not shown)

  Planarity restraints: 884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 209 "   -0.015 2.00e-02 2.50e+03   1.81e-02 6.53e+00
        pdb=" CG  TYR B 209 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 209 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 209 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 209 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 209 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 209 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 209 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 251 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.29e+00
        pdb=" N   PRO B 252 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 252 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 252 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  51 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO B  52 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B  52 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  52 "    0.022 5.00e-02 4.00e+02
  ... (remaining 881 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 121
        2.66 -     3.22: 4905
        3.22 -     3.78: 7818
        3.78 -     4.34: 10519
        4.34 -     4.90: 17589
  Nonbonded interactions: 40952
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B  83 "
            pdb=" O   GLU B 178 "
     model   vdw
     2.097 3.120
  nonbonded pdb=" OG1 THR B 292 "
            pdb=" OD2 ASP B 295 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER A 145 "
            pdb=" O   GLN C   0 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" NE2 GLN A  19 "
            pdb=" OD1 ASN A 119 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR A 224 "
            pdb=" OD1 ASP A 263 "
     model   vdw
     2.227 3.040
  ... (remaining 40947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.69 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.190
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
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      :  0.005   0.049   5010  Z= 0.329
  Angle     :  0.720   7.342   6800  Z= 0.389
  Chirality :  0.042   0.133    766
  Planarity :  0.005   0.045    884
  Dihedral  : 13.223  89.878   1794
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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: -1.35 (0.34), residues: 626
  helix:  0.93 (0.43), residues: 154
  sheet: -3.05 (0.48), residues: 108
  loop : -0.97 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  31 
 HIS   0.005   0.001   HIS A  41 
 PHE   0.026   0.002   PHE B 185 
 TYR   0.040   0.003   TYR B 209 
 ARG   0.007   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A  119 ASN cc_start: 0.8211 (t0) cc_final: 0.7954 (t0)
REVERT: A  240 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: C    4 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7755 (ttt-90)
REVERT: B   16 CYS cc_start: 0.7927 (p) cc_final: 0.7536 (p)
REVERT: B  130 MET cc_start: 0.8387 (tpp) cc_final: 0.8178 (ttt)
REVERT: B  175 THR cc_start: 0.8938 (p) cc_final: 0.8668 (t)
REVERT: B  240 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7554 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1423
  time to fit residues: 25.3206
Evaluate side-chains
  108 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A  74 GLN
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
A 299 GLN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.127404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.107000 restraints weight = 8537.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.111263 restraints weight = 4331.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.114239 restraints weight = 2755.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5010  Z= 0.320
  Angle     :  0.691   7.994   6800  Z= 0.354
  Chirality :  0.043   0.150    766
  Planarity :  0.005   0.051    884
  Dihedral  :  5.274  31.269    678
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.58 %
    Favored  : 87.13 %
  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: -1.38 (0.33), residues: 626
  helix:  0.87 (0.41), residues: 152
  sheet: -3.97 (0.48), residues: 64
  loop : -1.11 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  31 
 HIS   0.005   0.001   HIS B  41 
 PHE   0.017   0.001   PHE A 181 
 TYR   0.019   0.002   TYR B 209 
 ARG   0.006   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8381 (t0) cc_final: 0.7985 (t0)
REVERT: A  289 ASP cc_start: 0.8428 (p0) cc_final: 0.8122 (p0)
REVERT: B   16 CYS cc_start: 0.8125 (p) cc_final: 0.7612 (p)
REVERT: B   82 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (ttt)
REVERT: B  130 MET cc_start: 0.8480 (tpp) cc_final: 0.8236 (ttt)
REVERT: B  175 THR cc_start: 0.9062 (p) cc_final: 0.8707 (t)
REVERT: B  240 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7520 (tm-30)
REVERT: D    0 GLN cc_start: 0.8317 (mm110) cc_final: 0.8085 (mm-40)
  outliers start: 7
  outliers final: 4
  residues processed: 116
  average time/residue: 0.1362
  time to fit residues: 21.5829
Evaluate side-chains
  115 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  177 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 61 optimal weight:    0.4980
   chunk 51 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  19 GLN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.132590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.112716 restraints weight = 8416.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.117157 restraints weight = 4170.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.120214 restraints weight = 2577.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5010  Z= 0.176
  Angle     :  0.612   6.383   6800  Z= 0.311
  Chirality :  0.042   0.198    766
  Planarity :  0.004   0.045    884
  Dihedral  :  4.885  25.712    678
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.68 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.33), residues: 626
  helix:  1.04 (0.42), residues: 152
  sheet: -2.87 (0.52), residues: 88
  loop : -1.10 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  31 
 HIS   0.013   0.002   HIS B  41 
 PHE   0.011   0.001   PHE A 181 
 TYR   0.030   0.002   TYR A 161 
 ARG   0.004   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8248 (t0) cc_final: 0.7863 (t0)
REVERT: A  276 MET cc_start: 0.8761 (tpp) cc_final: 0.8408 (mmm)
REVERT: A  289 ASP cc_start: 0.8237 (p0) cc_final: 0.8009 (p0)
REVERT: B    6 MET cc_start: 0.7781 (tpt) cc_final: 0.7129 (tpt)
REVERT: B   16 CYS cc_start: 0.7938 (p) cc_final: 0.7500 (p)
REVERT: B  119 ASN cc_start: 0.8205 (t0) cc_final: 0.7949 (t0)
REVERT: B  175 THR cc_start: 0.8964 (p) cc_final: 0.8635 (t)
  outliers start: 10
  outliers final: 1
  residues processed: 137
  average time/residue: 0.1452
  time to fit residues: 26.8024
Evaluate side-chains
  115 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    1 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 60 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 11 optimal weight:    0.2980
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 246 HIS
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.130912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.110950 restraints weight = 8538.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.115351 restraints weight = 4211.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.118449 restraints weight = 2613.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5010  Z= 0.215
  Angle     :  0.638   7.209   6800  Z= 0.319
  Chirality :  0.041   0.148    766
  Planarity :  0.004   0.047    884
  Dihedral  :  4.784  23.571    678
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 17.65 %
    Favored  : 81.62 %
  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: -1.20 (0.33), residues: 626
  helix:  1.15 (0.42), residues: 152
  sheet: -3.68 (0.53), residues: 64
  loop : -1.09 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  31 
 HIS   0.004   0.001   HIS A  41 
 PHE   0.010   0.001   PHE B 140 
 TYR   0.029   0.002   TYR A 161 
 ARG   0.007   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8327 (t0) cc_final: 0.7881 (t0)
REVERT: A  270 GLU cc_start: 0.7910 (tp30) cc_final: 0.7507 (tp30)
REVERT: A  289 ASP cc_start: 0.8417 (p0) cc_final: 0.8082 (p0)
REVERT: B   16 CYS cc_start: 0.8106 (p) cc_final: 0.7696 (p)
REVERT: B   83 GLN cc_start: 0.8189 (tt0) cc_final: 0.7893 (tt0)
REVERT: B  119 ASN cc_start: 0.8303 (t0) cc_final: 0.8019 (t0)
REVERT: B  130 MET cc_start: 0.8440 (tpp) cc_final: 0.8024 (ttt)
REVERT: B  175 THR cc_start: 0.9023 (p) cc_final: 0.8574 (t)
  outliers start: 4
  outliers final: 4
  residues processed: 122
  average time/residue: 0.1361
  time to fit residues: 22.7253
Evaluate side-chains
  118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  19 GLN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.128163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.108334 restraints weight = 8649.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.112611 restraints weight = 4346.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.115557 restraints weight = 2726.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5010  Z= 0.246
  Angle     :  0.632   6.987   6800  Z= 0.313
  Chirality :  0.042   0.163    766
  Planarity :  0.004   0.047    884
  Dihedral  :  4.767  23.321    678
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.10 %
    Favored  : 80.70 %
  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: -1.11 (0.33), residues: 626
  helix:  1.31 (0.43), residues: 152
  sheet: -3.46 (0.53), residues: 64
  loop : -1.10 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  31 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.029   0.002   TYR B 161 
 ARG   0.008   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8489 (p0) cc_final: 0.8269 (p0)
REVERT: A  119 ASN cc_start: 0.8330 (t0) cc_final: 0.7899 (t0)
REVERT: A  270 GLU cc_start: 0.7878 (tp30) cc_final: 0.7475 (tp30)
REVERT: A  276 MET cc_start: 0.8824 (tpp) cc_final: 0.8157 (mmm)
REVERT: B   16 CYS cc_start: 0.8196 (p) cc_final: 0.7762 (p)
REVERT: B   83 GLN cc_start: 0.8144 (tt0) cc_final: 0.7939 (tt0)
REVERT: B  119 ASN cc_start: 0.8334 (t0) cc_final: 0.8032 (t0)
REVERT: B  175 THR cc_start: 0.8995 (p) cc_final: 0.8547 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 130
  average time/residue: 0.1466
  time to fit residues: 24.8002
Evaluate side-chains
  121 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain C residue   -2 VAL
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.106543 restraints weight = 8712.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.110562 restraints weight = 4479.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.113251 restraints weight = 2854.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5010  Z= 0.212
  Angle     :  0.653   7.421   6800  Z= 0.321
  Chirality :  0.042   0.178    766
  Planarity :  0.004   0.048    884
  Dihedral  :  4.753  24.614    678
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.30 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.33), residues: 626
  helix:  1.31 (0.43), residues: 152
  sheet: -2.66 (0.54), residues: 88
  loop : -1.13 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  31 
 HIS   0.006   0.001   HIS A  41 
 PHE   0.015   0.001   PHE B 150 
 TYR   0.029   0.002   TYR B 161 
 ARG   0.008   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8518 (p0) cc_final: 0.8285 (p0)
REVERT: A  119 ASN cc_start: 0.8334 (t0) cc_final: 0.7894 (t0)
REVERT: A  270 GLU cc_start: 0.7930 (tp30) cc_final: 0.7512 (tp30)
REVERT: A  276 MET cc_start: 0.8794 (tpp) cc_final: 0.8192 (mmm)
REVERT: B   16 CYS cc_start: 0.8270 (p) cc_final: 0.7892 (p)
REVERT: B   54 TYR cc_start: 0.7586 (m-80) cc_final: 0.7351 (m-80)
REVERT: B  119 ASN cc_start: 0.8334 (t0) cc_final: 0.8042 (t0)
REVERT: B  130 MET cc_start: 0.8419 (tpp) cc_final: 0.7926 (ttt)
REVERT: B  175 THR cc_start: 0.9031 (p) cc_final: 0.8539 (t)
REVERT: D    4 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7590 (ptm-80)
  outliers start: 13
  outliers final: 9
  residues processed: 124
  average time/residue: 0.1325
  time to fit residues: 22.4687
Evaluate side-chains
  117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.112712 restraints weight = 8341.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.116913 restraints weight = 4312.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.119775 restraints weight = 2751.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5010  Z= 0.193
  Angle     :  0.653   9.869   6800  Z= 0.317
  Chirality :  0.042   0.148    766
  Planarity :  0.004   0.048    884
  Dihedral  :  4.650  22.273    678
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.40 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.33), residues: 626
  helix:  1.15 (0.42), residues: 154
  sheet: -3.16 (0.58), residues: 64
  loop : -1.14 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  31 
 HIS   0.006   0.001   HIS A 164 
 PHE   0.011   0.001   PHE B 230 
 TYR   0.026   0.002   TYR B 161 
 ARG   0.009   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8280 (t0) cc_final: 0.7836 (t0)
REVERT: A  175 THR cc_start: 0.8987 (p) cc_final: 0.8736 (p)
REVERT: A  270 GLU cc_start: 0.7850 (tp30) cc_final: 0.7538 (tp30)
REVERT: A  276 MET cc_start: 0.8769 (tpp) cc_final: 0.8170 (mmm)
REVERT: A  289 ASP cc_start: 0.8379 (p0) cc_final: 0.7962 (p0)
REVERT: B   16 CYS cc_start: 0.8195 (p) cc_final: 0.7812 (p)
REVERT: B  119 ASN cc_start: 0.8262 (t0) cc_final: 0.7976 (t0)
REVERT: B  130 MET cc_start: 0.8345 (tpp) cc_final: 0.7807 (ttt)
REVERT: B  175 THR cc_start: 0.9009 (p) cc_final: 0.8534 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 124
  average time/residue: 0.1409
  time to fit residues: 23.2376
Evaluate side-chains
  115 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 HIS
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.132416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.112176 restraints weight = 8684.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.116435 restraints weight = 4382.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.119305 restraints weight = 2750.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5010  Z= 0.195
  Angle     :  0.661  11.106   6800  Z= 0.321
  Chirality :  0.042   0.164    766
  Planarity :  0.005   0.061    884
  Dihedral  :  4.681  21.135    678
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 22.06 %
    Favored  : 76.10 %
  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: -1.19 (0.33), residues: 626
  helix:  1.22 (0.42), residues: 154
  sheet: -3.36 (0.54), residues: 74
  loop : -1.11 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  31 
 HIS   0.006   0.001   HIS A 164 
 PHE   0.011   0.001   PHE B 150 
 TYR   0.027   0.002   TYR B 161 
 ARG   0.008   0.001   ARG C   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8352 (t0) cc_final: 0.7885 (t0)
REVERT: A  270 GLU cc_start: 0.7869 (tp30) cc_final: 0.7536 (tp30)
REVERT: A  276 MET cc_start: 0.8775 (tpp) cc_final: 0.8415 (mmm)
REVERT: A  289 ASP cc_start: 0.8385 (p0) cc_final: 0.7943 (p0)
REVERT: B   16 CYS cc_start: 0.8282 (p) cc_final: 0.7956 (p)
REVERT: B  119 ASN cc_start: 0.8325 (t0) cc_final: 0.8048 (t0)
REVERT: B  130 MET cc_start: 0.8382 (tpp) cc_final: 0.7765 (ttt)
REVERT: B  175 THR cc_start: 0.9019 (p) cc_final: 0.8530 (t)
REVERT: B  279 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7736 (ptt90)
  outliers start: 10
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1517
  time to fit residues: 25.4144
Evaluate side-chains
  121 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  279 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 11 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.3564

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.131178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.111109 restraints weight = 8417.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.115357 restraints weight = 4297.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.118243 restraints weight = 2720.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5010  Z= 0.230
  Angle     :  0.673   9.833   6800  Z= 0.326
  Chirality :  0.043   0.178    766
  Planarity :  0.005   0.051    884
  Dihedral  :  4.704  20.655    678
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 22.98 %
    Favored  : 75.37 %
  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: -1.16 (0.33), residues: 626
  helix:  1.23 (0.42), residues: 154
  sheet: -3.36 (0.54), residues: 74
  loop : -1.08 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  31 
 HIS   0.006   0.001   HIS B  41 
 PHE   0.011   0.001   PHE B 150 
 TYR   0.026   0.003   TYR B 161 
 ARG   0.012   0.001   ARG D   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8314 (t0) cc_final: 0.7854 (t0)
REVERT: A  166 GLU cc_start: 0.8353 (tt0) cc_final: 0.8034 (tt0)
REVERT: A  175 THR cc_start: 0.9018 (p) cc_final: 0.8756 (p)
REVERT: A  270 GLU cc_start: 0.7837 (tp30) cc_final: 0.7525 (tp30)
REVERT: A  276 MET cc_start: 0.8754 (tpp) cc_final: 0.8036 (mmm)
REVERT: A  289 ASP cc_start: 0.8417 (p0) cc_final: 0.7996 (p0)
REVERT: B   16 CYS cc_start: 0.8402 (p) cc_final: 0.8056 (p)
REVERT: B  119 ASN cc_start: 0.8312 (t0) cc_final: 0.8065 (t0)
REVERT: B  130 MET cc_start: 0.8412 (tpp) cc_final: 0.7806 (ttt)
REVERT: B  175 THR cc_start: 0.9008 (p) cc_final: 0.8505 (t)
  outliers start: 9
  outliers final: 7
  residues processed: 116
  average time/residue: 0.1231
  time to fit residues: 19.7935
Evaluate side-chains
  114 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.131578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.111595 restraints weight = 8419.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.115905 restraints weight = 4147.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.118850 restraints weight = 2609.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5010  Z= 0.272
  Angle     :  0.688   9.772   6800  Z= 0.339
  Chirality :  0.043   0.179    766
  Planarity :  0.005   0.052    884
  Dihedral  :  4.796  20.194    678
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 22.24 %
    Favored  : 76.29 %
  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: -1.16 (0.33), residues: 626
  helix:  1.22 (0.42), residues: 154
  sheet: -3.41 (0.53), residues: 74
  loop : -1.05 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  31 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.012   0.001   PHE B 140 
 TYR   0.050   0.003   TYR A 209 
 ARG   0.008   0.001   ARG D   4 

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8347 (t0) cc_final: 0.7899 (t0)
REVERT: A  166 GLU cc_start: 0.8426 (tt0) cc_final: 0.8121 (tt0)
REVERT: A  175 THR cc_start: 0.9026 (p) cc_final: 0.8781 (p)
REVERT: A  270 GLU cc_start: 0.7867 (tp30) cc_final: 0.7550 (tp30)
REVERT: A  276 MET cc_start: 0.8758 (tpp) cc_final: 0.8039 (mmm)
REVERT: A  289 ASP cc_start: 0.8457 (p0) cc_final: 0.8197 (p0)
REVERT: B   16 CYS cc_start: 0.8511 (p) cc_final: 0.8215 (p)
REVERT: B   26 THR cc_start: 0.8030 (m) cc_final: 0.7764 (m)
REVERT: B  119 ASN cc_start: 0.8379 (t0) cc_final: 0.8173 (t0)
REVERT: B  130 MET cc_start: 0.8432 (tpp) cc_final: 0.7967 (ttt)
REVERT: B  162 MET cc_start: 0.8595 (ttm) cc_final: 0.8324 (ttt)
  outliers start: 8
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1357
  time to fit residues: 20.5228
Evaluate side-chains
  110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0870
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.132703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.112449 restraints weight = 8643.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.116610 restraints weight = 4466.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.119435 restraints weight = 2849.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5010  Z= 0.218
  Angle     :  0.668  10.588   6800  Z= 0.324
  Chirality :  0.042   0.175    766
  Planarity :  0.004   0.050    884
  Dihedral  :  4.708  20.148    678
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 23.53 %
    Favored  : 75.55 %
  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: -1.18 (0.33), residues: 626
  helix:  1.21 (0.42), residues: 154
  sheet: -3.00 (0.48), residues: 98
  loop : -0.99 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  31 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.023   0.002   TYR B 161 
 ARG   0.008   0.001   ARG C   4 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1892.10 seconds
wall clock time: 34 minutes 40.71 seconds (2080.71 seconds total)