Starting phenix.real_space_refine
on Tue Mar  3 20:48:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s82_24889/03_2026/7s82_24889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s82_24889/03_2026/7s82_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_24889/03_2026/7s82_24889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s82_24889/03_2026/7s82_24889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s82_24889/03_2026/7s82_24889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s82_24889/03_2026/7s82_24889.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.01, per 1000 atoms: 0.21
  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: 0.31
  Conformation dependent library (CDL) restraints added in 288.0 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: 0.19
  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: 0.63

  Time building geometry restraints manager: 0.46 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: 0.01
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.900
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.060
-------------------------------------------------------------------------------
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= 0.223
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG C   4 
 TYR   0.040   0.003   TYR B 209 
 PHE   0.026   0.002   PHE B 185 
 TRP   0.010   0.001   TRP A  31 
 HIS   0.005   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 5010)
  covalent geometry    : angle       0.72045 ( 6800)
  hydrogen bonds       : bond        0.20743 (  157)
  hydrogen bonds       : angle       9.17757 (  462)

*********************** 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  : 0.157 
Fit side-chains
REVERT: A  119 ASN cc_start: 0.8212 (t0) cc_final: 0.7955 (t0)
REVERT: A  240 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: C    4 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7754 (ttt-90)
REVERT: B   16 CYS cc_start: 0.7927 (p) cc_final: 0.7534 (p)
REVERT: B  130 MET cc_start: 0.8387 (tpp) cc_final: 0.8178 (ttt)
REVERT: B  175 THR cc_start: 0.8937 (p) cc_final: 0.8668 (t)
REVERT: B  240 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7555 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0552
  time to fit residues: 10.1178
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  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
A 299 GLN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.127777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.107618 restraints weight = 8651.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.111815 restraints weight = 4324.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.114719 restraints weight = 2747.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116627 restraints weight = 1984.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.118021 restraints weight = 1566.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1610

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= 0.152
  Angle     :  0.666   7.485   6800  Z= 0.340
  Chirality :  0.042   0.152    766
  Planarity :  0.005   0.050    884
  Dihedral  :  5.162  31.491    678
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.11 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.32), residues: 626
  helix:  0.90 (0.41), residues: 152
  sheet: -3.91 (0.48), residues: 64
  loop : -1.09 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C   4 
 TYR   0.019   0.002   TYR A 161 
 PHE   0.017   0.001   PHE A 181 
 TRP   0.008   0.001   TRP A  31 
 HIS   0.005   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5010)
  covalent geometry    : angle       0.66644 ( 6800)
  hydrogen bonds       : bond        0.04970 (  157)
  hydrogen bonds       : angle       6.41577 (  462)

*********************** 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
  126 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8812 (mt) cc_final: 0.8396 (mt)
REVERT: A  119 ASN cc_start: 0.8327 (t0) cc_final: 0.7934 (t0)
REVERT: A  240 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: A  289 ASP cc_start: 0.8404 (p0) cc_final: 0.8143 (p0)
REVERT: B   16 CYS cc_start: 0.8024 (p) cc_final: 0.7575 (p)
REVERT: B  130 MET cc_start: 0.8439 (tpp) cc_final: 0.8215 (ttt)
REVERT: B  175 THR cc_start: 0.9012 (p) cc_final: 0.8696 (t)
REVERT: B  240 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7512 (tm-30)
  outliers start: 7
  outliers final: 2
  residues processed: 120
  average time/residue: 0.0620
  time to fit residues: 10.1351
Evaluate side-chains
  114 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
B  19 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 = 0.3768 r_free = 0.3768 target = 0.129360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109509 restraints weight = 8580.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.113711 restraints weight = 4399.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116695 restraints weight = 2804.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.118652 restraints weight = 2016.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.120051 restraints weight = 1584.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5010  Z= 0.162
  Angle     :  0.642   7.025   6800  Z= 0.325
  Chirality :  0.042   0.143    766
  Planarity :  0.005   0.046    884
  Dihedral  :  4.981  27.446    678
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.05 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.33), residues: 626
  helix:  1.06 (0.42), residues: 152
  sheet: -3.72 (0.51), residues: 64
  loop : -1.09 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C   4 
 TYR   0.032   0.002   TYR A 161 
 PHE   0.010   0.001   PHE B 140 
 TRP   0.003   0.001   TRP A  31 
 HIS   0.008   0.002   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 5010)
  covalent geometry    : angle       0.64175 ( 6800)
  hydrogen bonds       : bond        0.04372 (  157)
  hydrogen bonds       : angle       5.95957 (  462)

*********************** 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
  128 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 123
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8304 (t0) cc_final: 0.7892 (t0)
REVERT: A  289 ASP cc_start: 0.8391 (p0) cc_final: 0.8132 (p0)
REVERT: B    6 MET cc_start: 0.8023 (tpt) cc_final: 0.7407 (tpt)
REVERT: B   16 CYS cc_start: 0.8061 (p) cc_final: 0.7637 (p)
REVERT: B  119 ASN cc_start: 0.8231 (t0) cc_final: 0.7991 (t0)
REVERT: B  175 THR cc_start: 0.9051 (p) cc_final: 0.8679 (t)
REVERT: B  240 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7703 (tm-30)
  outliers start: 5
  outliers final: 3
  residues processed: 124
  average time/residue: 0.0582
  time to fit residues: 9.8430
Evaluate side-chains
  114 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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
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 = 0.3721 r_free = 0.3721 target = 0.126205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.106206 restraints weight = 8590.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.110468 restraints weight = 4288.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.113407 restraints weight = 2691.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115371 restraints weight = 1930.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.116591 restraints weight = 1510.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5010  Z= 0.215
  Angle     :  0.668   7.348   6800  Z= 0.336
  Chirality :  0.043   0.148    766
  Planarity :  0.005   0.048    884
  Dihedral  :  5.047  23.968    678
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.36 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.33), residues: 626
  helix:  1.09 (0.43), residues: 152
  sheet: -3.76 (0.54), residues: 60
  loop : -1.21 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   4 
 TYR   0.029   0.003   TYR B 161 
 PHE   0.010   0.001   PHE B 230 
 TRP   0.005   0.001   TRP A  31 
 HIS   0.005   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 5010)
  covalent geometry    : angle       0.66818 ( 6800)
  hydrogen bonds       : bond        0.04052 (  157)
  hydrogen bonds       : angle       5.79562 (  462)

*********************** 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
  119 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8342 (t0) cc_final: 0.7906 (t0)
REVERT: A  270 GLU cc_start: 0.7864 (tp30) cc_final: 0.7465 (tp30)
REVERT: A  276 MET cc_start: 0.8788 (tpp) cc_final: 0.8206 (mmm)
REVERT: A  289 ASP cc_start: 0.8495 (p0) cc_final: 0.8184 (p0)
REVERT: B   16 CYS cc_start: 0.8327 (p) cc_final: 0.7936 (p)
REVERT: B  119 ASN cc_start: 0.8298 (t0) cc_final: 0.8082 (t0)
REVERT: B  130 MET cc_start: 0.8444 (tpp) cc_final: 0.8159 (ttt)
REVERT: B  175 THR cc_start: 0.9056 (p) cc_final: 0.8540 (t)
REVERT: B  240 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7616 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 114
  average time/residue: 0.0536
  time to fit residues: 8.5429
Evaluate side-chains
  110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   32 LEU
Chi-restraints excluded: chain B residue  264 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 GLN
** 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 = 0.3719 r_free = 0.3719 target = 0.126261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.106220 restraints weight = 8702.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.110262 restraints weight = 4512.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.113060 restraints weight = 2886.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114887 restraints weight = 2097.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.116006 restraints weight = 1669.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2603

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= 0.123
  Angle     :  0.623   6.497   6800  Z= 0.309
  Chirality :  0.041   0.135    766
  Planarity :  0.004   0.048    884
  Dihedral  :  4.818  23.706    678
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.10 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.33), residues: 626
  helix:  1.26 (0.43), residues: 152
  sheet: -3.74 (0.50), residues: 64
  loop : -1.13 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C   4 
 TYR   0.026   0.002   TYR B 161 
 PHE   0.011   0.001   PHE B 230 
 TRP   0.006   0.001   TRP A  31 
 HIS   0.004   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5010)
  covalent geometry    : angle       0.62323 ( 6800)
  hydrogen bonds       : bond        0.03686 (  157)
  hydrogen bonds       : angle       5.57610 (  462)

*********************** 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
  135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8315 (t0) cc_final: 0.7859 (t0)
REVERT: A  270 GLU cc_start: 0.7865 (tp30) cc_final: 0.7480 (tp30)
REVERT: A  276 MET cc_start: 0.8758 (tpp) cc_final: 0.8231 (mmm)
REVERT: A  289 ASP cc_start: 0.8365 (p0) cc_final: 0.8040 (p0)
REVERT: B   16 CYS cc_start: 0.8260 (p) cc_final: 0.7920 (p)
REVERT: B   17 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7765 (mtm)
REVERT: B   83 GLN cc_start: 0.8157 (tt0) cc_final: 0.7929 (tt0)
REVERT: B  119 ASN cc_start: 0.8284 (t0) cc_final: 0.8006 (t0)
REVERT: B  130 MET cc_start: 0.8412 (tpp) cc_final: 0.8011 (ttt)
REVERT: B  175 THR cc_start: 0.8989 (p) cc_final: 0.8494 (t)
REVERT: B  240 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7524 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 130
  average time/residue: 0.0590
  time to fit residues: 10.3384
Evaluate side-chains
  116 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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  290 GLU
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  264 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 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**
B  19 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 = 0.3731 r_free = 0.3731 target = 0.127111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.106972 restraints weight = 8712.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.111152 restraints weight = 4401.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.114052 restraints weight = 2771.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.116023 restraints weight = 1993.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.117161 restraints weight = 1560.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5010  Z= 0.148
  Angle     :  0.653   6.695   6800  Z= 0.320
  Chirality :  0.042   0.165    766
  Planarity :  0.005   0.058    884
  Dihedral  :  4.764  21.960    678
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.57 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.33), residues: 626
  helix:  1.28 (0.43), residues: 152
  sheet: -3.54 (0.52), residues: 64
  loop : -1.14 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C   4 
 TYR   0.024   0.002   TYR B 161 
 PHE   0.011   0.001   PHE B 140 
 TRP   0.007   0.001   TRP B  31 
 HIS   0.007   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5010)
  covalent geometry    : angle       0.65295 ( 6800)
  hydrogen bonds       : bond        0.03673 (  157)
  hydrogen bonds       : angle       5.61403 (  462)

*********************** 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  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8495 (p0) cc_final: 0.8134 (p0)
REVERT: A  119 ASN cc_start: 0.8368 (t0) cc_final: 0.7912 (t0)
REVERT: A  270 GLU cc_start: 0.7850 (tp30) cc_final: 0.7537 (tp30)
REVERT: A  276 MET cc_start: 0.8776 (tpp) cc_final: 0.8239 (mmm)
REVERT: B   16 CYS cc_start: 0.8362 (p) cc_final: 0.7983 (p)
REVERT: B  119 ASN cc_start: 0.8293 (t0) cc_final: 0.8011 (t0)
REVERT: B  175 THR cc_start: 0.9001 (p) cc_final: 0.8538 (t)
REVERT: B  240 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7475 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 124
  average time/residue: 0.0544
  time to fit residues: 9.2815
Evaluate side-chains
  118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  290 GLU
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  264 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 16 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.5980
   chunk 58 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 10 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 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 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.127517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.107574 restraints weight = 8635.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.111731 restraints weight = 4381.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.114586 restraints weight = 2777.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.116271 restraints weight = 2000.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.117805 restraints weight = 1600.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5010  Z= 0.143
  Angle     :  0.657   7.375   6800  Z= 0.322
  Chirality :  0.043   0.153    766
  Planarity :  0.004   0.049    884
  Dihedral  :  4.743  21.163    678
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.40 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.32), residues: 626
  helix:  1.29 (0.42), residues: 154
  sheet: -3.43 (0.53), residues: 64
  loop : -1.18 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   4 
 TYR   0.024   0.002   TYR B 161 
 PHE   0.012   0.001   PHE B 150 
 TRP   0.006   0.001   TRP A  31 
 HIS   0.005   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5010)
  covalent geometry    : angle       0.65677 ( 6800)
  hydrogen bonds       : bond        0.03539 (  157)
  hydrogen bonds       : angle       5.53500 (  462)

*********************** 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
  129 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8493 (p0) cc_final: 0.8287 (p0)
REVERT: A  119 ASN cc_start: 0.8334 (t0) cc_final: 0.7879 (t0)
REVERT: A  270 GLU cc_start: 0.7848 (tp30) cc_final: 0.7539 (tp30)
REVERT: A  276 MET cc_start: 0.8719 (tpp) cc_final: 0.8455 (mmm)
REVERT: C    0 GLN cc_start: 0.8132 (mp10) cc_final: 0.7534 (mp10)
REVERT: B   16 CYS cc_start: 0.8379 (p) cc_final: 0.8047 (p)
REVERT: B  119 ASN cc_start: 0.8301 (t0) cc_final: 0.8042 (t0)
REVERT: B  130 MET cc_start: 0.8467 (tpp) cc_final: 0.7891 (ttt)
REVERT: B  175 THR cc_start: 0.9039 (p) cc_final: 0.8504 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 124
  average time/residue: 0.0548
  time to fit residues: 9.4747
Evaluate side-chains
  119 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  264 MET
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 61 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0370
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.1662

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 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 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.126893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.106817 restraints weight = 8774.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.110898 restraints weight = 4554.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.113750 restraints weight = 2916.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115586 restraints weight = 2108.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.116949 restraints weight = 1670.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5010  Z= 0.137
  Angle     :  0.637   7.049   6800  Z= 0.316
  Chirality :  0.042   0.145    766
  Planarity :  0.004   0.049    884
  Dihedral  :  4.680  20.632    678
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.59 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.33), residues: 626
  helix:  1.29 (0.42), residues: 154
  sheet: -3.30 (0.54), residues: 64
  loop : -1.17 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   4 
 TYR   0.023   0.002   TYR B 161 
 PHE   0.015   0.001   PHE B 150 
 TRP   0.008   0.001   TRP A  31 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5010)
  covalent geometry    : angle       0.63663 ( 6800)
  hydrogen bonds       : bond        0.03605 (  157)
  hydrogen bonds       : angle       5.53254 (  462)

*********************** 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
  127 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8292 (t0) cc_final: 0.7833 (t0)
REVERT: A  166 GLU cc_start: 0.8353 (tt0) cc_final: 0.8127 (tt0)
REVERT: A  175 THR cc_start: 0.8998 (p) cc_final: 0.8727 (p)
REVERT: A  270 GLU cc_start: 0.7830 (tp30) cc_final: 0.7537 (tp30)
REVERT: A  276 MET cc_start: 0.8766 (tpp) cc_final: 0.8185 (mmm)
REVERT: C    0 GLN cc_start: 0.8079 (mp10) cc_final: 0.7440 (mp10)
REVERT: B   16 CYS cc_start: 0.8426 (p) cc_final: 0.8118 (p)
REVERT: B  119 ASN cc_start: 0.8288 (t0) cc_final: 0.8033 (t0)
REVERT: B  130 MET cc_start: 0.8434 (tpp) cc_final: 0.7875 (ttt)
REVERT: B  175 THR cc_start: 0.9006 (p) cc_final: 0.8490 (t)
REVERT: B  262 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8772 (mm)
  outliers start: 15
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0563
  time to fit residues: 9.2165
Evaluate side-chains
  118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
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   21 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 MET
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 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**
B 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.130140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.109908 restraints weight = 8588.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114150 restraints weight = 4394.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.117064 restraints weight = 2792.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.119095 restraints weight = 2008.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.120396 restraints weight = 1580.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3663 r_free = 0.3663    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3663 r_free = 0.3663    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5010  Z= 0.148
  Angle     :  0.653   7.547   6800  Z= 0.322
  Chirality :  0.043   0.171    766
  Planarity :  0.004   0.048    884
  Dihedral  :  4.714  20.478    678
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.59 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.33), residues: 626
  helix:  1.42 (0.43), residues: 152
  sheet: -3.54 (0.52), residues: 74
  loop : -1.14 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   4 
 TYR   0.024   0.003   TYR A 209 
 PHE   0.015   0.001   PHE B 150 
 TRP   0.009   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5010)
  covalent geometry    : angle       0.65292 ( 6800)
  hydrogen bonds       : bond        0.03568 (  157)
  hydrogen bonds       : angle       5.51850 (  462)

*********************** 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
  124 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8296 (t0) cc_final: 0.7820 (t0)
REVERT: A  166 GLU cc_start: 0.8367 (tt0) cc_final: 0.8162 (tt0)
REVERT: A  175 THR cc_start: 0.9008 (p) cc_final: 0.8747 (p)
REVERT: A  270 GLU cc_start: 0.7789 (tp30) cc_final: 0.7515 (tp30)
REVERT: A  276 MET cc_start: 0.8773 (tpp) cc_final: 0.8252 (mmm)
REVERT: A  289 ASP cc_start: 0.8411 (p0) cc_final: 0.8085 (p0)
REVERT: C    0 GLN cc_start: 0.8129 (mp10) cc_final: 0.7482 (mp10)
REVERT: C    4 ARG cc_start: 0.7989 (ttt-90) cc_final: 0.7449 (ttp80)
REVERT: B   16 CYS cc_start: 0.8439 (p) cc_final: 0.8191 (p)
REVERT: B  119 ASN cc_start: 0.8317 (t0) cc_final: 0.8070 (t0)
REVERT: B  130 MET cc_start: 0.8453 (tpp) cc_final: 0.7926 (ttt)
REVERT: B  175 THR cc_start: 0.9015 (p) cc_final: 0.8508 (t)
REVERT: B  262 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8782 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0496
  time to fit residues: 8.0137
Evaluate side-chains
  117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
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   21 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 MET
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 28 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** 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**
B 214 ASN
B 299 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.133683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.113816 restraints weight = 8604.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.118182 restraints weight = 4339.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.121129 restraints weight = 2708.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.123148 restraints weight = 1935.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124531 restraints weight = 1501.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5010  Z= 0.125
  Angle     :  0.636   7.333   6800  Z= 0.316
  Chirality :  0.042   0.158    766
  Planarity :  0.004   0.048    884
  Dihedral  :  4.665  20.547    678
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 20.40 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.33), residues: 626
  helix:  1.37 (0.43), residues: 152
  sheet: -3.44 (0.53), residues: 74
  loop : -1.11 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   4 
 TYR   0.042   0.003   TYR A 209 
 PHE   0.013   0.001   PHE B 230 
 TRP   0.007   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5010)
  covalent geometry    : angle       0.63638 ( 6800)
  hydrogen bonds       : bond        0.03642 (  157)
  hydrogen bonds       : angle       5.48212 (  462)

********************** 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
  129 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASN cc_start: 0.8360 (t0) cc_final: 0.7855 (t0)
REVERT: A  166 GLU cc_start: 0.8345 (tt0) cc_final: 0.8126 (tt0)
REVERT: A  175 THR cc_start: 0.8904 (p) cc_final: 0.8699 (p)
REVERT: A  238 ASN cc_start: 0.8587 (t0) cc_final: 0.8337 (t0)
REVERT: A  270 GLU cc_start: 0.7749 (tp30) cc_final: 0.7486 (tp30)
REVERT: A  276 MET cc_start: 0.8754 (tpp) cc_final: 0.8230 (mmm)
REVERT: A  289 ASP cc_start: 0.8425 (p0) cc_final: 0.8086 (p0)
REVERT: A  294 PHE cc_start: 0.8300 (t80) cc_final: 0.8070 (t80)
REVERT: C    0 GLN cc_start: 0.8014 (mp10) cc_final: 0.7392 (mp10)
REVERT: C    4 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7574 (ptm-80)
REVERT: B   16 CYS cc_start: 0.8472 (p) cc_final: 0.8265 (p)
REVERT: B  119 ASN cc_start: 0.8253 (t0) cc_final: 0.8011 (t0)
REVERT: B  130 MET cc_start: 0.8405 (tpp) cc_final: 0.7865 (ttt)
REVERT: B  175 THR cc_start: 0.8973 (p) cc_final: 0.8537 (t)
REVERT: B  262 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8745 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 124
  average time/residue: 0.0543
  time to fit residues: 9.1941
Evaluate side-chains
  120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 MET
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 31 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 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 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.132031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.112054 restraints weight = 8600.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.116367 restraints weight = 4368.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119294 restraints weight = 2748.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.121299 restraints weight = 1974.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.122699 restraints weight = 1545.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5010  Z= 0.138
  Angle     :  0.647   7.973   6800  Z= 0.317
  Chirality :  0.041   0.138    766
  Planarity :  0.004   0.048    884
  Dihedral  :  4.601  20.357    678
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.33), residues: 626
  helix:  1.43 (0.42), residues: 152
  sheet: -3.50 (0.50), residues: 78
  loop : -1.18 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   4 
 TYR   0.027   0.003   TYR A 209 
 PHE   0.011   0.001   PHE B 150 
 TRP   0.009   0.001   TRP A 207 
 HIS   0.005   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5010)
  covalent geometry    : angle       0.64731 ( 6800)
  hydrogen bonds       : bond        0.03485 (  157)
  hydrogen bonds       : angle       5.40500 (  462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 963.65 seconds
wall clock time: 17 minutes 16.75 seconds (1036.75 seconds total)