Starting phenix.real_space_refine
on Sat May  2 09:21:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11ou_75893/05_2026/11ou_75893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11ou_75893/05_2026/11ou_75893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/11ou_75893/05_2026/11ou_75893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11ou_75893/05_2026/11ou_75893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/11ou_75893/05_2026/11ou_75893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11ou_75893/05_2026/11ou_75893.cif"
  }
  resolution = 3.2
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2608      2.51       5
     N     712      2.21       5
     O     829      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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4163
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "K"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1634
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201}
    Chain: "H"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1604
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 201}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 1.20, per 1000 atoms: 0.29
  Number of scatterers: 4163
  At special positions: 0
  Unit cell: (56.166, 76.406, 96.646, 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      14     16.00
     O     829      8.00
     N     712      7.00
     C    2608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.03

  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: 0.41
  Conformation dependent library (CDL) restraints added in 126.0 milliseconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1000

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 13 sheets defined
      7.7% alpha, 46.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'K' and resid 74 through 76
      No H-bonds generated for 'chain 'K' and resid 74 through 76'
    Processing helix  chain 'K' and resid 87 through 91
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.057A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 130
      removed outlier: 3.517A  pdb=" N   GLY L 130 " --> pdb=" O   GLN L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 191
      removed outlier: 3.566A  pdb=" N   HIS L 191 " --> pdb=" O   ASP L 187 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 159 through 161
      No H-bonds generated for 'chain 'H' and resid 159 through 161'
    Processing helix  chain 'H' and resid 190 through 195
      removed outlier: 4.633A  pdb=" N   THR H 194 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 6 through 7
    Processing sheet with id=AA2, first strand: chain 'K' and resid 46 through 51
      removed outlier: 5.581A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   TYR K 110 " --> pdb=" O   ILE K  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 46 through 51
      removed outlier: 5.581A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.528A  pdb=" N   LEU L  13 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.528A  pdb=" N   LEU L  13 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 116 through 120
      removed outlier: 3.564A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 155 through 157
      removed outlier: 4.597A  pdb=" N   TRP L 150 " --> pdb=" O   GLN L 157 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7
      removed outlier: 3.699A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  81 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU H  81 " --> pdb=" O   LEU H  20 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.917A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   TYR H  59 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 127
      removed outlier: 6.460A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 123 through 127
      removed outlier: 6.460A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 154 through 157
      removed outlier: 3.605A  pdb=" N   LYS H 212 " --> pdb=" O   CYS H 199 " (cutoff:3.500A)

    186 hydrogen bonds defined for protein.
    471 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: 0.62

  Time building geometry restraints manager: 0.54 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 1357
        1.34 -     1.46: 1027
        1.46 -     1.58: 1856
        1.58 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 4258
  Sorted by residual:
  bond pdb=" C   LYS H 204 "
       pdb=" N   PRO H 205 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.38e-02 5.25e+03 2.67e+00
  bond pdb=" CA  VAL H 187 "
       pdb=" C   VAL H 187 "
    ideal  model  delta    sigma   weight residual
    1.516  1.526 -0.011 1.11e-02 8.12e+03 9.15e-01
  bond pdb=" C   ILE L  59 "
       pdb=" O   ILE L  59 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.007 8.90e-03 1.26e+04 6.72e-01
  bond pdb=" CB  PRO H 152 "
       pdb=" CG  PRO H 152 "
    ideal  model  delta    sigma   weight residual
    1.506  1.535 -0.029 3.90e-02 6.57e+02 5.60e-01
  bond pdb=" CG  PRO L   8 "
       pdb=" CD  PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.512  1.494  0.018 2.70e-02 1.37e+03 4.49e-01
  ... (remaining 4253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 5546
        1.01 -     2.03: 192
        2.03 -     3.04: 36
        3.04 -     4.06: 10
        4.06 -     5.07: 3
  Bond angle restraints: 5787
  Sorted by residual:
  angle pdb=" C   VAL H 187 "
        pdb=" CA  VAL H 187 "
        pdb=" CB  VAL H 187 "
      ideal   model   delta    sigma   weight residual
     109.33  112.35   -3.02 9.80e-01 1.04e+00 9.53e+00
  angle pdb=" CA  VAL H 187 "
        pdb=" C   VAL H 187 "
        pdb=" N   PRO H 188 "
      ideal   model   delta    sigma   weight residual
     116.57  119.42   -2.85 9.80e-01 1.04e+00 8.44e+00
  angle pdb=" C   ASP K  73 "
        pdb=" N   ASP K  74 "
        pdb=" CA  ASP K  74 "
      ideal   model   delta    sigma   weight residual
     121.54  125.68   -4.14 1.91e+00 2.74e-01 4.69e+00
  angle pdb=" N   ALA K  92 "
        pdb=" CA  ALA K  92 "
        pdb=" C   ALA K  92 "
      ideal   model   delta    sigma   weight residual
     107.88  110.82   -2.94 1.41e+00 5.03e-01 4.34e+00
  angle pdb=" C   SER L  94 "
        pdb=" N   SER L  95 "
        pdb=" CA  SER L  95 "
      ideal   model   delta    sigma   weight residual
     121.80  126.87   -5.07 2.44e+00 1.68e-01 4.32e+00
  ... (remaining 5782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 2270
       17.90 -    35.80: 209
       35.80 -    53.69: 37
       53.69 -    71.59: 10
       71.59 -    89.49: 7
  Dihedral angle restraints: 2533
    sinusoidal: 959
      harmonic: 1574
  Sorted by residual:
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.02  -37.02     1      1.00e+01 1.00e-02 1.93e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.99   35.01     1      1.00e+01 1.00e-02 1.74e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.64   30.36     1      1.00e+01 1.00e-02 1.32e+01
  ... (remaining 2530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 408
       0.029 -    0.058: 153
       0.058 -    0.087: 34
       0.087 -    0.117: 38
       0.117 -    0.146: 5
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  ILE K  98 "
            pdb=" N   ILE K  98 "
            pdb=" C   ILE K  98 "
            pdb=" CB  ILE K  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CA  VAL K  79 "
            pdb=" N   VAL K  79 "
            pdb=" C   VAL K  79 "
            pdb=" CB  VAL K  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality pdb=" CA  ILE L 108 "
            pdb=" N   ILE L 108 "
            pdb=" C   ILE L 108 "
            pdb=" CB  ILE L 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  ... (remaining 635 not shown)

  Planarity restraints: 749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU L  80 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.24e+00
        pdb=" N   PRO L  81 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 151 "   -0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO H 152 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO H 152 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO H 152 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 187 "   -0.021 5.00e-02 4.00e+02   3.17e-02 1.61e+00
        pdb=" N   PRO H 188 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO H 188 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H 188 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 746 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 2225
        3.01 -     3.48: 3867
        3.48 -     3.96: 6630
        3.96 -     4.43: 7735
        4.43 -     4.90: 13034
  Nonbonded interactions: 33491
  Sorted by model distance:
  nonbonded pdb=" O   PRO L   8 "
            pdb=" OG1 THR L 104 "
     model   vdw
     2.541 3.040
  nonbonded pdb=" N   SER L  68 "
            pdb=" O   SER L  68 "
     model   vdw
     2.620 2.496
  nonbonded pdb=" C   SER K  71 "
            pdb=" OG  SER K  71 "
     model   vdw
     2.623 2.616
  nonbonded pdb=" N   ALA H  92 "
            pdb=" O   ALA H  92 "
     model   vdw
     2.632 2.496
  nonbonded pdb=" O   THR H 154 "
            pdb=" OG1 THR H 154 "
     model   vdw
     2.632 3.040
  ... (remaining 33486 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.930
  Find NCS groups from input model:        0.020
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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      :  0.002   0.029   4263  Z= 0.106
  Angle     :  0.471   5.073   5797  Z= 0.264
  Chirality :  0.040   0.146    638
  Planarity :  0.004   0.037    749
  Dihedral  : 14.875  89.490   1518
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.46 (0.39), residues: 541
  helix:  1.94 (1.37), residues: 16
  sheet:  0.56 (0.35), residues: 236
  loop :  0.09 (0.41), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 213 
 TYR   0.013   0.001   TYR H  59 
 PHE   0.007   0.001   PHE H  29 
 TRP   0.005   0.001   TRP H  52 
 HIS   0.001   0.000   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4258)
  covalent geometry    : angle       0.47114 ( 5787)
  SS BOND              : bond        0.00150 (    5)
  SS BOND              : angle       0.44516 (   10)
  hydrogen bonds       : bond        0.21453 (  157)
  hydrogen bonds       : angle      10.15778 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.097 
Fit side-chains
REVERT: K   80 TYR cc_start: 0.8093 (m-80) cc_final: 0.7808 (m-80)
REVERT: L   94 SER cc_start: 0.7857 (p) cc_final: 0.7613 (p)
REVERT: L  144 ARG cc_start: 0.7999 (tpt-90) cc_final: 0.7679 (ttt180)
REVERT: L  149 GLN cc_start: 0.8048 (mt0) cc_final: 0.7647 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0533
  time to fit residues: 3.7614
Evaluate side-chains
  49 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 157 GLN
H 200 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.162414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.124831 restraints weight = 4517.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.75
r_work: 0.3253 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4263  Z= 0.149
  Angle     :  0.522   5.553   5797  Z= 0.280
  Chirality :  0.043   0.163    638
  Planarity :  0.005   0.038    749
  Dihedral  :  3.672  14.828    600
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 11.84 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.64 (0.39), residues: 541
  helix:  2.22 (1.41), residues: 16
  sheet:  0.77 (0.35), residues: 242
  loop :  0.10 (0.41), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 213 
 TYR   0.010   0.001   TYR H 148 
 PHE   0.011   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 4258)
  covalent geometry    : angle       0.52138 ( 5787)
  SS BOND              : bond        0.00246 (    5)
  SS BOND              : angle       0.85655 (   10)
  hydrogen bonds       : bond        0.03903 (  157)
  hydrogen bonds       : angle       6.96202 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.151 
Fit side-chains
REVERT: K   80 TYR cc_start: 0.7811 (m-80) cc_final: 0.7530 (m-80)
REVERT: L   94 SER cc_start: 0.7914 (p) cc_final: 0.7673 (p)
REVERT: L  144 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.7750 (ttt180)
REVERT: L  149 GLN cc_start: 0.8231 (mt0) cc_final: 0.7605 (mm110)
REVERT: L  187 ASP cc_start: 0.6987 (m-30) cc_final: 0.6782 (m-30)
REVERT: H   60 TYR cc_start: 0.8536 (m-80) cc_final: 0.8177 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0529
  time to fit residues: 4.3451
Evaluate side-chains
  60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue  210 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    0.4980
   chunk 18 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.161167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.123592 restraints weight = 4491.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.72
r_work: 0.3236 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4263  Z= 0.136
  Angle     :  0.501   5.529   5797  Z= 0.267
  Chirality :  0.042   0.157    638
  Planarity :  0.004   0.036    749
  Dihedral  :  3.781  15.030    600
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 12.28 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.58 (0.38), residues: 541
  helix:  2.43 (1.45), residues: 16
  sheet:  0.77 (0.34), residues: 242
  loop : -0.00 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 213 
 TYR   0.007   0.001   TYR K  95 
 PHE   0.011   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4258)
  covalent geometry    : angle       0.50063 ( 5787)
  SS BOND              : bond        0.00253 (    5)
  SS BOND              : angle       0.78906 (   10)
  hydrogen bonds       : bond        0.03447 (  157)
  hydrogen bonds       : angle       6.23311 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.149 
Fit side-chains
REVERT: K   80 TYR cc_start: 0.7801 (m-80) cc_final: 0.7545 (m-80)
REVERT: L   39 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7379 (tt0)
REVERT: L  144 ARG cc_start: 0.8024 (tpt-90) cc_final: 0.7774 (ttt180)
REVERT: L  149 GLN cc_start: 0.8217 (mt0) cc_final: 0.7601 (mm110)
REVERT: H   52 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.6453 (t-100)
  outliers start: 20
  outliers final: 14
  residues processed: 65
  average time/residue: 0.0519
  time to fit residues: 4.6999
Evaluate side-chains
  68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.160014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.122612 restraints weight = 4439.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.72
r_work: 0.3176 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4263  Z= 0.137
  Angle     :  0.498   5.520   5797  Z= 0.264
  Chirality :  0.042   0.148    638
  Planarity :  0.004   0.037    749
  Dihedral  :  3.808  15.134    600
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 14.04 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.55 (0.38), residues: 541
  helix:  2.31 (1.41), residues: 16
  sheet:  0.68 (0.33), residues: 253
  loop :  0.03 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 213 
 TYR   0.007   0.001   TYR K  95 
 PHE   0.011   0.001   PHE L 141 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4258)
  covalent geometry    : angle       0.49762 ( 5787)
  SS BOND              : bond        0.00176 (    5)
  SS BOND              : angle       0.79120 (   10)
  hydrogen bonds       : bond        0.03159 (  157)
  hydrogen bonds       : angle       5.93230 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.163 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7343 (tt0)
REVERT: L  144 ARG cc_start: 0.8019 (tpt-90) cc_final: 0.7763 (ttt180)
REVERT: L  149 GLN cc_start: 0.8258 (mt0) cc_final: 0.7592 (mm110)
  outliers start: 20
  outliers final: 16
  residues processed: 67
  average time/residue: 0.0523
  time to fit residues: 4.7982
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.153059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.116854 restraints weight = 4519.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.63
r_work: 0.3086 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   4263  Z= 0.261
  Angle     :  0.598   6.854   5797  Z= 0.313
  Chirality :  0.045   0.163    638
  Planarity :  0.005   0.037    749
  Dihedral  :  4.317  15.737    600
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 13.60 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.28 (0.37), residues: 541
  helix:  2.43 (1.43), residues: 15
  sheet:  0.59 (0.33), residues: 239
  loop : -0.23 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K  67 
 TYR   0.012   0.002   TYR K  95 
 PHE   0.013   0.002   PHE H 169 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 4258)
  covalent geometry    : angle       0.59707 ( 5787)
  SS BOND              : bond        0.00182 (    5)
  SS BOND              : angle       1.15406 (   10)
  hydrogen bonds       : bond        0.03536 (  157)
  hydrogen bonds       : angle       6.32990 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 49
  time to evaluate  : 0.100 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7470 (tt0)
REVERT: L  144 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7792 (ttt180)
REVERT: L  149 GLN cc_start: 0.8360 (mt0) cc_final: 0.7701 (mm110)
REVERT: H   52 TRP cc_start: 0.7748 (OUTLIER) cc_final: 0.6660 (t-100)
  outliers start: 27
  outliers final: 21
  residues processed: 68
  average time/residue: 0.0538
  time to fit residues: 4.9808
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   70 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  144 ARG
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  199 CYS
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120677 restraints weight = 4502.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.72
r_work: 0.3170 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4263  Z= 0.152
  Angle     :  0.520   5.904   5797  Z= 0.273
  Chirality :  0.042   0.145    638
  Planarity :  0.004   0.036    749
  Dihedral  :  4.117  16.038    600
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 15.13 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.32 (0.37), residues: 541
  helix:  2.24 (1.42), residues: 16
  sheet:  0.59 (0.33), residues: 251
  loop : -0.20 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.010   0.001   TYR H 148 
 PHE   0.013   0.001   PHE L 141 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4258)
  covalent geometry    : angle       0.51911 ( 5787)
  SS BOND              : bond        0.00182 (    5)
  SS BOND              : angle       0.80363 (   10)
  hydrogen bonds       : bond        0.03106 (  157)
  hydrogen bonds       : angle       5.98953 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 49
  time to evaluate  : 0.176 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7341 (tt0)
REVERT: L  144 ARG cc_start: 0.8006 (tpt-90) cc_final: 0.7746 (ttt180)
REVERT: L  149 GLN cc_start: 0.8320 (mt0) cc_final: 0.7710 (mm110)
  outliers start: 23
  outliers final: 22
  residues processed: 65
  average time/residue: 0.0518
  time to fit residues: 4.5841
Evaluate side-chains
  71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 48
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   70 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  199 CYS
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0010
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.4790

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.154796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.117557 restraints weight = 4541.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.71
r_work: 0.3120 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   4263  Z= 0.210
  Angle     :  0.559   6.395   5797  Z= 0.291
  Chirality :  0.043   0.148    638
  Planarity :  0.004   0.036    749
  Dihedral  :  4.245  15.660    600
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 15.13 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.15 (0.36), residues: 541
  helix:  2.12 (1.40), residues: 16
  sheet:  0.55 (0.33), residues: 230
  loop : -0.33 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  46 
 TYR   0.011   0.001   TYR H 148 
 PHE   0.013   0.002   PHE L 141 
 TRP   0.011   0.002   TRP H  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 4258)
  covalent geometry    : angle       0.55836 ( 5787)
  SS BOND              : bond        0.00174 (    5)
  SS BOND              : angle       0.98172 (   10)
  hydrogen bonds       : bond        0.03246 (  157)
  hydrogen bonds       : angle       6.08852 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 46
  time to evaluate  : 0.186 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7398 (tt0)
REVERT: L  144 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7806 (ttt180)
REVERT: L  149 GLN cc_start: 0.8368 (mt0) cc_final: 0.7714 (mm110)
REVERT: H   52 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.6785 (t-100)
  outliers start: 27
  outliers final: 22
  residues processed: 65
  average time/residue: 0.0538
  time to fit residues: 4.7084
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 45
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   70 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  144 ARG
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   52 TRP
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  199 CYS
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0000
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.157884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120886 restraints weight = 4490.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.71
r_work: 0.3211 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4263  Z= 0.129
  Angle     :  0.505   5.626   5797  Z= 0.266
  Chirality :  0.042   0.143    638
  Planarity :  0.004   0.036    749
  Dihedral  :  4.063  15.624    600
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 15.79 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.30 (0.37), residues: 541
  helix:  2.31 (1.42), residues: 16
  sheet:  0.57 (0.33), residues: 250
  loop : -0.21 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 213 
 TYR   0.007   0.001   TYR H 148 
 PHE   0.013   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4258)
  covalent geometry    : angle       0.50511 ( 5787)
  SS BOND              : bond        0.00208 (    5)
  SS BOND              : angle       0.66585 (   10)
  hydrogen bonds       : bond        0.02998 (  157)
  hydrogen bonds       : angle       5.78699 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 47
  time to evaluate  : 0.114 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7296 (tt0)
REVERT: L  149 GLN cc_start: 0.8324 (mt0) cc_final: 0.7716 (mm110)
  outliers start: 24
  outliers final: 21
  residues processed: 63
  average time/residue: 0.0603
  time to fit residues: 5.0591
Evaluate side-chains
  69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   70 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  199 CYS
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.158849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.121563 restraints weight = 4543.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.74
r_work: 0.3173 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4263  Z= 0.150
  Angle     :  0.515   5.857   5797  Z= 0.270
  Chirality :  0.042   0.142    638
  Planarity :  0.004   0.036    749
  Dihedral  :  4.061  15.472    600
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 16.23 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.30 (0.37), residues: 541
  helix:  2.27 (1.41), residues: 16
  sheet:  0.59 (0.33), residues: 250
  loop : -0.21 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.008   0.001   TYR H 148 
 PHE   0.013   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4258)
  covalent geometry    : angle       0.51467 ( 5787)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.74910 (   10)
  hydrogen bonds       : bond        0.03015 (  157)
  hydrogen bonds       : angle       5.77947 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 45
  time to evaluate  : 0.153 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7316 (tt0)
REVERT: L  149 GLN cc_start: 0.8313 (mt0) cc_final: 0.7717 (mm110)
  outliers start: 22
  outliers final: 20
  residues processed: 60
  average time/residue: 0.0433
  time to fit residues: 3.7833
Evaluate side-chains
  66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   70 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  199 CYS
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.157776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120760 restraints weight = 4431.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.69
r_work: 0.3172 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4263  Z= 0.136
  Angle     :  0.507   5.735   5797  Z= 0.266
  Chirality :  0.042   0.141    638
  Planarity :  0.004   0.036    749
  Dihedral  :  4.029  15.356    600
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 16.23 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.36 (0.37), residues: 541
  helix:  2.29 (1.41), residues: 16
  sheet:  0.54 (0.33), residues: 255
  loop : -0.09 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.007   0.001   TYR H 148 
 PHE   0.013   0.001   PHE L 141 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4258)
  covalent geometry    : angle       0.50614 ( 5787)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       0.69365 (   10)
  hydrogen bonds       : bond        0.02946 (  157)
  hydrogen bonds       : angle       5.70184 (  471)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.168 
Fit side-chains
REVERT: L   39 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7321 (tt0)
REVERT: L  149 GLN cc_start: 0.8308 (mt0) cc_final: 0.7716 (mm110)
  outliers start: 21
  outliers final: 20
  residues processed: 60
  average time/residue: 0.0502
  time to fit residues: 4.1876
Evaluate side-chains
  66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   70 VAL
Chi-restraints excluded: chain K residue   71 SER
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain K residue  119 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  184 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  199 CYS
Chi-restraints excluded: chain H residue  210 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 162 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.157123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.119597 restraints weight = 4510.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.75
r_work: 0.3166 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4263  Z= 0.179
  Angle     :  0.539   6.201   5797  Z= 0.282
  Chirality :  0.043   0.143    638
  Planarity :  0.004   0.037    749
  Dihedral  :  4.169  16.252    600
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 16.89 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.25 (0.37), residues: 541
  helix:  2.15 (1.40), residues: 16
  sheet:  0.54 (0.33), residues: 250
  loop : -0.24 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.009   0.001   TYR H 148 
 PHE   0.013   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 4258)
  covalent geometry    : angle       0.53822 ( 5787)
  SS BOND              : bond        0.00178 (    5)
  SS BOND              : angle       0.83619 (   10)
  hydrogen bonds       : bond        0.03078 (  157)
  hydrogen bonds       : angle       5.86371 (  471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1223.28 seconds
wall clock time: 21 minutes 40.65 seconds (1300.65 seconds total)