Starting phenix.real_space_refine
on Fri Aug 22 13:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hnn_34917/08_2025/8hnn_34917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hnn_34917/08_2025/8hnn_34917.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hnn_34917/08_2025/8hnn_34917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hnn_34917/08_2025/8hnn_34917.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hnn_34917/08_2025/8hnn_34917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hnn_34917/08_2025/8hnn_34917.map"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.080
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     Cl      2      4.86       5
     C    1993      2.51       5
     N     527      2.21       5
     O     524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3063
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "N"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 852
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 112}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 2150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2150
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 9, 'TRANS': 268}
    Chain: "R"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 61
          Unusual residues: {'43I': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.22, per 1000 atoms: 0.40
  Number of scatterers: 3063
  At special positions: 0
  Unit cell: (71.4, 52.7, 123.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      17     16.00
     O     524      8.00
     N     527      7.00
     C    1993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  24 " - pdb=" SG  CYS N  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 124 " - pdb=" SG  CYS R 203 " 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: 0.29
  Conformation dependent library (CDL) restraints added in 121.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 4 sheets defined
      56.6% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'N' and resid 88 through 92
    Processing helix  chain 'R' and resid 55 through 80
    Processing helix  chain 'R' and resid 86 through 105
      removed outlier: 3.851A  pdb=" N   ASP R  99 " --> pdb=" O   LEU R  95 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LEU R 101 " --> pdb=" O   VAL R  97 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   LEU R 102 " --> pdb=" O   ALA R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 115
      removed outlier: 3.909A  pdb=" N   TRP R 109 " --> pdb=" O   THR R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 120 through 154
      removed outlier: 4.064A  pdb=" N   PHE R 135 " --> pdb=" O   PHE R 131 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR R 136 " --> pdb=" O   ASN R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 189
      Proline residue:  R 185  - end of helix
    Processing helix  chain 'R' and resid 211 through 244
      Proline residue:  R 227  - end of helix
      removed outlier: 3.889A  pdb=" N   SER R 244 " --> pdb=" O   ALA R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 291
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 300 through 329
      removed outlier: 4.207A  pdb=" N   CYS R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   CYS R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
      removed outlier: 3.675A  pdb=" N   VAL R 329 " --> pdb=" O   LEU R 325 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'N' and resid 4 through 9
    Processing sheet with id=AA2, first strand: chain 'N' and resid 59 through 61
      removed outlier: 6.842A  pdb=" N   TRP N  38 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   SER N  52 " --> pdb=" O   MET N  36 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   MET N  36 " --> pdb=" O   SER N  52 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   LEU N  33 " --> pdb=" O   ARG N 102 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ARG N 102 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP N  35 " --> pdb=" O   GLU N 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'N' and resid 59 through 61
      removed outlier: 6.842A  pdb=" N   TRP N  38 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   SER N  52 " --> pdb=" O   MET N  36 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   MET N  36 " --> pdb=" O   SER N  52 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   LEU N  33 " --> pdb=" O   ARG N 102 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ARG N 102 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP N  35 " --> pdb=" O   GLU N 100 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'R' and resid 190 through 191
      removed outlier: 4.145A  pdb=" N   SER R 191 " --> pdb=" O   GLN R 204 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLN R 204 " --> pdb=" O   SER R 191 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    205 hydrogen bonds defined for protein.
    591 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: 0.36

  Time building geometry restraints manager: 0.37 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: 972
        1.34 -     1.46: 711
        1.46 -     1.58: 1424
        1.58 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3131
  Sorted by residual:
  bond pdb=" C19 43I R 401 "
       pdb=" C22 43I R 401 "
    ideal  model  delta    sigma   weight residual
    1.437  1.379  0.058 2.00e-02 2.50e+03 8.44e+00
  bond pdb=" C10 43I R 401 "
       pdb=" C11 43I R 401 "
    ideal  model  delta    sigma   weight residual
    1.524  1.488  0.036 2.00e-02 2.50e+03 3.18e+00
  bond pdb=" C22 43I R 401 "
       pdb="CL2  43I R 401 "
    ideal  model  delta    sigma   weight residual
    1.763  1.730  0.033 2.00e-02 2.50e+03 2.73e+00
  bond pdb=" C23 43I R 401 "
       pdb=" N6  43I R 401 "
    ideal  model  delta    sigma   weight residual
    1.347  1.318  0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C14 43I R 401 "
       pdb=" C15 43I R 401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.359  0.029 2.00e-02 2.50e+03 2.07e+00
  ... (remaining 3126 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 4138
        1.61 -     3.21: 101
        3.21 -     4.82: 17
        4.82 -     6.42: 14
        6.42 -     8.03: 2
  Bond angle restraints: 4272
  Sorted by residual:
  angle pdb=" C8  43I R 401 "
        pdb=" C7  43I R 401 "
        pdb=" N2  43I R 401 "
      ideal   model   delta    sigma   weight residual
     115.50  123.35   -7.85 3.00e+00 1.11e-01 6.84e+00
  angle pdb=" C   LEU R 225 "
        pdb=" N   LEU R 226 "
        pdb=" CA  LEU R 226 "
      ideal   model   delta    sigma   weight residual
     121.80  115.59    6.21 2.44e+00 1.68e-01 6.47e+00
  angle pdb=" C   HIS R  94 "
        pdb=" N   LEU R  95 "
        pdb=" CA  LEU R  95 "
      ideal   model   delta    sigma   weight residual
     121.58  117.00    4.58 1.95e+00 2.63e-01 5.52e+00
  angle pdb=" CA  LEU R  95 "
        pdb=" CB  LEU R  95 "
        pdb=" CG  LEU R  95 "
      ideal   model   delta    sigma   weight residual
     116.30  124.33   -8.03 3.50e+00 8.16e-02 5.26e+00
  angle pdb=" C19 43I R 401 "
        pdb=" N1  43I R 401 "
        pdb=" C5  43I R 401 "
      ideal   model   delta    sigma   weight residual
     118.45  124.82   -6.37 3.00e+00 1.11e-01 4.50e+00
  ... (remaining 4267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.68: 1847
       32.68 -    65.37: 34
       65.37 -    98.05: 4
       98.05 -   130.74: 6
      130.74 -   163.42: 2
  Dihedral angle restraints: 1893
    sinusoidal: 765
      harmonic: 1128
  Sorted by residual:
  dihedral pdb=" CB  CYS R 124 "
           pdb=" SG  CYS R 124 "
           pdb=" SG  CYS R 203 "
           pdb=" CB  CYS R 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.02  -88.98     1      1.00e+01 1.00e-02 9.43e+01
  dihedral pdb=" C11 43I R 401 "
           pdb=" C7  43I R 401 "
           pdb=" N2  43I R 401 "
           pdb=" C3  43I R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     198.38   34.96  163.42     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" C11 43I R 401 "
           pdb=" C7  43I R 401 "
           pdb=" N2  43I R 401 "
           pdb=" C6  43I R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      63.87  -94.22  158.09     1      3.00e+01 1.11e-03 2.06e+01
  ... (remaining 1890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.818: 507
       0.818 -    1.635: 0
       1.635 -    2.453: 0
       2.453 -    3.271: 0
       3.271 -    4.089: 1
  Chirality restraints: 508
  Sorted by residual:
  chirality pdb=" C7  43I R 401 "
            pdb=" C11 43I R 401 "
            pdb=" C8  43I R 401 "
            pdb=" N2  43I R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.33   -1.76    4.09 2.00e-01 2.50e+01 4.18e+02
  chirality pdb=" CG  LEU R 321 "
            pdb=" CB  LEU R 321 "
            pdb=" CD1 LEU R 321 "
            pdb=" CD2 LEU R 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CA  LEU R 106 "
            pdb=" N   LEU R 106 "
            pdb=" C   LEU R 106 "
            pdb=" CB  LEU R 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 505 not shown)

  Planarity restraints: 521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 222 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   ALA R 222 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ALA R 222 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLY R 223 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 196 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.65e+00
        pdb=" C   GLU R 196 "    0.022 2.00e-02 2.50e+03
        pdb=" O   GLU R 196 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ARG R 197 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 135 "    0.010 2.00e-02 2.50e+03   7.74e-03 1.05e+00
        pdb=" CG  PHE R 135 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 135 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 135 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 135 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 135 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 135 "    0.004 2.00e-02 2.50e+03
  ... (remaining 518 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 318
        2.74 -     3.28: 2951
        3.28 -     3.82: 4849
        3.82 -     4.36: 5235
        4.36 -     4.90: 9449
  Nonbonded interactions: 22802
  Sorted by model distance:
  nonbonded pdb=" O   ALA R 273 "
            pdb=" OG1 THR R 277 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NZ  LYS R 125 "
            pdb=" O   LEU R 190 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OG  SER N   9 "
            pdb=" OG  SER N  23 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   GLN R 158 "
            pdb=" NH1 ARG R 162 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" O   GLU R 253 "
            pdb=" ND2 ASN R 257 "
     model   vdw
     2.351 3.120
  ... (remaining 22797 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.240
  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:1.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
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      :  0.004   0.058   3133  Z= 0.188
  Angle     :  0.688   8.025   4276  Z= 0.338
  Chirality :  0.186   4.089    508
  Planarity :  0.003   0.021    521
  Dihedral  : 17.325 163.420   1165
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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 aren not related in a simple way.
  whole:  0.62 (0.44), residues: 386
  helix:  1.05 (0.35), residues: 217
  sheet:  2.72 (0.80), residues: 44
  loop : -1.64 (0.54), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 263 
 TYR   0.010   0.001   TYR R 233 
 PHE   0.017   0.001   PHE R 135 
 TRP   0.009   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3131)
  covalent geometry    : angle       0.68828 ( 4272)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.55949 (    4)
  hydrogen bonds       : bond        0.11129 (  197)
  hydrogen bonds       : angle       4.86515 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  101 TYR cc_start: 0.8965 (p90) cc_final: 0.8449 (p90)
REVERT: N  113 TRP cc_start: 0.8339 (m100) cc_final: 0.7985 (m-90)
REVERT: R  254 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7233 (ttpt)
REVERT: R  274 LEU cc_start: 0.8379 (tt) cc_final: 0.8176 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0539
  time to fit residues: 4.1038
Evaluate side-chains
  56 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0270
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
R 116 GLN
R 318 HIS
R 322 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.193394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.126041 restraints weight = 2890.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130546 restraints weight = 1832.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.133153 restraints weight = 1439.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.134132 restraints weight = 1272.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.134132 restraints weight = 1204.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3133  Z= 0.146
  Angle     :  0.649   8.346   4276  Z= 0.310
  Chirality :  0.040   0.120    508
  Planarity :  0.003   0.020    521
  Dihedral  : 13.058 140.686    538
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  8.97 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.44), residues: 386
  helix:  1.20 (0.36), residues: 217
  sheet:  2.17 (0.77), residues: 49
  loop : -1.31 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 162 
 TYR   0.010   0.001   TYR R 233 
 PHE   0.023   0.002   PHE R 328 
 TRP   0.010   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3131)
  covalent geometry    : angle       0.64924 ( 4272)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       0.39145 (    4)
  hydrogen bonds       : bond        0.04584 (  197)
  hydrogen bonds       : angle       4.09453 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N   36 MET cc_start: 0.7879 (mtt) cc_final: 0.7610 (mmm)
REVERT: N  113 TRP cc_start: 0.8307 (m100) cc_final: 0.7913 (m-90)
REVERT: R  189 PHE cc_start: 0.8021 (m-10) cc_final: 0.7728 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0596
  time to fit residues: 4.3666
Evaluate side-chains
  61 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  243 LYS
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0000
   chunk 8 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0670
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4722

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.195105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127847 restraints weight = 2885.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.132562 restraints weight = 1772.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.135308 restraints weight = 1378.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.136645 restraints weight = 1208.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.137838 restraints weight = 1131.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3133  Z= 0.125
  Angle     :  0.599   9.214   4276  Z= 0.287
  Chirality :  0.038   0.120    508
  Planarity :  0.003   0.021    521
  Dihedral  : 12.616 142.008    538
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.38 %
    Favored  : 81.41 %
  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 aren not related in a simple way.
  whole:  1.07 (0.44), residues: 386
  helix:  1.44 (0.37), residues: 217
  sheet:  2.16 (0.76), residues: 49
  loop : -1.30 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 162 
 TYR   0.012   0.001   TYR N 101 
 PHE   0.018   0.002   PHE R 187 
 TRP   0.008   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3131)
  covalent geometry    : angle       0.59961 ( 4272)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       0.37660 (    4)
  hydrogen bonds       : bond        0.04103 (  197)
  hydrogen bonds       : angle       3.94322 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N   36 MET cc_start: 0.7817 (mtt) cc_final: 0.7572 (mmm)
REVERT: N  113 TRP cc_start: 0.8311 (m100) cc_final: 0.7889 (m-90)
REVERT: R  189 PHE cc_start: 0.8025 (m-10) cc_final: 0.7753 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0478
  time to fit residues: 3.6989
Evaluate side-chains
  60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  291 LEU
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
N  75 ASN
R 322 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.182956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.115026 restraints weight = 2946.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.118688 restraints weight = 1970.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120632 restraints weight = 1601.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120900 restraints weight = 1442.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.122143 restraints weight = 1409.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3133  Z= 0.254
  Angle     :  0.777  12.672   4276  Z= 0.374
  Chirality :  0.044   0.174    508
  Planarity :  0.003   0.019    521
  Dihedral  : 12.810 142.319    538
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 18.27 %
    Favored  : 76.92 %
  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 aren not related in a simple way.
  whole:  0.65 (0.44), residues: 386
  helix:  1.00 (0.36), residues: 218
  sheet:  2.08 (0.77), residues: 49
  loop : -1.32 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 259 
 TYR   0.018   0.002   TYR R 235 
 PHE   0.021   0.002   PHE R 135 
 TRP   0.010   0.001   TRP N 106 
 HIS   0.004   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 ( 3131)
  covalent geometry    : angle       0.77752 ( 4272)
  SS BOND              : bond        0.00546 (    2)
  SS BOND              : angle       0.62967 (    4)
  hydrogen bonds       : bond        0.06153 (  197)
  hydrogen bonds       : angle       4.44406 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8353 (m100) cc_final: 0.7933 (m-90)
REVERT: R  189 PHE cc_start: 0.8168 (m-10) cc_final: 0.7793 (m-10)
  outliers start: 15
  outliers final: 10
  residues processed: 61
  average time/residue: 0.0500
  time to fit residues: 3.9878
Evaluate side-chains
  60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  291 LEU
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  317 MET
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4202 r_free = 0.4202 target = 0.203202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.142098 restraints weight = 2884.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146819 restraints weight = 1749.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.149316 restraints weight = 1362.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.150927 restraints weight = 1206.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.151220 restraints weight = 1125.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3133  Z= 0.135
  Angle     :  0.637   9.408   4276  Z= 0.302
  Chirality :  0.038   0.117    508
  Planarity :  0.003   0.020    521
  Dihedral  : 12.207 144.656    538
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 19.55 %
    Favored  : 76.60 %
  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 aren not related in a simple way.
  whole:  0.96 (0.44), residues: 386
  helix:  1.30 (0.37), residues: 218
  sheet:  2.16 (0.76), residues: 49
  loop : -1.28 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 296 
 TYR   0.013   0.001   TYR N 101 
 PHE   0.015   0.001   PHE R 135 
 TRP   0.009   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3131)
  covalent geometry    : angle       0.63744 ( 4272)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       0.44020 (    4)
  hydrogen bonds       : bond        0.04469 (  197)
  hydrogen bonds       : angle       4.04704 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8253 (m100) cc_final: 0.7939 (m-90)
REVERT: R  189 PHE cc_start: 0.8164 (m-10) cc_final: 0.7840 (m-10)
  outliers start: 12
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0493
  time to fit residues: 3.9455
Evaluate side-chains
  64 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  317 MET
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
N  75 ASN
R 194 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.195006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.133270 restraints weight = 2940.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.137599 restraints weight = 1845.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.140172 restraints weight = 1457.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141599 restraints weight = 1287.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.141769 restraints weight = 1210.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3133  Z= 0.203
  Angle     :  0.730  13.119   4276  Z= 0.347
  Chirality :  0.041   0.144    508
  Planarity :  0.003   0.019    521
  Dihedral  : 12.484 150.581    538
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.15 %
    Favored  : 74.68 %
  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 aren not related in a simple way.
  whole:  0.72 (0.44), residues: 386
  helix:  1.11 (0.36), residues: 218
  sheet:  2.08 (0.75), residues: 49
  loop : -1.43 (0.53), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 259 
 TYR   0.015   0.002   TYR R 235 
 PHE   0.025   0.002   PHE R 187 
 TRP   0.009   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 3131)
  covalent geometry    : angle       0.72980 ( 4272)
  SS BOND              : bond        0.00435 (    2)
  SS BOND              : angle       0.54242 (    4)
  hydrogen bonds       : bond        0.05510 (  197)
  hydrogen bonds       : angle       4.23407 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8289 (m100) cc_final: 0.7949 (m-90)
REVERT: R  189 PHE cc_start: 0.8196 (m-10) cc_final: 0.7892 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0483
  time to fit residues: 3.8760
Evaluate side-chains
  64 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0970
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.4150 r_free = 0.4150 target = 0.197941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.136302 restraints weight = 2910.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.140612 restraints weight = 1847.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.143158 restraints weight = 1460.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144306 restraints weight = 1302.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144399 restraints weight = 1229.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3133  Z= 0.132
  Angle     :  0.643  11.435   4276  Z= 0.302
  Chirality :  0.038   0.118    508
  Planarity :  0.003   0.020    521
  Dihedral  : 12.453 156.518    538
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.47 %
    Favored  : 75.00 %
  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 aren not related in a simple way.
  whole:  0.99 (0.44), residues: 386
  helix:  1.36 (0.37), residues: 218
  sheet:  2.13 (0.74), residues: 49
  loop : -1.33 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 259 
 TYR   0.011   0.001   TYR N 101 
 PHE   0.016   0.001   PHE R 135 
 TRP   0.007   0.001   TRP N 106 
 HIS   0.006   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3131)
  covalent geometry    : angle       0.64358 ( 4272)
  SS BOND              : bond        0.00291 (    2)
  SS BOND              : angle       0.43688 (    4)
  hydrogen bonds       : bond        0.04467 (  197)
  hydrogen bonds       : angle       3.99569 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8242 (m100) cc_final: 0.7946 (m-90)
REVERT: R  187 PHE cc_start: 0.8388 (m-80) cc_final: 0.8047 (m-80)
REVERT: R  189 PHE cc_start: 0.8132 (m-10) cc_final: 0.7820 (m-10)
  outliers start: 11
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0497
  time to fit residues: 3.8771
Evaluate side-chains
  66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  317 MET
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 194 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.194152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.131390 restraints weight = 2909.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.135609 restraints weight = 1867.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138100 restraints weight = 1487.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.139066 restraints weight = 1325.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.139142 restraints weight = 1254.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3133  Z= 0.142
  Angle     :  0.651  10.939   4276  Z= 0.308
  Chirality :  0.038   0.122    508
  Planarity :  0.003   0.021    521
  Dihedral  : 12.701 162.112    538
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 20.19 %
    Favored  : 75.00 %
  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 aren not related in a simple way.
  whole:  0.98 (0.44), residues: 386
  helix:  1.38 (0.37), residues: 218
  sheet:  2.17 (0.74), residues: 49
  loop : -1.42 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 259 
 TYR   0.011   0.001   TYR N 101 
 PHE   0.017   0.001   PHE R 135 
 TRP   0.007   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3131)
  covalent geometry    : angle       0.65163 ( 4272)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       0.44963 (    4)
  hydrogen bonds       : bond        0.04605 (  197)
  hydrogen bonds       : angle       3.99261 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8227 (m100) cc_final: 0.7925 (m-90)
REVERT: R  187 PHE cc_start: 0.8433 (m-80) cc_final: 0.8096 (m-80)
REVERT: R  189 PHE cc_start: 0.8121 (m-10) cc_final: 0.7822 (m-10)
  outliers start: 15
  outliers final: 15
  residues processed: 62
  average time/residue: 0.0468
  time to fit residues: 3.7996
Evaluate side-chains
  71 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  132 ASN
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  291 LEU
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  317 MET
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 194 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.202708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142408 restraints weight = 2904.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.147098 restraints weight = 1770.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.149825 restraints weight = 1377.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.150909 restraints weight = 1215.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.150908 restraints weight = 1149.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3133  Z= 0.141
  Angle     :  0.646  10.513   4276  Z= 0.304
  Chirality :  0.038   0.121    508
  Planarity :  0.003   0.021    521
  Dihedral  : 12.826 164.744    538
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 20.51 %
    Favored  : 74.36 %
  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 aren not related in a simple way.
  whole:  1.00 (0.44), residues: 386
  helix:  1.40 (0.37), residues: 218
  sheet:  2.21 (0.75), residues: 49
  loop : -1.44 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 259 
 TYR   0.011   0.001   TYR N 101 
 PHE   0.017   0.001   PHE R 135 
 TRP   0.006   0.001   TRP N 106 
 HIS   0.007   0.002   HIS R 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3131)
  covalent geometry    : angle       0.64638 ( 4272)
  SS BOND              : bond        0.00309 (    2)
  SS BOND              : angle       0.45404 (    4)
  hydrogen bonds       : bond        0.04552 (  197)
  hydrogen bonds       : angle       3.98343 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8225 (m100) cc_final: 0.7927 (m-90)
REVERT: R  187 PHE cc_start: 0.8449 (m-80) cc_final: 0.8126 (m-80)
REVERT: R  189 PHE cc_start: 0.8120 (m-10) cc_final: 0.7827 (m-10)
  outliers start: 16
  outliers final: 15
  residues processed: 61
  average time/residue: 0.0513
  time to fit residues: 4.0520
Evaluate side-chains
  70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   36 MET
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  132 ASN
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  317 MET
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.190031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.126245 restraints weight = 2863.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127603 restraints weight = 2744.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.130772 restraints weight = 2060.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.129788 restraints weight = 1577.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.130278 restraints weight = 1569.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3133  Z= 0.130
  Angle     :  0.635  10.387   4276  Z= 0.298
  Chirality :  0.038   0.115    508
  Planarity :  0.003   0.021    521
  Dihedral  : 13.085 170.949    538
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 20.19 %
    Favored  : 74.36 %
  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 aren not related in a simple way.
  whole:  1.07 (0.44), residues: 386
  helix:  1.47 (0.37), residues: 218
  sheet:  2.24 (0.74), residues: 49
  loop : -1.46 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 259 
 TYR   0.010   0.001   TYR N 101 
 PHE   0.016   0.001   PHE R 135 
 TRP   0.006   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3131)
  covalent geometry    : angle       0.63516 ( 4272)
  SS BOND              : bond        0.00276 (    2)
  SS BOND              : angle       0.40411 (    4)
  hydrogen bonds       : bond        0.04257 (  197)
  hydrogen bonds       : angle       3.91557 (  591)

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

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

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  772 Ramachandran restraints generated.
    386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  113 TRP cc_start: 0.8230 (m100) cc_final: 0.7930 (m-90)
REVERT: R  187 PHE cc_start: 0.8326 (m-80) cc_final: 0.7982 (m-80)
REVERT: R  189 PHE cc_start: 0.8066 (m-10) cc_final: 0.7729 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 64
  average time/residue: 0.0527
  time to fit residues: 4.3665
Evaluate side-chains
  70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   36 MET
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   97 VAL
Chi-restraints excluded: chain R residue  121 SER
Chi-restraints excluded: chain R residue  132 ASN
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  317 MET
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain R residue  328 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0980
   chunk 35 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
R 194 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.190225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.122345 restraints weight = 2940.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.126383 restraints weight = 1969.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.128698 restraints weight = 1592.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.129782 restraints weight = 1437.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.129940 restraints weight = 1360.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3133  Z= 0.138
  Angle     :  0.644  10.276   4276  Z= 0.304
  Chirality :  0.038   0.120    508
  Planarity :  0.003   0.021    521
  Dihedral  : 13.416 176.338    538
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 20.19 %
    Favored  : 74.36 %
  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 aren not related in a simple way.
  whole:  1.04 (0.44), residues: 386
  helix:  1.43 (0.37), residues: 218
  sheet:  2.31 (0.74), residues: 49
  loop : -1.47 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 259 
 TYR   0.010   0.001   TYR N 101 
 PHE   0.017   0.001   PHE R 135 
 TRP   0.006   0.001   TRP N 106 
 HIS   0.005   0.001   HIS R 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3131)
  covalent geometry    : angle       0.64462 ( 4272)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       0.44840 (    4)
  hydrogen bonds       : bond        0.04463 (  197)
  hydrogen bonds       : angle       3.96256 (  591)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 825.76 seconds
wall clock time: 14 minutes 53.90 seconds (893.90 seconds total)