Starting phenix.real_space_refine
on Tue Aug  4 15:01:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9thk_55929/08_2026/9thk_55929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9thk_55929/08_2026/9thk_55929.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9thk_55929/08_2026/9thk_55929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9thk_55929/08_2026/9thk_55929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9thk_55929/08_2026/9thk_55929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9thk_55929/08_2026/9thk_55929.cif"
  }
  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=   0.000 sd=   0.012
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
     P       6      5.49       5
     S      32      5.16       5
     C    2746      2.51       5
     N     674      2.21       5
     O     678      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4136
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2020
          Classifications: {'peptide': 247}
          Link IDs: {'PTRANS': 5, 'TRANS': 241}
    Chain: "D"
      Number of atoms: 2020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2020
          Classifications: {'peptide': 247}
          Link IDs: {'PTRANS': 5, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.82, per 1000 atoms: 0.20
  Number of scatterers: 4136
  At special positions: 0
  Unit cell: (62.694, 57.591, 88.209, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       6     15.00
     O     678      8.00
     N     674      7.00
     C    2746      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 148.7 milliseconds
  

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      91.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'B' and resid 20 through 50
    Processing helix  chain 'B' and resid 50 through 56
      removed outlier: 3.601A  pdb=" N   ARG B  54 " --> pdb=" O   ASN B  50 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER B  55 " --> pdb=" O   ALA B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 87
    Processing helix  chain 'B' and resid 88 through 94
      removed outlier: 3.730A  pdb=" N   HIS B  92 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 129
      removed outlier: 3.763A  pdb=" N   HIS B 106 " --> pdb=" O   TRP B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 152
    Processing helix  chain 'B' and resid 157 through 166
      removed outlier: 3.537A  pdb=" N   LEU B 166 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 183
      removed outlier: 4.683A  pdb=" N   PHE B 172 " --> pdb=" O   MET B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 218
    Processing helix  chain 'B' and resid 218 through 226
    Processing helix  chain 'B' and resid 227 through 244
    Processing helix  chain 'B' and resid 244 through 259
      removed outlier: 3.507A  pdb=" N   LEU B 258 " --> pdb=" O   THR B 254 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 50
    Processing helix  chain 'D' and resid 50 through 56
      removed outlier: 3.600A  pdb=" N   ARG D  54 " --> pdb=" O   ASN D  50 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER D  55 " --> pdb=" O   ALA D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 87
    Processing helix  chain 'D' and resid 88 through 94
      removed outlier: 3.730A  pdb=" N   HIS D  92 " --> pdb=" O   ASP D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 129
      removed outlier: 3.763A  pdb=" N   HIS D 106 " --> pdb=" O   TRP D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 152
    Processing helix  chain 'D' and resid 157 through 166
      removed outlier: 3.538A  pdb=" N   LEU D 166 " --> pdb=" O   THR D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 183
      removed outlier: 4.684A  pdb=" N   PHE D 172 " --> pdb=" O   MET D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 187 through 218
    Processing helix  chain 'D' and resid 218 through 226
    Processing helix  chain 'D' and resid 227 through 244
    Processing helix  chain 'D' and resid 244 through 259
      removed outlier: 3.507A  pdb=" N   LEU D 258 " --> pdb=" O   THR D 254 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.63

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1164
        1.34 -     1.46: 1318
        1.46 -     1.58: 1746
        1.58 -     1.70: 10
        1.70 -     1.82: 48
  Bond restraints: 4286
  Sorted by residual:
  bond pdb=" O3B COA D 301 "
       pdb=" P3B COA D 301 "
    ideal  model  delta    sigma   weight residual
    1.683  1.627  0.056 2.00e-02 2.50e+03 7.72e+00
  bond pdb=" O3B COA B 301 "
       pdb=" P3B COA B 301 "
    ideal  model  delta    sigma   weight residual
    1.683  1.628  0.055 2.00e-02 2.50e+03 7.69e+00
  bond pdb=" C   THR B 170 "
       pdb=" N   PRO B 171 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.38e-02 5.25e+03 3.75e+00
  bond pdb=" C   THR D 170 "
       pdb=" N   PRO D 171 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.38e-02 5.25e+03 3.71e+00
  bond pdb=" C   ASP D  88 "
       pdb=" N   PRO D  89 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.23e-02 6.61e+03 3.48e+00
  ... (remaining 4281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 5023
        1.81 -     3.63: 762
        3.63 -     5.44: 71
        5.44 -     7.26: 9
        7.26 -     9.07: 3
  Bond angle restraints: 5868
  Sorted by residual:
  angle pdb=" C   GLN B 256 "
        pdb=" N   LEU B 257 "
        pdb=" CA  LEU B 257 "
      ideal   model   delta    sigma   weight residual
     120.38  126.92   -6.54 1.37e+00 5.33e-01 2.28e+01
  angle pdb=" C   GLN D 256 "
        pdb=" N   LEU D 257 "
        pdb=" CA  LEU D 257 "
      ideal   model   delta    sigma   weight residual
     120.38  126.87   -6.49 1.37e+00 5.33e-01 2.24e+01
  angle pdb=" CG  ARG B  97 "
        pdb=" CD  ARG B  97 "
        pdb=" NE  ARG B  97 "
      ideal   model   delta    sigma   weight residual
     112.00  102.93    9.07 2.20e+00 2.07e-01 1.70e+01
  angle pdb=" CG  ARG D  97 "
        pdb=" CD  ARG D  97 "
        pdb=" NE  ARG D  97 "
      ideal   model   delta    sigma   weight residual
     112.00  102.96    9.04 2.20e+00 2.07e-01 1.69e+01
  angle pdb=" CA  ASP B  94 "
        pdb=" CB  ASP B  94 "
        pdb=" CG  ASP B  94 "
      ideal   model   delta    sigma   weight residual
     112.60  116.56   -3.96 1.00e+00 1.00e+00 1.57e+01
  ... (remaining 5863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 2156
       17.17 -    34.35: 169
       34.35 -    51.52: 37
       51.52 -    68.69: 36
       68.69 -    85.86: 18
  Dihedral angle restraints: 2416
    sinusoidal: 978
      harmonic: 1438
  Sorted by residual:
  dihedral pdb=" CA  LEU D  86 "
           pdb=" C   LEU D  86 "
           pdb=" N   GLY D  87 "
           pdb=" CA  GLY D  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.34  -25.66     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  LEU B  86 "
           pdb=" C   LEU B  86 "
           pdb=" N   GLY B  87 "
           pdb=" CA  GLY B  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.37  -25.63     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  LEU D  49 "
           pdb=" C   LEU D  49 "
           pdb=" N   ASN D  50 "
           pdb=" CA  ASN D  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.40  -24.60     0      5.00e+00 4.00e-02 2.42e+01
  ... (remaining 2413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 419
       0.077 -    0.154: 181
       0.154 -    0.230: 32
       0.230 -    0.307: 9
       0.307 -    0.384: 5
  Chirality restraints: 646
  Sorted by residual:
  chirality pdb=" CA  TYR D  35 "
            pdb=" N   TYR D  35 "
            pdb=" C   TYR D  35 "
            pdb=" CB  TYR D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.68e+00
  chirality pdb=" CA  TYR B  35 "
            pdb=" N   TYR B  35 "
            pdb=" C   TYR B  35 "
            pdb=" CB  TYR B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CA  PHE B 146 "
            pdb=" N   PHE B 146 "
            pdb=" C   PHE B 146 "
            pdb=" CB  PHE B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 643 not shown)

  Planarity restraints: 686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  97 "    0.478 9.50e-02 1.11e+02   2.15e-01 3.23e+01
        pdb=" NE  ARG D  97 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  97 "   -0.040 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  97 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  97 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  97 "    0.476 9.50e-02 1.11e+02   2.14e-01 3.21e+01
        pdb=" NE  ARG B  97 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  97 "   -0.041 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  97 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  97 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 129 "    0.455 9.50e-02 1.11e+02   2.04e-01 2.73e+01
        pdb=" NE  ARG D 129 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 129 "    0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 129 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 129 "    0.008 2.00e-02 2.50e+03
  ... (remaining 683 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1492
        2.89 -     3.39: 4184
        3.39 -     3.90: 7283
        3.90 -     4.40: 8114
        4.40 -     4.90: 13797
  Nonbonded interactions: 34870
  Sorted by model distance:
  nonbonded pdb=" O4B COA B 301 "
            pdb=" O2A COA D 301 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" ND1 HIS D 210 "
            pdb=" O1A COA D 301 "
     model   vdw
     2.481 3.120
  nonbonded pdb=" ND1 HIS B 210 "
            pdb=" O1A COA B 301 "
     model   vdw
     2.483 3.120
  nonbonded pdb=" O   ASN B 259 "
            pdb=" C   PRO B 260 "
     model   vdw
     2.575 3.270
  nonbonded pdb=" O   ASN D 259 "
            pdb=" C   PRO D 260 "
     model   vdw
     2.577 3.270
  ... (remaining 34865 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             3.680
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.070
  Find NCS groups from input model:        0.040
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   4286  Z= 0.463
  Angle     :  1.287   9.069   5868  Z= 0.862
  Chirality :  0.088   0.384    646
  Planarity :  0.018   0.215    686
  Dihedral  : 17.466  85.865   1484
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.33), residues: 490
  helix: -0.04 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.00 (0.77), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.035   0.005   ARG B  97 
 TYR   0.020   0.003   TYR B  18 
 PHE   0.016   0.002   PHE D 128 
 TRP   0.029   0.003   TRP B  64 
 HIS   0.014   0.003   HIS B  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00724 /  0.46 ( 4286)
  covalent geometry    : angle       1.28670 /  0.86 ( 5868)
  hydrogen bonds       : bond        0.19105 / 12.70 (  342)
  hydrogen bonds       : angle       7.42885 /  5.50 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B   43 HIS cc_start: 0.6658 (t70) cc_final: 0.5985 (t70)
REVERT: B   54 ARG cc_start: 0.6308 (mtm-85) cc_final: 0.6097 (mtm-85)
REVERT: B   60 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7470 (mp0)
REVERT: B   83 TRP cc_start: 0.7525 (t-100) cc_final: 0.7311 (t-100)
REVERT: B  178 MET cc_start: 0.7891 (mtp) cc_final: 0.7652 (mtm)
REVERT: D  195 TRP cc_start: 0.7335 (m100) cc_final: 0.6916 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0524
  time to fit residues: 9.5507
Evaluate side-chains
  67 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 138 HIS
B 193 ASN
B 230 HIS
D  43 HIS
D 101 ASN
D 106 HIS
D 125 ASN
D 193 ASN
D 202 HIS
D 230 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.173110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.147474 restraints weight = 5996.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.152687 restraints weight = 3317.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.156368 restraints weight = 2238.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.158787 restraints weight = 1679.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.160482 restraints weight = 1363.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4286  Z= 0.152
  Angle     :  0.635   9.898   5868  Z= 0.316
  Chirality :  0.042   0.270    646
  Planarity :  0.004   0.023    686
  Dihedral  : 16.581  67.322    640
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 11.45 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.90 (0.36), residues: 490
  helix:  2.16 (0.23), residues: 430
  sheet:  None (None), residues: 0
  loop :  0.23 (0.90), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  97 
 TYR   0.018   0.002   TYR D  35 
 PHE   0.026   0.002   PHE D  73 
 TRP   0.025   0.002   TRP D  64 
 HIS   0.008   0.002   HIS B 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 ( 4286)
  covalent geometry    : angle       0.63499 /  0.32 ( 5868)
  hydrogen bonds       : bond        0.05222 /  3.44 (  342)
  hydrogen bonds       : angle       4.38079 /  3.13 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.085 
Fit side-chains
REVERT: B   83 TRP cc_start: 0.7940 (t-100) cc_final: 0.7670 (t-100)
REVERT: B  168 MET cc_start: 0.8614 (ptm) cc_final: 0.8404 (ptm)
  outliers start: 12
  outliers final: 5
  residues processed: 87
  average time/residue: 0.0345
  time to fit residues: 4.0318
Evaluate side-chains
  71 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 106 HIS
B 139 HIS
D 125 ASN
D 138 HIS
D 230 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.161447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.134588 restraints weight = 6141.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.140111 restraints weight = 3336.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.143825 restraints weight = 2210.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.146151 restraints weight = 1659.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.147888 restraints weight = 1360.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4286  Z= 0.151
  Angle     :  0.578   8.155   5868  Z= 0.289
  Chirality :  0.042   0.296    646
  Planarity :  0.004   0.032    686
  Dihedral  : 14.361  64.544    640
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 12.15 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.83 (0.35), residues: 490
  helix:  2.85 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop :  0.58 (0.75), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  54 
 TYR   0.022   0.002   TYR D  35 
 PHE   0.019   0.002   PHE B  39 
 TRP   0.016   0.002   TRP B 213 
 HIS   0.006   0.001   HIS B 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.15 ( 4286)
  covalent geometry    : angle       0.57790 /  0.29 ( 5868)
  hydrogen bonds       : bond        0.04965 /  3.27 (  342)
  hydrogen bonds       : angle       3.96937 /  2.83 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.083 
Fit side-chains
REVERT: B   50 ASN cc_start: 0.7588 (t0) cc_final: 0.7386 (t0)
REVERT: B   83 TRP cc_start: 0.8160 (t-100) cc_final: 0.7809 (t-100)
REVERT: B  141 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6045 (t80)
REVERT: B  192 LEU cc_start: 0.8526 (tp) cc_final: 0.8196 (tp)
REVERT: B  235 LEU cc_start: 0.8801 (tp) cc_final: 0.8464 (tp)
REVERT: D  134 PHE cc_start: 0.5368 (t80) cc_final: 0.5109 (t80)
REVERT: D  154 GLN cc_start: 0.8096 (mp10) cc_final: 0.7800 (mp10)
REVERT: D  161 MET cc_start: 0.8128 (mmm) cc_final: 0.7365 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0454
  time to fit residues: 5.2640
Evaluate side-chains
  82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   70 ARG
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  125 ASN
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  230 HIS
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  43 HIS
B 122 HIS
D 125 ASN
D 139 HIS
D 230 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.160321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132834 restraints weight = 6204.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.138254 restraints weight = 3406.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.141619 restraints weight = 2307.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144088 restraints weight = 1791.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145483 restraints weight = 1476.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4286  Z= 0.148
  Angle     :  0.577   8.662   5868  Z= 0.278
  Chirality :  0.042   0.285    646
  Planarity :  0.004   0.034    686
  Dihedral  : 13.391  67.065    640
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 14.49 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.07 (0.36), residues: 490
  helix:  3.01 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop :  0.68 (0.76), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 204 
 TYR   0.021   0.002   TYR D  35 
 PHE   0.015   0.002   PHE B  39 
 TRP   0.014   0.001   TRP D  64 
 HIS   0.008   0.001   HIS D 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.15 ( 4286)
  covalent geometry    : angle       0.57654 /  0.28 ( 5868)
  hydrogen bonds       : bond        0.04684 /  3.08 (  342)
  hydrogen bonds       : angle       3.84387 /  2.75 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.080 
Fit side-chains
REVERT: B   50 ASN cc_start: 0.7708 (t0) cc_final: 0.7504 (t0)
REVERT: B   83 TRP cc_start: 0.8227 (t-100) cc_final: 0.7926 (t-100)
REVERT: B  141 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6259 (t80)
REVERT: B  192 LEU cc_start: 0.8534 (tp) cc_final: 0.8264 (tp)
REVERT: B  235 LEU cc_start: 0.8864 (tp) cc_final: 0.8528 (tp)
REVERT: D  154 GLN cc_start: 0.8158 (mp10) cc_final: 0.7863 (mp10)
REVERT: D  161 MET cc_start: 0.8219 (mmm) cc_final: 0.7968 (mmm)
REVERT: D  220 ASP cc_start: 0.7154 (m-30) cc_final: 0.6922 (p0)
  outliers start: 20
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0501
  time to fit residues: 5.7866
Evaluate side-chains
  88 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 122 HIS
D  92 HIS
D 230 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.128107 restraints weight = 5984.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.132520 restraints weight = 3583.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.135304 restraints weight = 2520.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137254 restraints weight = 1981.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138879 restraints weight = 1647.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.6089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4286  Z= 0.142
  Angle     :  0.569   7.198   5868  Z= 0.276
  Chirality :  0.040   0.257    646
  Planarity :  0.004   0.034    686
  Dihedral  : 12.831  69.277    640
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 16.82 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.18 (0.36), residues: 490
  helix:  3.14 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop :  0.38 (0.75), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  24 
 TYR   0.019   0.002   TYR D  35 
 PHE   0.016   0.002   PHE B  39 
 TRP   0.016   0.001   TRP D  64 
 HIS   0.012   0.001   HIS D  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 4286)
  covalent geometry    : angle       0.56948 /  0.28 ( 5868)
  hydrogen bonds       : bond        0.04507 /  2.95 (  342)
  hydrogen bonds       : angle       3.73699 /  2.66 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B   50 ASN cc_start: 0.7676 (t0) cc_final: 0.7474 (t0)
REVERT: B   83 TRP cc_start: 0.8216 (t-100) cc_final: 0.7875 (t-100)
REVERT: B  141 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6262 (t80)
REVERT: B  192 LEU cc_start: 0.8484 (tp) cc_final: 0.8259 (tp)
REVERT: D  154 GLN cc_start: 0.8250 (mp10) cc_final: 0.7903 (mp10)
REVERT: D  161 MET cc_start: 0.8212 (mmm) cc_final: 0.7947 (mmm)
  outliers start: 18
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0527
  time to fit residues: 5.8964
Evaluate side-chains
  85 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain D residue   70 ARG
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  230 HIS
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 230 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.150656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.126731 restraints weight = 6024.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.131013 restraints weight = 3586.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.133841 restraints weight = 2524.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.136000 restraints weight = 1993.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137309 restraints weight = 1656.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.6354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4286  Z= 0.147
  Angle     :  0.556   7.324   5868  Z= 0.274
  Chirality :  0.040   0.264    646
  Planarity :  0.004   0.036    686
  Dihedral  : 12.619  69.479    640
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 17.29 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.08 (0.36), residues: 490
  helix:  3.09 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop :  0.22 (0.73), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  24 
 TYR   0.022   0.002   TYR D  35 
 PHE   0.014   0.002   PHE D  73 
 TRP   0.013   0.001   TRP D  64 
 HIS   0.014   0.001   HIS D 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.15 ( 4286)
  covalent geometry    : angle       0.55577 /  0.27 ( 5868)
  hydrogen bonds       : bond        0.04465 /  2.93 (  342)
  hydrogen bonds       : angle       3.75842 /  2.68 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.153 
Fit side-chains
REVERT: B   50 ASN cc_start: 0.7817 (t0) cc_final: 0.7593 (t0)
REVERT: B   83 TRP cc_start: 0.8236 (t-100) cc_final: 0.7873 (t-100)
REVERT: B  141 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6225 (t80)
REVERT: B  192 LEU cc_start: 0.8502 (tp) cc_final: 0.8277 (tp)
REVERT: D   20 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7580 (p)
REVERT: D  154 GLN cc_start: 0.8243 (mp10) cc_final: 0.7866 (mp10)
REVERT: D  161 MET cc_start: 0.8178 (mmm) cc_final: 0.7946 (mmm)
  outliers start: 22
  outliers final: 19
  residues processed: 85
  average time/residue: 0.0608
  time to fit residues: 6.7203
Evaluate side-chains
  86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   70 ARG
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    0.0770
   chunk 43 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 230 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.153592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.131731 restraints weight = 5963.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.135879 restraints weight = 3550.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.138601 restraints weight = 2481.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.140641 restraints weight = 1922.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.141980 restraints weight = 1579.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.6592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4286  Z= 0.119
  Angle     :  0.526   7.508   5868  Z= 0.257
  Chirality :  0.038   0.249    646
  Planarity :  0.003   0.032    686
  Dihedral  : 12.275  68.496    640
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 17.52 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.22 (0.36), residues: 490
  helix:  3.22 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.04 (0.71), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  97 
 TYR   0.020   0.002   TYR D  35 
 PHE   0.015   0.001   PHE B  39 
 TRP   0.017   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.12 ( 4286)
  covalent geometry    : angle       0.52562 /  0.26 ( 5868)
  hydrogen bonds       : bond        0.04141 /  2.70 (  342)
  hydrogen bonds       : angle       3.63159 /  2.60 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.161 
Fit side-chains
REVERT: B  141 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6439 (t80)
REVERT: D  161 MET cc_start: 0.8227 (mmm) cc_final: 0.8022 (mmm)
  outliers start: 22
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0502
  time to fit residues: 5.9582
Evaluate side-chains
  86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain D residue   70 ARG
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  230 HIS
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 ASN
D 230 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.151595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.130464 restraints weight = 5947.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134527 restraints weight = 3641.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.137276 restraints weight = 2561.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139073 restraints weight = 1979.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.140406 restraints weight = 1645.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.6856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4286  Z= 0.148
  Angle     :  0.560   7.448   5868  Z= 0.279
  Chirality :  0.040   0.260    646
  Planarity :  0.003   0.033    686
  Dihedral  : 12.335  69.414    640
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 19.16 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.00 (0.36), residues: 490
  helix:  3.09 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.26 (0.70), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  54 
 TYR   0.023   0.002   TYR D  35 
 PHE   0.013   0.001   PHE B  39 
 TRP   0.014   0.001   TRP B 102 
 HIS   0.011   0.001   HIS D 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.15 ( 4286)
  covalent geometry    : angle       0.55957 /  0.28 ( 5868)
  hydrogen bonds       : bond        0.04389 /  2.86 (  342)
  hydrogen bonds       : angle       3.71601 /  2.65 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B  141 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6491 (t80)
REVERT: D  161 MET cc_start: 0.8253 (mmm) cc_final: 0.7997 (mmm)
REVERT: D  231 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7246 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 85
  average time/residue: 0.0549
  time to fit residues: 6.1079
Evaluate side-chains
  84 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 122 HIS
D 230 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.152860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.131541 restraints weight = 5945.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.135680 restraints weight = 3501.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.138357 restraints weight = 2428.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.140492 restraints weight = 1882.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141707 restraints weight = 1531.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.7065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4286  Z= 0.133
  Angle     :  0.546   7.513   5868  Z= 0.271
  Chirality :  0.039   0.251    646
  Planarity :  0.003   0.032    686
  Dihedral  : 12.351  69.471    640
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 19.86 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.95 (0.36), residues: 490
  helix:  3.07 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.31 (0.70), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  97 
 TYR   0.025   0.002   TYR D  35 
 PHE   0.014   0.001   PHE B  39 
 TRP   0.017   0.001   TRP D  64 
 HIS   0.003   0.001   HIS B 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 ( 4286)
  covalent geometry    : angle       0.54632 /  0.27 ( 5868)
  hydrogen bonds       : bond        0.04265 /  2.78 (  342)
  hydrogen bonds       : angle       3.68778 /  2.65 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.144 
Fit side-chains
REVERT: B  141 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6446 (t80)
REVERT: D  161 MET cc_start: 0.8300 (mmm) cc_final: 0.8078 (mmm)
REVERT: D  231 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7262 (pp)
  outliers start: 23
  outliers final: 16
  residues processed: 83
  average time/residue: 0.0448
  time to fit residues: 4.9774
Evaluate side-chains
  79 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  154 GLN
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 3 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0000
   chunk 38 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0050
   overall best weight:    0.3398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 230 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.156001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134729 restraints weight = 5711.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.138813 restraints weight = 3390.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141723 restraints weight = 2350.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.143605 restraints weight = 1790.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145077 restraints weight = 1469.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.7173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4286  Z= 0.112
  Angle     :  0.530   7.607   5868  Z= 0.262
  Chirality :  0.037   0.232    646
  Planarity :  0.003   0.031    686
  Dihedral  : 12.078  68.531    640
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 20.79 %
    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 are not related in a simple way.
  whole:  4.18 (0.36), residues: 490
  helix:  3.21 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.20 (0.71), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  97 
 TYR   0.024   0.002   TYR D  35 
 PHE   0.017   0.001   PHE B  39 
 TRP   0.034   0.001   TRP B 102 
 HIS   0.004   0.001   HIS D 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.11 ( 4286)
  covalent geometry    : angle       0.53017 /  0.26 ( 5868)
  hydrogen bonds       : bond        0.03996 /  2.56 (  342)
  hydrogen bonds       : angle       3.58816 /  2.57 ( 1026)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.088 
Fit side-chains
REVERT: B  141 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6396 (t80)
REVERT: D  161 MET cc_start: 0.8167 (mmm) cc_final: 0.7943 (mmm)
  outliers start: 18
  outliers final: 15
  residues processed: 82
  average time/residue: 0.0432
  time to fit residues: 4.7969
Evaluate side-chains
  83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  154 GLN
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 230 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.152592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130973 restraints weight = 5933.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.135072 restraints weight = 3564.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.137864 restraints weight = 2495.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.139671 restraints weight = 1927.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140991 restraints weight = 1607.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.7268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4286  Z= 0.134
  Angle     :  0.565   9.045   5868  Z= 0.280
  Chirality :  0.039   0.241    646
  Planarity :  0.003   0.032    686
  Dihedral  : 12.112  69.430    640
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.50 %
    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 are not related in a simple way.
  whole:  3.98 (0.36), residues: 490
  helix:  3.08 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.27 (0.70), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  97 
 TYR   0.025   0.002   TYR D  35 
 PHE   0.014   0.001   PHE B  39 
 TRP   0.030   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 4286)
  covalent geometry    : angle       0.56452 /  0.28 ( 5868)
  hydrogen bonds       : bond        0.04201 /  2.71 (  342)
  hydrogen bonds       : angle       3.72295 /  2.66 ( 1026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 693.61 seconds
wall clock time: 12 minutes 38.38 seconds (758.38 seconds total)