Starting phenix.real_space_refine
on Wed Sep 17 11:56:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3j89_6123/09_2025/3j89_6123.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3j89_6123/09_2025/3j89_6123.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/3j89_6123/09_2025/3j89_6123.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3j89_6123/09_2025/3j89_6123.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/3j89_6123/09_2025/3j89_6123.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3j89_6123/09_2025/3j89_6123.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=   0.047 sd=   0.273
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     C    2755      2.51       5
     N     855      2.21       5
     O     817      1.98       5
     H    4598      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9025
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 475
          Classifications: {'peptide': 29}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 28}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S
  Time building chain proxies: 0.92, per 1000 atoms: 0.10
  Number of scatterers: 9025
  At special positions: 0
  Unit cell: (90.78, 90.78, 67.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O     817      8.00
     N     855      7.00
     C    2755      6.00
     H    4598      1.00
    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: 0.77
  Conformation dependent library (CDL) restraints added in 282.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      96.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 29
      removed outlier: 3.543A  pdb=" N   ALA A   7 " --> pdb=" O   ARG A   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA B   7 " --> pdb=" O   ARG B   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA C   7 " --> pdb=" O   ARG C   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA D   7 " --> pdb=" O   ARG D   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA E   7 " --> pdb=" O   ARG E   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA F   7 " --> pdb=" O   ARG F   3 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA G   7 " --> pdb=" O   ARG G   3 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA H   7 " --> pdb=" O   ARG H   3 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA I   7 " --> pdb=" O   ARG I   3 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA J   7 " --> pdb=" O   ARG J   3 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA K   7 " --> pdb=" O   ARG K   3 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA L   7 " --> pdb=" O   ARG L   3 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA M   7 " --> pdb=" O   ARG M   3 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA N   7 " --> pdb=" O   ARG N   3 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA O   7 " --> pdb=" O   ARG O   3 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA P   7 " --> pdb=" O   ARG P   3 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 2 through 29
      removed outlier: 3.543A  pdb=" N   ALA Q   7 " --> pdb=" O   ARG Q   3 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA R   7 " --> pdb=" O   ARG R   3 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 2 through 29
      removed outlier: 3.542A  pdb=" N   ALA S   7 " --> pdb=" O   ARG S   3 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        0.96 -     1.08: 1102
        1.08 -     1.19: 3496
        1.19 -     1.31: 928
        1.31 -     1.43: 1005
        1.43 -     1.54: 2513
  Bond restraints: 9044
  Sorted by residual:
  bond pdb=" N   ALA P   7 "
       pdb=" H   ALA P   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.032 -0.172 2.00e-02 2.50e+03 7.39e+01
  bond pdb=" N   ALA D   7 "
       pdb=" H   ALA D   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.032 -0.172 2.00e-02 2.50e+03 7.38e+01
  bond pdb=" N   ALA J   7 "
       pdb=" H   ALA J   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.032 -0.172 2.00e-02 2.50e+03 7.35e+01
  bond pdb=" N   ALA E   7 "
       pdb=" H   ALA E   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.031 -0.171 2.00e-02 2.50e+03 7.35e+01
  bond pdb=" N   ALA F   7 "
       pdb=" H   ALA F   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.031 -0.171 2.00e-02 2.50e+03 7.35e+01
  ... (remaining 9039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 12390
        1.65 -     3.30: 2619
        3.30 -     4.95: 588
        4.95 -     6.60: 648
        6.60 -     8.25: 95
  Bond angle restraints: 16340
  Sorted by residual:
  angle pdb=" N   ILE R   4 "
        pdb=" CA  ILE R   4 "
        pdb=" C   ILE R   4 "
      ideal   model   delta    sigma   weight residual
     112.83  108.63    4.20 9.90e-01 1.02e+00 1.80e+01
  angle pdb=" N   ILE C   4 "
        pdb=" CA  ILE C   4 "
        pdb=" C   ILE C   4 "
      ideal   model   delta    sigma   weight residual
     112.83  108.67    4.16 9.90e-01 1.02e+00 1.76e+01
  angle pdb=" N   ILE Q   4 "
        pdb=" CA  ILE Q   4 "
        pdb=" C   ILE Q   4 "
      ideal   model   delta    sigma   weight residual
     112.83  108.70    4.13 9.90e-01 1.02e+00 1.74e+01
  angle pdb=" N   ILE H   4 "
        pdb=" CA  ILE H   4 "
        pdb=" C   ILE H   4 "
      ideal   model   delta    sigma   weight residual
     112.83  108.70    4.13 9.90e-01 1.02e+00 1.74e+01
  angle pdb=" N   ILE K   4 "
        pdb=" CA  ILE K   4 "
        pdb=" C   ILE K   4 "
      ideal   model   delta    sigma   weight residual
     112.83  108.71    4.12 9.90e-01 1.02e+00 1.73e+01
  ... (remaining 16335 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.65: 3769
       11.65 -    23.30: 221
       23.30 -    34.95: 38
       34.95 -    46.59: 19
       46.59 -    58.24: 19
  Dihedral angle restraints: 4066
    sinusoidal: 2280
      harmonic: 1786
  Sorted by residual:
  dihedral pdb=" CA  ILE C   4 "
           pdb=" C   ILE C   4 "
           pdb=" N   LEU C   5 "
           pdb=" CA  LEU C   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ILE F   4 "
           pdb=" C   ILE F   4 "
           pdb=" N   LEU F   5 "
           pdb=" CA  LEU F   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.50   18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ILE O   4 "
           pdb=" C   ILE O   4 "
           pdb=" N   LEU O   5 "
           pdb=" CA  LEU O   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.50   18.50     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 4063 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 119
       0.040 -    0.079: 197
       0.079 -    0.118: 208
       0.118 -    0.157: 109
       0.157 -    0.197: 70
  Chirality restraints: 703
  Sorted by residual:
  chirality pdb=" CA  GLU N  10 "
            pdb=" N   GLU N  10 "
            pdb=" C   GLU N  10 "
            pdb=" CB  GLU N  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  GLU B  10 "
            pdb=" N   GLU B  10 "
            pdb=" C   GLU B  10 "
            pdb=" CB  GLU B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.57e-01
  chirality pdb=" CA  GLU O  10 "
            pdb=" N   GLU O  10 "
            pdb=" C   GLU O  10 "
            pdb=" CB  GLU O  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 700 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  22 "    0.020 2.00e-02 2.50e+03   3.11e-02 2.18e+01
        pdb=" CG  HIS E  22 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  22 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  22 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  22 "    0.015 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  22 "   -0.014 2.00e-02 2.50e+03
        pdb=" HD1 HIS E  22 "   -0.071 2.00e-02 2.50e+03
        pdb=" HD2 HIS E  22 "   -0.026 2.00e-02 2.50e+03
        pdb=" HE1 HIS E  22 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H  22 "    0.020 2.00e-02 2.50e+03   3.10e-02 2.17e+01
        pdb=" CG  HIS H  22 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS H  22 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 HIS H  22 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS H  22 "    0.016 2.00e-02 2.50e+03
        pdb=" NE2 HIS H  22 "   -0.014 2.00e-02 2.50e+03
        pdb=" HD1 HIS H  22 "   -0.071 2.00e-02 2.50e+03
        pdb=" HD2 HIS H  22 "   -0.026 2.00e-02 2.50e+03
        pdb=" HE1 HIS H  22 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS R  22 "   -0.019 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" CG  HIS R  22 "   -0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS R  22 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 HIS R  22 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS R  22 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 HIS R  22 "    0.014 2.00e-02 2.50e+03
        pdb=" HD1 HIS R  22 "    0.070 2.00e-02 2.50e+03
        pdb=" HD2 HIS R  22 "    0.025 2.00e-02 2.50e+03
        pdb=" HE1 HIS R  22 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.29: 1304
        2.29 -     2.84: 20083
        2.84 -     3.40: 22086
        3.40 -     3.95: 29734
        3.95 -     4.50: 42641
  Nonbonded interactions: 115848
  Sorted by model distance:
  nonbonded pdb="HH22 ARG H   3 "
            pdb=" OE1 GLU H   6 "
     model   vdw
     1.738 2.450
  nonbonded pdb="HH22 ARG S   3 "
            pdb=" OE1 GLU S   6 "
     model   vdw
     1.738 2.450
  nonbonded pdb="HH22 ARG Q   3 "
            pdb=" OE1 GLU Q   6 "
     model   vdw
     1.738 2.450
  nonbonded pdb="HH22 ARG N   3 "
            pdb=" OE1 GLU N   6 "
     model   vdw
     1.738 2.450
  nonbonded pdb="HH22 ARG M   3 "
            pdb=" OE1 GLU M   6 "
     model   vdw
     1.738 2.450
  ... (remaining 115843 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
}

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:             0.030
  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:             0.060
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.250
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
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      :  0.022   0.065   4446  Z= 1.440
  Angle     :  1.639   5.689   5985  Z= 1.159
  Chirality :  0.101   0.197    703
  Planarity :  0.010   0.046    798
  Dihedral  : 11.967  58.243   1710
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.96 (0.29), residues: 513
  helix: -0.44 (0.18), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  17 
 TYR   0.015   0.006   TYR F  15 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.02218 ( 4446)
  covalent geometry    : angle       1.63931 ( 5985)
  hydrogen bonds       : bond        0.23422 (  438)
  hydrogen bonds       : angle       7.36226 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.3428
  time to fit residues: 54.8496
Evaluate side-chains
  75 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
R  29 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.113233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.091008 restraints weight = 29226.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.094297 restraints weight = 14368.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.096268 restraints weight = 9839.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.097506 restraints weight = 7924.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.098297 restraints weight = 6951.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4446  Z= 0.268
  Angle     :  0.684   5.726   5985  Z= 0.385
  Chirality :  0.030   0.090    703
  Planarity :  0.007   0.040    798
  Dihedral  :  4.912  16.912    646
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.53 %
    Favored  : 83.71 %
  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 aren not related in a simple way.
  whole:  2.41 (0.34), residues: 513
  helix:  1.64 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG N  13 
 TYR   0.016   0.004   TYR E  15 
 HIS   0.006   0.002   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 4446)
  covalent geometry    : angle       0.68357 ( 5985)
  hydrogen bonds       : bond        0.07308 (  438)
  hydrogen bonds       : angle       5.91846 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   10 GLU cc_start: 0.8269 (tt0) cc_final: 0.7978 (tt0)
  outliers start: 11
  outliers final: 9
  residues processed: 127
  average time/residue: 0.3529
  time to fit residues: 50.3455
Evaluate side-chains
  106 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   19 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain I residue    8 ASP
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue    8 ASP
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain N residue   26 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.091861 restraints weight = 29194.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.095133 restraints weight = 14418.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.097173 restraints weight = 9931.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.098469 restraints weight = 7988.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.099285 restraints weight = 6973.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.5285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4446  Z= 0.178
  Angle     :  0.522   4.102   5985  Z= 0.305
  Chirality :  0.029   0.099    703
  Planarity :  0.005   0.037    798
  Dihedral  :  4.403  15.234    646
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.05 %
    Favored  : 76.69 %
  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:  3.41 (0.34), residues: 513
  helix:  2.25 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG M  27 
 TYR   0.014   0.003   TYR R  15 
 HIS   0.005   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4446)
  covalent geometry    : angle       0.52212 ( 5985)
  hydrogen bonds       : bond        0.05486 (  438)
  hydrogen bonds       : angle       4.83930 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7771 (mt-10)
REVERT: G   24 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7693 (mm-30)
REVERT: H   24 GLU cc_start: 0.7707 (tt0) cc_final: 0.7355 (tt0)
REVERT: I   10 GLU cc_start: 0.8422 (tt0) cc_final: 0.8148 (mt-10)
REVERT: L   27 ARG cc_start: 0.7358 (mtt-85) cc_final: 0.7046 (mtt-85)
  outliers start: 13
  outliers final: 8
  residues processed: 124
  average time/residue: 0.3473
  time to fit residues: 48.5628
Evaluate side-chains
  108 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.109290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.087043 restraints weight = 30144.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.090495 restraints weight = 14832.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.092562 restraints weight = 10123.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.093905 restraints weight = 8145.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.094746 restraints weight = 7111.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.5808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4446  Z= 0.315
  Angle     :  0.663   6.463   5985  Z= 0.387
  Chirality :  0.033   0.094    703
  Planarity :  0.008   0.051    798
  Dihedral  :  4.928  19.167    646
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.06 %
    Favored  : 72.93 %
  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 aren not related in a simple way.
  whole:  1.75 (0.34), residues: 513
  helix:  1.23 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  13 
 TYR   0.022   0.006   TYR R  15 
 HIS   0.008   0.002   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 ( 4446)
  covalent geometry    : angle       0.66272 ( 5985)
  hydrogen bonds       : bond        0.06812 (  438)
  hydrogen bonds       : angle       5.48115 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   20 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: I   10 GLU cc_start: 0.8475 (tt0) cc_final: 0.8210 (mt-10)
REVERT: I   24 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7597 (tt0)
REVERT: L   27 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.7087 (mtt90)
  outliers start: 20
  outliers final: 14
  residues processed: 88
  average time/residue: 0.4328
  time to fit residues: 42.0772
Evaluate side-chains
  89 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   19 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain I residue   12 LEU
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Chi-restraints excluded: chain R residue   25 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.110865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.088662 restraints weight = 29476.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.092016 restraints weight = 14607.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.094099 restraints weight = 10074.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.095446 restraints weight = 8090.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.096239 restraints weight = 7072.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4446  Z= 0.204
  Angle     :  0.512   4.573   5985  Z= 0.304
  Chirality :  0.029   0.103    703
  Planarity :  0.005   0.035    798
  Dihedral  :  4.525  17.446    646
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.31 %
    Favored  : 72.43 %
  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:  2.75 (0.35), residues: 513
  helix:  1.84 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M  27 
 TYR   0.014   0.004   TYR E  15 
 HIS   0.006   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 4446)
  covalent geometry    : angle       0.51232 ( 5985)
  hydrogen bonds       : bond        0.05523 (  438)
  hydrogen bonds       : angle       4.89095 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   10 GLU cc_start: 0.8371 (tt0) cc_final: 0.8131 (mt-10)
REVERT: L   27 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.7168 (mtt90)
  outliers start: 17
  outliers final: 16
  residues processed: 97
  average time/residue: 0.3966
  time to fit residues: 42.8263
Evaluate side-chains
  100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain C residue   15 TYR
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain I residue   12 LEU
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain O residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.110613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088493 restraints weight = 29642.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.091972 restraints weight = 14634.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.094037 restraints weight = 10006.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.095365 restraints weight = 8043.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.096212 restraints weight = 7034.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.6329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4446  Z= 0.189
  Angle     :  0.493   4.561   5985  Z= 0.293
  Chirality :  0.029   0.110    703
  Planarity :  0.006   0.049    798
  Dihedral  :  4.459  19.438    646
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.06 %
    Favored  : 72.68 %
  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:  2.95 (0.34), residues: 513
  helix:  1.96 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG P  27 
 TYR   0.014   0.004   TYR K  15 
 HIS   0.005   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4446)
  covalent geometry    : angle       0.49327 ( 5985)
  hydrogen bonds       : bond        0.05231 (  438)
  hydrogen bonds       : angle       4.74484 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   10 GLU cc_start: 0.8351 (tt0) cc_final: 0.8108 (mt-10)
REVERT: I   24 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7673 (tt0)
REVERT: L   27 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.7123 (mtt90)
  outliers start: 17
  outliers final: 14
  residues processed: 93
  average time/residue: 0.3863
  time to fit residues: 40.0695
Evaluate side-chains
  100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain C residue   15 TYR
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain K residue   25 ILE
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain O residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.110282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.088283 restraints weight = 29825.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.091681 restraints weight = 14951.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.093731 restraints weight = 10260.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.095037 restraints weight = 8280.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.095863 restraints weight = 7240.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.6398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4446  Z= 0.232
  Angle     :  0.546   5.330   5985  Z= 0.323
  Chirality :  0.031   0.148    703
  Planarity :  0.006   0.030    798
  Dihedral  :  4.576  21.237    646
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 23.56 %
    Favored  : 71.43 %
  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:  2.49 (0.34), residues: 513
  helix:  1.68 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  27 
 TYR   0.016   0.004   TYR K  15 
 HIS   0.007   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 4446)
  covalent geometry    : angle       0.54629 ( 5985)
  hydrogen bonds       : bond        0.05657 (  438)
  hydrogen bonds       : angle       4.96543 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   15 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6977 (m-80)
REVERT: I   10 GLU cc_start: 0.8321 (tt0) cc_final: 0.8095 (mt-10)
REVERT: I   24 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7615 (tt0)
  outliers start: 20
  outliers final: 17
  residues processed: 89
  average time/residue: 0.3960
  time to fit residues: 39.2495
Evaluate side-chains
  96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain C residue   15 TYR
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain G residue   15 TYR
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain K residue   25 ILE
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain O residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Chi-restraints excluded: chain R residue   25 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.110789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.089041 restraints weight = 29602.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.092374 restraints weight = 14701.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.094371 restraints weight = 10236.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.095683 restraints weight = 8298.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.096503 restraints weight = 7258.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.6489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4446  Z= 0.194
  Angle     :  0.497   4.303   5985  Z= 0.296
  Chirality :  0.030   0.162    703
  Planarity :  0.005   0.032    798
  Dihedral  :  4.398  22.261    646
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.06 %
    Favored  : 71.68 %
  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:  2.97 (0.34), residues: 513
  helix:  1.98 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  27 
 TYR   0.014   0.004   TYR K  15 
 HIS   0.006   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4446)
  covalent geometry    : angle       0.49729 ( 5985)
  hydrogen bonds       : bond        0.05188 (  438)
  hydrogen bonds       : angle       4.76063 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   15 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.6969 (m-80)
REVERT: I   10 GLU cc_start: 0.8294 (tt0) cc_final: 0.8091 (mt-10)
REVERT: I   24 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7687 (tm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 95
  average time/residue: 0.3827
  time to fit residues: 40.6319
Evaluate side-chains
  103 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain C residue   15 TYR
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain G residue   15 TYR
Chi-restraints excluded: chain I residue   12 LEU
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain K residue   25 ILE
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain O residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Chi-restraints excluded: chain R residue   25 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.111212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.088492 restraints weight = 28766.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.091853 restraints weight = 14290.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.093897 restraints weight = 9884.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.095227 restraints weight = 7986.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.096076 restraints weight = 6983.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.6551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4446  Z= 0.201
  Angle     :  0.516   4.604   5985  Z= 0.305
  Chirality :  0.030   0.150    703
  Planarity :  0.005   0.039    798
  Dihedral  :  4.427  23.182    646
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 24.31 %
    Favored  : 70.68 %
  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:  2.84 (0.34), residues: 513
  helix:  1.90 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  27 
 TYR   0.014   0.004   TYR K  15 
 HIS   0.006   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 4446)
  covalent geometry    : angle       0.51585 ( 5985)
  hydrogen bonds       : bond        0.05236 (  438)
  hydrogen bonds       : angle       4.79186 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   15 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.6980 (m-80)
REVERT: I   10 GLU cc_start: 0.8394 (tt0) cc_final: 0.8193 (mt-10)
REVERT: I   24 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7612 (tm-30)
  outliers start: 20
  outliers final: 18
  residues processed: 92
  average time/residue: 0.3786
  time to fit residues: 38.8002
Evaluate side-chains
  102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain C residue   15 TYR
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain G residue   15 TYR
Chi-restraints excluded: chain I residue   12 LEU
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain K residue   25 ILE
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain O residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Chi-restraints excluded: chain R residue   25 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.111304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.088643 restraints weight = 28691.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.092021 restraints weight = 14131.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.094075 restraints weight = 9737.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.095421 restraints weight = 7880.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.096255 restraints weight = 6886.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.6602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4446  Z= 0.187
  Angle     :  0.501   4.363   5985  Z= 0.297
  Chirality :  0.030   0.158    703
  Planarity :  0.005   0.031    798
  Dihedral  :  4.342  22.595    646
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 24.31 %
    Favored  : 70.68 %
  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:  3.01 (0.34), residues: 513
  helix:  2.01 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  27 
 TYR   0.013   0.004   TYR K  15 
 HIS   0.006   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4446)
  covalent geometry    : angle       0.50052 ( 5985)
  hydrogen bonds       : bond        0.05107 (  438)
  hydrogen bonds       : angle       4.73425 ( 1314)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   15 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.6976 (m-80)
REVERT: I   24 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7649 (tm-30)
  outliers start: 20
  outliers final: 18
  residues processed: 94
  average time/residue: 0.3828
  time to fit residues: 40.1337
Evaluate side-chains
  102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain C residue   15 TYR
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain G residue   15 TYR
Chi-restraints excluded: chain I residue   12 LEU
Chi-restraints excluded: chain I residue   24 GLU
Chi-restraints excluded: chain K residue   25 ILE
Chi-restraints excluded: chain L residue   25 ILE
Chi-restraints excluded: chain M residue   25 ILE
Chi-restraints excluded: chain N residue   25 ILE
Chi-restraints excluded: chain O residue   25 ILE
Chi-restraints excluded: chain Q residue   25 ILE
Chi-restraints excluded: chain R residue   19 LEU
Chi-restraints excluded: chain R residue   25 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.110531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.087973 restraints weight = 28765.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.091328 restraints weight = 14369.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.093400 restraints weight = 9898.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.094667 restraints weight = 7952.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.095550 restraints weight = 6985.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.6614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4446  Z= 0.235
  Angle     :  0.554   5.104   5985  Z= 0.327
  Chirality :  0.031   0.156    703
  Planarity :  0.006   0.039    798
  Dihedral  :  4.586  29.601    646
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 25.06 %
    Favored  : 69.92 %
  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:  2.58 (0.34), residues: 513
  helix:  1.74 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  27 
 TYR   0.016   0.004   TYR K  15 
 HIS   0.007   0.001   HIS P  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 4446)
  covalent geometry    : angle       0.55397 ( 5985)
  hydrogen bonds       : bond        0.05504 (  438)
  hydrogen bonds       : angle       4.92272 ( 1314)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1663.08 seconds
wall clock time: 28 minutes 58.04 seconds (1738.04 seconds total)