Starting phenix.real_space_refine
on Tue Mar  3 23:48:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x57_33010/03_2026/7x57_33010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x57_33010/03_2026/7x57_33010.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2026/7x57_33010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2026/7x57_33010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2026/7x57_33010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2026/7x57_33010.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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     242      5.49       5
     S      20      5.16       5
     C    5373      2.51       5
     N    1845      2.21       5
     O    2287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9767
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 568
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "G"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "H"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2463
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2498
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 2.35, per 1000 atoms: 0.24
  Number of scatterers: 9767
  At special positions: 0
  Unit cell: (120.75, 93.45, 111.3, 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      20     16.00
     P     242     15.00
     O    2287      8.00
     N    1845      7.00
     C    5373      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: 0.80
  Conformation dependent library (CDL) restraints added in 180.0 milliseconds
  

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1126

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 6 sheets defined
      78.8% alpha, 2.0% beta
      120 base pairs and 187 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.798A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 3.517A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 132
    Processing helix  chain 'D' and resid 25 through 29
      removed outlier: 3.559A  pdb=" N   ILE D  29 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
    Processing helix  chain 'D' and resid 82 through 93
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.720A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.527A  pdb=" N   PHE G  67 " --> pdb=" O   ARG G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 131
    Processing helix  chain 'H' and resid 24 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.862A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA5, first strand: chain 'G' and resid 83 through 84
      removed outlier: 6.812A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 118 through 119

    358 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      312 hydrogen bonds
      624 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      187 stacking parallelities
  Total time for adding SS restraints: 1.78

  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:
        1.22 -     1.33: 1875
        1.33 -     1.45: 3371
        1.45 -     1.57: 4658
        1.57 -     1.69: 482
        1.69 -     1.81: 32
  Bond restraints: 10418
  Sorted by residual:
  bond pdb=" C3'  DT I  14 "
       pdb=" O3'  DT I  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.25e+00
  bond pdb=" C3'  DC I -48 "
       pdb=" O3'  DC I -48 "
    ideal  model  delta    sigma   weight residual
    1.422  1.466 -0.044 3.00e-02 1.11e+03 2.17e+00
  bond pdb=" C3'  DC I  51 "
       pdb=" O3'  DC I  51 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CG  LYS H  77 "
       pdb=" CD  LYS H  77 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" CB  MET B  84 "
       pdb=" CG  MET B  84 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.34e+00
  ... (remaining 10413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 14651
        1.76 -     3.53: 407
        3.53 -     5.29: 23
        5.29 -     7.06: 3
        7.06 -     8.82: 2
  Bond angle restraints: 15086
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  104.00    8.70 3.00e+00 1.11e-01 8.41e+00
  angle pdb=" CA  ARG H  92 "
        pdb=" CB  ARG H  92 "
        pdb=" CG  ARG H  92 "
      ideal   model   delta    sigma   weight residual
     114.10  119.61   -5.51 2.00e+00 2.50e-01 7.59e+00
  angle pdb=" C   ALA F  76 "
        pdb=" N   LYS F  77 "
        pdb=" CA  LYS F  77 "
      ideal   model   delta    sigma   weight residual
     121.54  126.72   -5.18 1.91e+00 2.74e-01 7.35e+00
  angle pdb=" C   TYR D  51 "
        pdb=" N   GLU D  52 "
        pdb=" CA  GLU D  52 "
      ideal   model   delta    sigma   weight residual
     120.28  116.66    3.62 1.34e+00 5.57e-01 7.31e+00
  angle pdb=" N   GLY D  56 "
        pdb=" CA  GLY D  56 "
        pdb=" C   GLY D  56 "
      ideal   model   delta    sigma   weight residual
     112.50  109.51    2.99 1.16e+00 7.43e-01 6.62e+00
  ... (remaining 15081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.68: 4448
       34.68 -    69.35: 1165
       69.35 -   104.02: 32
      104.02 -   138.70: 1
      138.70 -   173.37: 3
  Dihedral angle restraints: 5649
    sinusoidal: 3920
      harmonic: 1729
  Sorted by residual:
  dihedral pdb=" C4'  DC I  51 "
           pdb=" C3'  DC I  51 "
           pdb=" O3'  DC I  51 "
           pdb=" P    DA I  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.63  173.37     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC I -48 "
           pdb=" C3'  DC I -48 "
           pdb=" O3'  DC I -48 "
           pdb=" P    DG I -47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   49.06  170.94     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT I  14 "
           pdb=" C3'  DT I  14 "
           pdb=" O3'  DT I  14 "
           pdb=" P    DT I  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.32  169.68     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 5646 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1330
       0.036 -    0.072: 300
       0.072 -    0.108: 78
       0.108 -    0.143: 14
       0.143 -    0.179: 1
  Chirality restraints: 1723
  Sorted by residual:
  chirality pdb=" CB  VAL H  70 "
            pdb=" CA  VAL H  70 "
            pdb=" CG1 VAL H  70 "
            pdb=" CG2 VAL H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CA  LYS H  77 "
            pdb=" N   LYS H  77 "
            pdb=" C   LYS H  77 "
            pdb=" CB  LYS H  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CB  ILE F  50 "
            pdb=" CA  ILE F  50 "
            pdb=" CG1 ILE F  50 "
            pdb=" CG2 ILE F  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 1720 not shown)

  Planarity restraints: 1072
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  67 "   -0.021 2.00e-02 2.50e+03   4.20e-02 1.77e+01
        pdb=" C   ARG B  67 "    0.073 2.00e-02 2.50e+03
        pdb=" O   ARG B  67 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ASP B  68 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  49 "    0.019 2.00e-02 2.50e+03   3.88e-02 1.50e+01
        pdb=" C   LEU D  49 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   LEU D  49 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE D  50 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D  67 "    0.019 2.00e-02 2.50e+03   3.83e-02 1.47e+01
        pdb=" C   ARG D  67 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ARG D  67 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ASP D  68 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1069 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2199
        2.81 -     3.33: 9187
        3.33 -     3.85: 19761
        3.85 -     4.38: 21986
        4.38 -     4.90: 30534
  Nonbonded interactions: 83667
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 125 "
            pdb=" OE2 GLU B  53 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" NH1 ARG F  35 "
            pdb=" OP2  DC I  39 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" NH1 ARG B  78 "
            pdb=" OP2  DC I  -2 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" N   SER A  86 "
            pdb=" OP1  DT J   7 "
     model   vdw
     2.375 3.120
  ... (remaining 83662 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 'A'
  selection = (chain 'C' and resid 59 through 134)
  selection = chain 'E'
  selection = (chain 'G' and resid 59 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 94)
  selection = (chain 'D' and resid 25 through 94)
  selection = (chain 'F' and resid 25 through 94)
  selection = (chain 'H' and resid 25 through 94)
}

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:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.320
  Find NCS groups from input model:        0.120
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
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      :  0.003   0.045  10418  Z= 0.177
  Angle     :  0.633   8.819  15086  Z= 0.411
  Chirality :  0.034   0.179   1723
  Planarity :  0.007   0.061   1072
  Dihedral  : 28.743 173.373   4523
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.56 %
    Favored  : 96.24 %
  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:  0.39 (0.29), residues: 579
  helix:  0.79 (0.21), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.62 (0.38), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F  78 
 TYR   0.017   0.001   TYR B  88 
 PHE   0.016   0.001   PHE C  84 
 HIS   0.004   0.002   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (10418)
  covalent geometry    : angle       0.63321 (15086)
  hydrogen bonds       : bond        0.11428 (  670)
  hydrogen bonds       : angle       4.41167 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 SER cc_start: 0.8582 (t) cc_final: 0.8232 (m)
REVERT: E   64 LYS cc_start: 0.8483 (tptt) cc_final: 0.8135 (tptm)
REVERT: F   55 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7792 (mtt180)
REVERT: G   86 SER cc_start: 0.8605 (t) cc_final: 0.8132 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1769
  time to fit residues: 37.9593
Evaluate side-chains
  118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
E  93 GLN
E 125 GLN
G  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.166108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.121662 restraints weight = 19811.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.123284 restraints weight = 12218.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.124023 restraints weight = 8990.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.124174 restraints weight = 9510.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.125400 restraints weight = 8417.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  10418  Z= 0.238
  Angle     :  0.656   6.787  15086  Z= 0.376
  Chirality :  0.035   0.130   1723
  Planarity :  0.005   0.039   1072
  Dihedral  : 32.340 172.272   3289
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 13.66 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.33), residues: 579
  helix:  1.84 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.64 (0.39), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  40 
 TYR   0.012   0.002   TYR B  88 
 PHE   0.013   0.002   PHE A  78 
 HIS   0.008   0.002   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (10418)
  covalent geometry    : angle       0.65628 (15086)
  hydrogen bonds       : bond        0.04831 (  670)
  hydrogen bonds       : angle       3.30109 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9066 (m) cc_final: 0.8735 (t)
REVERT: A  120 MET cc_start: 0.7374 (mmm) cc_final: 0.7129 (mtt)
REVERT: C   90 MET cc_start: 0.7309 (mmm) cc_final: 0.7086 (tpt)
REVERT: G   86 SER cc_start: 0.8711 (t) cc_final: 0.8323 (p)
REVERT: G  112 ILE cc_start: 0.9142 (tp) cc_final: 0.8821 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 153
  average time/residue: 0.1195
  time to fit residues: 23.9287
Evaluate side-chains
  137 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 63 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E 125 GLN
** G  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.167472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.126165 restraints weight = 19524.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.128181 restraints weight = 13434.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.128672 restraints weight = 14035.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.128981 restraints weight = 11141.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.129145 restraints weight = 11044.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10418  Z= 0.168
  Angle     :  0.581   7.940  15086  Z= 0.342
  Chirality :  0.033   0.148   1723
  Planarity :  0.004   0.032   1072
  Dihedral  : 32.239 173.416   3289
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.62 %
    Favored  : 79.01 %
  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:  2.44 (0.34), residues: 579
  helix:  2.36 (0.24), residues: 457
  sheet:  None (None), residues: 0
  loop : -1.40 (0.42), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  40 
 TYR   0.010   0.001   TYR F  88 
 PHE   0.017   0.002   PHE C  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10418)
  covalent geometry    : angle       0.58113 (15086)
  hydrogen bonds       : bond        0.04036 (  670)
  hydrogen bonds       : angle       2.96955 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   90 MET cc_start: 0.7845 (tpp) cc_final: 0.7434 (mpp)
REVERT: F   40 ARG cc_start: 0.8306 (mtp180) cc_final: 0.8055 (ttp-170)
REVERT: G   86 SER cc_start: 0.8527 (t) cc_final: 0.8221 (p)
REVERT: G  112 ILE cc_start: 0.9132 (tp) cc_final: 0.8860 (tp)
  outliers start: 17
  outliers final: 14
  residues processed: 134
  average time/residue: 0.1265
  time to fit residues: 21.9910
Evaluate side-chains
  125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   54 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 74 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.168520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.127400 restraints weight = 19825.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.128320 restraints weight = 14565.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.129151 restraints weight = 13055.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.129526 restraints weight = 11716.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.129840 restraints weight = 10762.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10418  Z= 0.155
  Angle     :  0.576   7.776  15086  Z= 0.337
  Chirality :  0.033   0.144   1723
  Planarity :  0.004   0.030   1072
  Dihedral  : 32.160 174.038   3289
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.00 %
    Favored  : 76.63 %
  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:  2.70 (0.34), residues: 579
  helix:  2.54 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.37 (0.45), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  67 
 TYR   0.008   0.001   TYR H  72 
 PHE   0.015   0.001   PHE C  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10418)
  covalent geometry    : angle       0.57551 (15086)
  hydrogen bonds       : bond        0.03809 (  670)
  hydrogen bonds       : angle       2.80331 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   90 MET cc_start: 0.7808 (tpp) cc_final: 0.7378 (mpp)
REVERT: D   84 MET cc_start: 0.6850 (ptt) cc_final: 0.6586 (tpp)
REVERT: E   73 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6588 (pt0)
REVERT: F   44 LYS cc_start: 0.8636 (mmpt) cc_final: 0.8294 (mmtm)
REVERT: G   86 SER cc_start: 0.8456 (t) cc_final: 0.8175 (p)
REVERT: G  112 ILE cc_start: 0.9133 (tp) cc_final: 0.8858 (tp)
  outliers start: 17
  outliers final: 12
  residues processed: 128
  average time/residue: 0.1295
  time to fit residues: 21.7699
Evaluate side-chains
  121 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 66 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
C  68 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.165329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.122973 restraints weight = 19389.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.125006 restraints weight = 12920.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.125112 restraints weight = 12477.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.125439 restraints weight = 10903.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.126198 restraints weight = 9908.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10418  Z= 0.184
  Angle     :  0.598   7.829  15086  Z= 0.347
  Chirality :  0.034   0.162   1723
  Planarity :  0.004   0.032   1072
  Dihedral  : 32.276 175.413   3289
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.59 %
    Favored  : 74.06 %
  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:  2.58 (0.34), residues: 579
  helix:  2.45 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.42 (0.45), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.010   0.001   TYR B  88 
 PHE   0.025   0.002   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (10418)
  covalent geometry    : angle       0.59788 (15086)
  hydrogen bonds       : bond        0.04053 (  670)
  hydrogen bonds       : angle       2.95534 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7813 (tpp) cc_final: 0.7448 (tpp)
REVERT: B   84 MET cc_start: 0.7494 (tpp) cc_final: 0.7283 (tpp)
REVERT: G   86 SER cc_start: 0.8497 (t) cc_final: 0.8253 (p)
REVERT: G  112 ILE cc_start: 0.9147 (tp) cc_final: 0.8902 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1376
  time to fit residues: 24.0703
Evaluate side-chains
  130 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.168356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.123926 restraints weight = 20198.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.127427 restraints weight = 11549.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.129673 restraints weight = 8466.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.130882 restraints weight = 7255.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.131312 restraints weight = 6751.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10418  Z= 0.153
  Angle     :  0.581   7.398  15086  Z= 0.339
  Chirality :  0.033   0.144   1723
  Planarity :  0.004   0.031   1072
  Dihedral  : 32.121 176.383   3289
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 21.98 %
    Favored  : 73.66 %
  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:  2.72 (0.34), residues: 579
  helix:  2.55 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.35 (0.45), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  40 
 TYR   0.008   0.001   TYR H  72 
 PHE   0.010   0.001   PHE C  67 
 HIS   0.002   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10418)
  covalent geometry    : angle       0.58070 (15086)
  hydrogen bonds       : bond        0.03717 (  670)
  hydrogen bonds       : angle       2.79492 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   90 MET cc_start: 0.7758 (tpp) cc_final: 0.7468 (tpp)
REVERT: C   82 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7394 (mt)
REVERT: C   90 MET cc_start: 0.7213 (mmm) cc_final: 0.6744 (tpt)
REVERT: F   84 MET cc_start: 0.6916 (tpp) cc_final: 0.6714 (tpp)
REVERT: G   86 SER cc_start: 0.8469 (t) cc_final: 0.8244 (p)
REVERT: G  112 ILE cc_start: 0.9129 (tp) cc_final: 0.8865 (tp)
  outliers start: 22
  outliers final: 17
  residues processed: 132
  average time/residue: 0.1242
  time to fit residues: 21.4302
Evaluate side-chains
  124 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.168173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.128500 restraints weight = 19904.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.130446 restraints weight = 14106.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.131116 restraints weight = 14420.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.131550 restraints weight = 11314.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.131959 restraints weight = 10919.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10418  Z= 0.178
  Angle     :  0.606  10.033  15086  Z= 0.348
  Chirality :  0.033   0.145   1723
  Planarity :  0.004   0.030   1072
  Dihedral  : 32.236 176.855   3289
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 22.18 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.34), residues: 579
  helix:  2.55 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.42 (0.45), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  40 
 TYR   0.006   0.001   TYR B  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (10418)
  covalent geometry    : angle       0.60555 (15086)
  hydrogen bonds       : bond        0.03919 (  670)
  hydrogen bonds       : angle       2.88932 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7800 (tpp) cc_final: 0.7503 (tpp)
REVERT: C   82 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7304 (mt)
REVERT: C   90 MET cc_start: 0.7260 (mmm) cc_final: 0.7058 (mmm)
REVERT: G   86 SER cc_start: 0.8502 (t) cc_final: 0.8269 (p)
REVERT: G  112 ILE cc_start: 0.9157 (tp) cc_final: 0.8901 (tp)
  outliers start: 24
  outliers final: 17
  residues processed: 132
  average time/residue: 0.1074
  time to fit residues: 18.9044
Evaluate side-chains
  125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue   30 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 67 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.168856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.129655 restraints weight = 19988.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.131817 restraints weight = 13966.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.132389 restraints weight = 13766.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.132785 restraints weight = 11078.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.133171 restraints weight = 10774.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10418  Z= 0.163
  Angle     :  0.593   9.651  15086  Z= 0.344
  Chirality :  0.033   0.139   1723
  Planarity :  0.004   0.031   1072
  Dihedral  : 32.136 177.409   3289
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 23.96 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.74 (0.34), residues: 579
  helix:  2.58 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.37 (0.45), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  92 
 TYR   0.007   0.001   TYR H  88 
 PHE   0.008   0.001   PHE C  67 
 HIS   0.003   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10418)
  covalent geometry    : angle       0.59307 (15086)
  hydrogen bonds       : bond        0.03774 (  670)
  hydrogen bonds       : angle       2.83044 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7748 (tpp) cc_final: 0.7491 (tpp)
REVERT: C   82 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7266 (mt)
REVERT: F   27 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8264 (mp10)
REVERT: G   86 SER cc_start: 0.8459 (t) cc_final: 0.8236 (p)
REVERT: G  112 ILE cc_start: 0.9164 (tp) cc_final: 0.8899 (tp)
REVERT: H   84 MET cc_start: 0.7514 (tpp) cc_final: 0.7006 (tpp)
  outliers start: 20
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1172
  time to fit residues: 19.4109
Evaluate side-chains
  123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   49 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 9 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 12 optimal weight:    0.4980
   chunk 29 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
E 125 GLN
F  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.168183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.128899 restraints weight = 19902.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.131162 restraints weight = 13496.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.131654 restraints weight = 13505.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.132054 restraints weight = 10802.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.132411 restraints weight = 10454.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10418  Z= 0.167
  Angle     :  0.615  11.218  15086  Z= 0.350
  Chirality :  0.033   0.150   1723
  Planarity :  0.004   0.031   1072
  Dihedral  : 32.131 177.413   3289
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 24.75 %
    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 are not related in a simple way.
  whole:  2.75 (0.34), residues: 579
  helix:  2.59 (0.24), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.41 (0.46), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  40 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.006   0.001   PHE G  78 
 HIS   0.003   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10418)
  covalent geometry    : angle       0.61502 (15086)
  hydrogen bonds       : bond        0.03803 (  670)
  hydrogen bonds       : angle       2.84000 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7771 (tpp) cc_final: 0.7505 (tpp)
REVERT: B   84 MET cc_start: 0.7446 (tpp) cc_final: 0.6918 (tpp)
REVERT: C   82 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7342 (mm)
REVERT: C   90 MET cc_start: 0.7219 (mmm) cc_final: 0.6833 (tpp)
REVERT: D   84 MET cc_start: 0.6798 (tpp) cc_final: 0.6492 (tpp)
REVERT: F   27 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8217 (mp10)
REVERT: G   86 SER cc_start: 0.8459 (t) cc_final: 0.8239 (p)
REVERT: G  112 ILE cc_start: 0.9165 (tp) cc_final: 0.8895 (tp)
  outliers start: 18
  outliers final: 15
  residues processed: 125
  average time/residue: 0.1315
  time to fit residues: 21.5996
Evaluate side-chains
  124 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue   30 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0170
   chunk 55 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.170176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.131160 restraints weight = 20018.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.132539 restraints weight = 14218.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.135460 restraints weight = 12829.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.135464 restraints weight = 9773.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.135487 restraints weight = 10216.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10418  Z= 0.154
  Angle     :  0.613  11.301  15086  Z= 0.348
  Chirality :  0.033   0.147   1723
  Planarity :  0.003   0.032   1072
  Dihedral  : 31.953 176.995   3289
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 25.35 %
    Favored  : 71.09 %
  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:  2.79 (0.35), residues: 579
  helix:  2.63 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.55 (0.46), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  78 
 TYR   0.008   0.001   TYR H  72 
 PHE   0.008   0.001   PHE C  84 
 HIS   0.003   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10418)
  covalent geometry    : angle       0.61347 (15086)
  hydrogen bonds       : bond        0.03675 (  670)
  hydrogen bonds       : angle       2.74385 ( 1671)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7699 (tpp) cc_final: 0.7453 (tpp)
REVERT: B   84 MET cc_start: 0.7330 (tpp) cc_final: 0.6761 (tpp)
REVERT: C   82 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7145 (mm)
REVERT: C   90 MET cc_start: 0.7110 (mmm) cc_final: 0.6820 (tpp)
REVERT: D   84 MET cc_start: 0.6745 (tpp) cc_final: 0.6446 (tpp)
REVERT: G   86 SER cc_start: 0.8443 (t) cc_final: 0.8235 (p)
REVERT: G  112 ILE cc_start: 0.9153 (tp) cc_final: 0.8867 (tp)
REVERT: H   84 MET cc_start: 0.7321 (tpp) cc_final: 0.7109 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 119
  average time/residue: 0.1137
  time to fit residues: 18.0223
Evaluate side-chains
  118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   80 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue   30 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.4528 r_free = 0.4528 target = 0.167171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.128006 restraints weight = 20022.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.129456 restraints weight = 14730.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.130316 restraints weight = 15094.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.130726 restraints weight = 11722.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.131222 restraints weight = 11331.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10418  Z= 0.190
  Angle     :  0.641  10.438  15086  Z= 0.361
  Chirality :  0.034   0.151   1723
  Planarity :  0.004   0.038   1072
  Dihedral  : 32.153 177.393   3289
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 24.55 %
    Favored  : 71.49 %
  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:  2.63 (0.35), residues: 579
  helix:  2.54 (0.24), residues: 461
  sheet:  None (None), residues: 0
  loop : -1.68 (0.45), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  78 
 TYR   0.011   0.001   TYR D  88 
 PHE   0.007   0.001   PHE C  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (10418)
  covalent geometry    : angle       0.64070 (15086)
  hydrogen bonds       : bond        0.03980 (  670)
  hydrogen bonds       : angle       2.92050 ( 1671)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1433.93 seconds
wall clock time: 25 minutes 24.29 seconds (1524.29 seconds total)