Starting phenix.real_space_refine
on Fri Aug 22 15:00:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoy_33990/08_2025/7yoy_33990.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoy_33990/08_2025/7yoy_33990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoy_33990/08_2025/7yoy_33990.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoy_33990/08_2025/7yoy_33990.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yoy_33990/08_2025/7yoy_33990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoy_33990/08_2025/7yoy_33990.map"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2859      2.51       5
     N     745      2.21       5
     O     886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4517
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1095
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "E"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 928
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 113}
    Chain: "F"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 853
          Classifications: {'peptide': 113}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
    Chain: "I"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 810
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 104}
    Chain: "J"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 831
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
  Time building chain proxies: 1.07, per 1000 atoms: 0.24
  Number of scatterers: 4517
  At special positions: 0
  Unit cell: (79.356, 102.696, 92.582, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O     886      8.00
     N     745      7.00
     C    2859      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  99 " - pdb=" SG  CYS C 138 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 102 " - pdb=" SG  CYS C 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 214 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 132 " - pdb=" SG  CYS C 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 192 " - pdb=" SG  CYS C 208 " distance=1.94
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  23 " - pdb=" SG  CYS I  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  23 " - pdb=" SG  CYS J  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 175.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1070

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 13 sheets defined
      2.7% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'C' and resid 127 through 134
      removed outlier: 3.654A  pdb=" N   ALA C 133 " --> pdb=" O   PHE C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 155
    Processing sheet with id=AA1, first strand: chain 'C' and resid 110 through 111
      removed outlier: 3.532A  pdb=" N   TYR C 140 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 162 through 163
    Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 58
      removed outlier: 6.509A  pdb=" N   TRP E  35 " --> pdb=" O   ILE E  47 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   THR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   MET E  33 " --> pdb=" O   THR E  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58
      removed outlier: 6.509A  pdb=" N   TRP E  35 " --> pdb=" O   ILE E  47 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   THR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   MET E  33 " --> pdb=" O   THR E  49 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR E 115 " --> pdb=" O   PHE E  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 99 through 100
      removed outlier: 3.644A  pdb=" N   ASP E 103 " --> pdb=" O   SER E 100 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 7
      removed outlier: 3.511A  pdb=" N   SER F   7 " --> pdb=" O   THR F  21 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR F  21 " --> pdb=" O   SER F   7 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU F  78 " --> pdb=" O   LEU F  20 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL F  76 " --> pdb=" O   CYS F  22 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLU F  77 " --> pdb=" O   SER F  70 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 57 through 59
      removed outlier: 6.734A  pdb=" N   TRP F  36 " --> pdb=" O   ILE F  48 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   THR F  50 " --> pdb=" O   MET F  34 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   MET F  34 " --> pdb=" O   THR F  50 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLN F  39 " --> pdb=" O   THR F  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 6
      removed outlier: 3.580A  pdb=" N   GLU I  70 " --> pdb=" O   SER I  67 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER I  67 " --> pdb=" O   GLU I  70 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 53 through 54
      removed outlier: 6.557A  pdb=" N   TRP I  35 " --> pdb=" O   LEU I  47 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   TYR I  49 " --> pdb=" O   LEU I  33 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   LEU I  33 " --> pdb=" O   TYR I  49 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN I  38 " --> pdb=" O   THR I  85 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR I  85 " --> pdb=" O   GLN I  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 11
      removed outlier: 6.971A  pdb=" N   GLN J  37 " --> pdb=" O   LEU J  46 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   LEU J  46 " --> pdb=" O   GLN J  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 11
      removed outlier: 3.524A  pdb=" N   ALA J 101 " --> pdb=" O   THR J  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 24
      removed outlier: 3.877A  pdb=" N   VAL J  19 " --> pdb=" O   ILE J  75 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN J  70 " --> pdb=" O   SER J  67 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   SER J  67 " --> pdb=" O   GLN J  70 " (cutoff:3.500A)

    126 hydrogen bonds defined for protein.
    330 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 729
        1.31 -     1.44: 1395
        1.44 -     1.56: 2481
        1.56 -     1.69: 0
        1.69 -     1.82: 32
  Bond restraints: 4637
  Sorted by residual:
  bond pdb=" CA  THR J  51 "
       pdb=" C   THR J  51 "
    ideal  model  delta    sigma   weight residual
    1.528  1.471  0.056 8.80e-03 1.29e+04 4.12e+01
  bond pdb=" C   THR J  51 "
       pdb=" O   THR J  51 "
    ideal  model  delta    sigma   weight residual
    1.242  1.185  0.056 1.00e-02 1.00e+04 3.19e+01
  bond pdb=" CA  ALA J  55 "
       pdb=" C   ALA J  55 "
    ideal  model  delta    sigma   weight residual
    1.528  1.455  0.073 1.37e-02 5.33e+03 2.84e+01
  bond pdb=" C   PHE J  62 "
       pdb=" N   ARG J  63 "
    ideal  model  delta    sigma   weight residual
    1.331  1.267  0.063 1.24e-02 6.50e+03 2.62e+01
  bond pdb=" CA  SER J  65 "
       pdb=" C   SER J  65 "
    ideal  model  delta    sigma   weight residual
    1.524  1.466  0.058 1.23e-02 6.61e+03 2.20e+01
  ... (remaining 4632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.39: 6271
        4.39 -     8.77: 47
        8.77 -    13.16: 7
       13.16 -    17.55: 0
       17.55 -    21.93: 1
  Bond angle restraints: 6326
  Sorted by residual:
  angle pdb=" N   SER J  76 "
        pdb=" CA  SER J  76 "
        pdb=" C   SER J  76 "
      ideal   model   delta    sigma   weight residual
     111.14  123.67  -12.53 1.08e+00 8.57e-01 1.35e+02
  angle pdb=" N   SER J  52 "
        pdb=" CA  SER J  52 "
        pdb=" C   SER J  52 "
      ideal   model   delta    sigma   weight residual
     108.41  120.68  -12.27 1.61e+00 3.86e-01 5.80e+01
  angle pdb=" N   ASN J  53 "
        pdb=" CA  ASN J  53 "
        pdb=" C   ASN J  53 "
      ideal   model   delta    sigma   weight residual
     108.76   99.11    9.65 1.58e+00 4.01e-01 3.73e+01
  angle pdb=" N   LEU J  47 "
        pdb=" CA  LEU J  47 "
        pdb=" C   LEU J  47 "
      ideal   model   delta    sigma   weight residual
     111.36  117.60   -6.24 1.09e+00 8.42e-01 3.28e+01
  angle pdb=" N   PHE J  62 "
        pdb=" CA  PHE J  62 "
        pdb=" C   PHE J  62 "
      ideal   model   delta    sigma   weight residual
     109.25  101.38    7.87 1.53e+00 4.27e-01 2.64e+01
  ... (remaining 6321 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 2432
       17.44 -    34.87: 213
       34.87 -    52.30: 41
       52.30 -    69.74: 4
       69.74 -    87.17: 3
  Dihedral angle restraints: 2693
    sinusoidal: 1001
      harmonic: 1692
  Sorted by residual:
  dihedral pdb=" CB  CYS C 102 "
           pdb=" SG  CYS C 102 "
           pdb=" SG  CYS C 115 "
           pdb=" CB  CYS C 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    5.83   87.17     1      1.00e+01 1.00e-02 9.13e+01
  dihedral pdb=" CA  ASP I 109 "
           pdb=" C   ASP I 109 "
           pdb=" N   ILE I 110 "
           pdb=" CA  ILE I 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.56   42.44     0      5.00e+00 4.00e-02 7.21e+01
  dihedral pdb=" CA  GLY C 189 "
           pdb=" C   GLY C 189 "
           pdb=" N   SER C 190 "
           pdb=" CA  SER C 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -140.53  -39.47     0      5.00e+00 4.00e-02 6.23e+01
  ... (remaining 2690 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 613
       0.091 -    0.183: 79
       0.183 -    0.274: 7
       0.274 -    0.365: 3
       0.365 -    0.456: 1
  Chirality restraints: 703
  Sorted by residual:
  chirality pdb=" CA  SER J  76 "
            pdb=" N   SER J  76 "
            pdb=" C   SER J  76 "
            pdb=" CB  SER J  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.20e+00
  chirality pdb=" CA  LEU J  47 "
            pdb=" N   LEU J  47 "
            pdb=" C   LEU J  47 "
            pdb=" CB  LEU J  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  SER J  52 "
            pdb=" N   SER J  52 "
            pdb=" C   SER J  52 "
            pdb=" CB  SER J  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  ... (remaining 700 not shown)

  Planarity restraints: 802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO I  43 "    0.044 5.00e-02 4.00e+02   6.65e-02 7.08e+00
        pdb=" N   PRO I  44 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO I  44 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO I  44 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  90 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO C  91 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN I  39 "   -0.039 5.00e-02 4.00e+02   5.99e-02 5.73e+00
        pdb=" N   PRO I  40 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO I  40 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO I  40 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 799 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1547
        2.82 -     3.34: 3764
        3.34 -     3.86: 7332
        3.86 -     4.38: 7626
        4.38 -     4.90: 13758
  Nonbonded interactions: 34027
  Sorted by model distance:
  nonbonded pdb=" O   ARG E   9 "
            pdb=" OG1 THR E 118 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER C 221 "
            pdb=" OH  TYR I  30 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   ARG I  61 "
            pdb=" OG  SER I  76 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   SER I  63 "
            pdb=" OG1 THR I  74 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OG1 THR C 100 "
            pdb=" O   ARG C 220 "
     model   vdw
     2.334 3.040
  ... (remaining 34022 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
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:             8.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.610
  Find NCS groups from input model:        0.030
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
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      :  0.008   0.093   4646  Z= 0.473
  Angle     :  1.154  24.361   6344  Z= 0.642
  Chirality :  0.065   0.456    703
  Planarity :  0.008   0.067    802
  Dihedral  : 13.197  76.582   1596
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 14.29 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -3.78 (0.31), residues: 583
  helix: -4.27 (0.74), residues: 16
  sheet: -1.95 (0.34), residues: 208
  loop : -2.90 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  94 
 TYR   0.015   0.002   TYR J  49 
 PHE   0.037   0.003   PHE E 108 
 TRP   0.016   0.002   TRP F  62 
 HIS   0.003   0.001   HIS I 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00807 ( 4637)
  covalent geometry    : angle       1.11360 ( 6326)
  SS BOND              : bond        0.03167 (    9)
  SS BOND              : angle       5.80932 (   18)
  hydrogen bonds       : bond        0.28899 (  112)
  hydrogen bonds       : angle      10.79796 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 ASN cc_start: 0.8646 (m-40) cc_final: 0.8408 (m110)
REVERT: E   85 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: E   86 ASP cc_start: 0.7505 (m-30) cc_final: 0.6515 (m-30)
REVERT: E  106 ASP cc_start: 0.8449 (t70) cc_final: 0.8195 (t70)
REVERT: I   22 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8927 (mmtt)
REVERT: I   24 GLN cc_start: 0.8424 (mt0) cc_final: 0.7980 (tm-30)
REVERT: I   32 ASP cc_start: 0.8323 (t0) cc_final: 0.7980 (t0)
REVERT: I   49 TYR cc_start: 0.8586 (p90) cc_final: 0.8290 (p90)
REVERT: I   53 ASN cc_start: 0.8061 (t0) cc_final: 0.7585 (t0)
REVERT: J   33 LEU cc_start: 0.8642 (mp) cc_final: 0.8209 (mp)
REVERT: J   78 LEU cc_start: 0.9304 (mp) cc_final: 0.8828 (mp)
REVERT: J   99 TYR cc_start: 0.9266 (p90) cc_final: 0.8748 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0733
  time to fit residues: 12.7584
Evaluate side-chains
  112 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
I   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.093223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.080011 restraints weight = 14458.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.082447 restraints weight = 7549.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.084196 restraints weight = 4938.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.085373 restraints weight = 3640.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.086236 restraints weight = 2907.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4646  Z= 0.141
  Angle     :  0.710  15.763   6344  Z= 0.349
  Chirality :  0.042   0.141    703
  Planarity :  0.006   0.050    802
  Dihedral  :  6.581  62.974    647
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.94 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -3.13 (0.32), residues: 583
  helix: -2.36 (1.32), residues: 15
  sheet: -1.50 (0.34), residues: 213
  loop : -2.55 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 220 
 TYR   0.015   0.001   TYR E 104 
 PHE   0.017   0.001   PHE E 108 
 TRP   0.009   0.001   TRP C 174 
 HIS   0.002   0.001   HIS I 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4637)
  covalent geometry    : angle       0.70789 ( 6326)
  SS BOND              : bond        0.00496 (    9)
  SS BOND              : angle       1.24280 (   18)
  hydrogen bonds       : bond        0.04449 (  112)
  hydrogen bonds       : angle       6.78726 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  106 GLU cc_start: 0.8976 (pt0) cc_final: 0.8753 (pm20)
REVERT: C  157 ASN cc_start: 0.8298 (m-40) cc_final: 0.8047 (m110)
REVERT: E    4 GLU cc_start: 0.9120 (tt0) cc_final: 0.8801 (tt0)
REVERT: E   86 ASP cc_start: 0.7602 (m-30) cc_final: 0.7093 (m-30)
REVERT: E  104 TYR cc_start: 0.8877 (m-80) cc_final: 0.8630 (m-10)
REVERT: I   22 LYS cc_start: 0.9351 (mtmm) cc_final: 0.9049 (mmtm)
REVERT: I   49 TYR cc_start: 0.8685 (p90) cc_final: 0.8366 (p90)
REVERT: I   53 ASN cc_start: 0.8087 (t0) cc_final: 0.7622 (t0)
REVERT: I   72 ILE cc_start: 0.9267 (pt) cc_final: 0.8894 (mm)
REVERT: J   33 LEU cc_start: 0.8467 (mp) cc_final: 0.8257 (mp)
REVERT: J   99 TYR cc_start: 0.9122 (p90) cc_final: 0.8560 (p90)
  outliers start: 17
  outliers final: 10
  residues processed: 141
  average time/residue: 0.0522
  time to fit residues: 9.4297
Evaluate side-chains
  123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  192 CYS
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0170
   chunk 32 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.8026

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.088854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.076437 restraints weight = 14041.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.079389 restraints weight = 7202.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.081307 restraints weight = 4100.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.082156 restraints weight = 2718.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.082482 restraints weight = 2343.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   4646  Z= 0.258
  Angle     :  0.783  18.590   6344  Z= 0.378
  Chirality :  0.043   0.158    703
  Planarity :  0.006   0.050    802
  Dihedral  :  6.682  60.775    647
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 19.18 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -2.83 (0.33), residues: 583
  helix: -1.51 (1.49), residues: 15
  sheet: -1.41 (0.34), residues: 223
  loop : -2.29 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  79 
 TYR   0.010   0.001   TYR J  36 
 PHE   0.020   0.002   PHE E 108 
 TRP   0.011   0.001   TRP F  62 
 HIS   0.003   0.001   HIS I 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 4637)
  covalent geometry    : angle       0.78239 ( 6326)
  SS BOND              : bond        0.00879 (    9)
  SS BOND              : angle       1.07032 (   18)
  hydrogen bonds       : bond        0.04066 (  112)
  hydrogen bonds       : angle       6.38919 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: E   86 ASP cc_start: 0.7258 (m-30) cc_final: 0.6509 (m-30)
REVERT: E  104 TYR cc_start: 0.8973 (m-80) cc_final: 0.8742 (m-80)
REVERT: F   20 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8891 (mm)
REVERT: I   24 GLN cc_start: 0.8278 (mt0) cc_final: 0.7945 (tm-30)
REVERT: I   49 TYR cc_start: 0.8871 (p90) cc_final: 0.8623 (p90)
REVERT: I   53 ASN cc_start: 0.8064 (t0) cc_final: 0.7589 (t0)
  outliers start: 30
  outliers final: 20
  residues processed: 130
  average time/residue: 0.0604
  time to fit residues: 9.9960
Evaluate side-chains
  125 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   20 LEU
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain F residue   85 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   48 ILE
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue    3 VAL
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   56 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.090447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.077334 restraints weight = 14178.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.079725 restraints weight = 7308.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.081384 restraints weight = 4773.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.082481 restraints weight = 3544.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.083315 restraints weight = 2874.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4646  Z= 0.161
  Angle     :  0.719  17.729   6344  Z= 0.345
  Chirality :  0.043   0.171    703
  Planarity :  0.005   0.046    802
  Dihedral  :  6.437  61.681    647
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 21.02 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -2.50 (0.34), residues: 583
  helix: -1.19 (1.58), residues: 15
  sheet: -1.00 (0.35), residues: 215
  loop : -2.19 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  79 
 TYR   0.010   0.001   TYR I  30 
 PHE   0.018   0.001   PHE E 108 
 TRP   0.009   0.001   TRP F  62 
 HIS   0.002   0.001   HIS I 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4637)
  covalent geometry    : angle       0.71820 ( 6326)
  SS BOND              : bond        0.00504 (    9)
  SS BOND              : angle       1.05430 (   18)
  hydrogen bonds       : bond        0.03506 (  112)
  hydrogen bonds       : angle       5.96431 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  104 TYR cc_start: 0.8936 (m-80) cc_final: 0.8671 (m-80)
REVERT: E  106 ASP cc_start: 0.8118 (t70) cc_final: 0.7857 (t0)
REVERT: F   20 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9003 (mm)
REVERT: I   24 GLN cc_start: 0.8208 (mt0) cc_final: 0.7892 (tm-30)
REVERT: I   49 TYR cc_start: 0.8821 (p90) cc_final: 0.8565 (p90)
REVERT: I   53 ASN cc_start: 0.8011 (t0) cc_final: 0.7522 (t0)
REVERT: I   54 LEU cc_start: 0.8499 (mm) cc_final: 0.8276 (mm)
REVERT: I   72 ILE cc_start: 0.9242 (pt) cc_final: 0.8977 (tp)
  outliers start: 28
  outliers final: 21
  residues processed: 130
  average time/residue: 0.0530
  time to fit residues: 8.7467
Evaluate side-chains
  129 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   20 LEU
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue    3 VAL
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   26 SER
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   52 SER
Chi-restraints excluded: chain J residue   56 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.090842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.078021 restraints weight = 13927.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080459 restraints weight = 6890.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082134 restraints weight = 4417.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.083304 restraints weight = 3231.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.084095 restraints weight = 2562.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4646  Z= 0.135
  Angle     :  0.705  17.215   6344  Z= 0.336
  Chirality :  0.042   0.142    703
  Planarity :  0.005   0.041    802
  Dihedral  :  6.201  62.679    647
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 22.65 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -2.32 (0.34), residues: 583
  helix: -1.27 (1.54), residues: 15
  sheet: -0.80 (0.36), residues: 206
  loop : -2.09 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  94 
 TYR   0.010   0.001   TYR I  30 
 PHE   0.017   0.001   PHE E 108 
 TRP   0.008   0.001   TRP C 163 
 HIS   0.003   0.001   HIS C 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4637)
  covalent geometry    : angle       0.70346 ( 6326)
  SS BOND              : bond        0.00441 (    9)
  SS BOND              : angle       1.02396 (   18)
  hydrogen bonds       : bond        0.03256 (  112)
  hydrogen bonds       : angle       5.66067 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: E   33 MET cc_start: 0.8801 (mmt) cc_final: 0.8474 (mmm)
REVERT: E  104 TYR cc_start: 0.8928 (m-80) cc_final: 0.8616 (m-80)
REVERT: E  106 ASP cc_start: 0.8048 (t70) cc_final: 0.7823 (t0)
REVERT: I   22 LYS cc_start: 0.9387 (mttm) cc_final: 0.9005 (mmtt)
REVERT: I   24 GLN cc_start: 0.8168 (mt0) cc_final: 0.7821 (tm-30)
REVERT: I   49 TYR cc_start: 0.8780 (p90) cc_final: 0.8504 (p90)
REVERT: I   53 ASN cc_start: 0.8004 (t0) cc_final: 0.7500 (t0)
REVERT: I   54 LEU cc_start: 0.8475 (mm) cc_final: 0.8240 (mm)
REVERT: I   72 ILE cc_start: 0.9243 (pt) cc_final: 0.8910 (mp)
  outliers start: 23
  outliers final: 20
  residues processed: 124
  average time/residue: 0.0603
  time to fit residues: 9.6592
Evaluate side-chains
  132 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  192 CYS
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain F residue   85 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   56 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
E  38 GLN
I  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.078739 restraints weight = 13989.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.081183 restraints weight = 6934.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.082883 restraints weight = 4442.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.084067 restraints weight = 3243.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.084856 restraints weight = 2568.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4646  Z= 0.121
  Angle     :  0.674  16.327   6344  Z= 0.319
  Chirality :  0.041   0.141    703
  Planarity :  0.004   0.037    802
  Dihedral  :  5.980  63.981    647
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 23.88 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -2.12 (0.34), residues: 583
  helix: -1.29 (1.51), residues: 15
  sheet: -0.57 (0.37), residues: 197
  loop : -1.99 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  94 
 TYR   0.009   0.001   TYR I  30 
 PHE   0.015   0.001   PHE E 108 
 TRP   0.008   0.001   TRP C 163 
 HIS   0.002   0.001   HIS I 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4637)
  covalent geometry    : angle       0.67343 ( 6326)
  SS BOND              : bond        0.00456 (    9)
  SS BOND              : angle       0.93829 (   18)
  hydrogen bonds       : bond        0.03073 (  112)
  hydrogen bonds       : angle       5.36182 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: E    5 GLU cc_start: 0.7158 (pm20) cc_final: 0.6816 (pm20)
REVERT: E   33 MET cc_start: 0.8822 (mmt) cc_final: 0.8455 (mmm)
REVERT: E  104 TYR cc_start: 0.8892 (m-80) cc_final: 0.8592 (m-80)
REVERT: I   22 LYS cc_start: 0.9392 (mttm) cc_final: 0.9004 (mmtt)
REVERT: I   24 GLN cc_start: 0.8142 (mt0) cc_final: 0.7852 (tm-30)
REVERT: I   49 TYR cc_start: 0.8744 (p90) cc_final: 0.8465 (p90)
REVERT: I   53 ASN cc_start: 0.8001 (t0) cc_final: 0.7507 (t0)
REVERT: I   54 LEU cc_start: 0.8473 (mm) cc_final: 0.8249 (mm)
REVERT: I   72 ILE cc_start: 0.9212 (pt) cc_final: 0.8892 (mm)
  outliers start: 22
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0657
  time to fit residues: 10.3085
Evaluate side-chains
  128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  192 CYS
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   56 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.0570
   chunk 32 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0980
   chunk 18 optimal weight:    0.2980
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
I  38 GLN
J  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.092051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.079541 restraints weight = 13821.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.082488 restraints weight = 7048.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.084791 restraints weight = 4003.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085942 restraints weight = 2461.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.086395 restraints weight = 1927.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3402 r_free = 0.3402    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3402
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   4646  Z= 0.112
  Angle     :  0.687  14.964   6344  Z= 0.328
  Chirality :  0.041   0.143    703
  Planarity :  0.004   0.038    802
  Dihedral  :  5.803  65.511    647
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 25.51 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.95 (0.34), residues: 583
  helix: -1.25 (1.49), residues: 15
  sheet: -0.39 (0.37), residues: 195
  loop : -1.91 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  79 
 TYR   0.007   0.001   TYR E  57 
 PHE   0.014   0.001   PHE E 108 
 TRP   0.008   0.001   TRP C 163 
 HIS   0.003   0.001   HIS C 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4637)
  covalent geometry    : angle       0.68637 ( 6326)
  SS BOND              : bond        0.00351 (    9)
  SS BOND              : angle       0.96447 (   18)
  hydrogen bonds       : bond        0.02906 (  112)
  hydrogen bonds       : angle       5.11111 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  106 GLU cc_start: 0.8548 (pm20) cc_final: 0.8308 (pm20)
REVERT: C  163 TRP cc_start: 0.8686 (m100) cc_final: 0.8480 (m100)
REVERT: E    5 GLU cc_start: 0.7177 (pm20) cc_final: 0.6930 (pm20)
REVERT: E  104 TYR cc_start: 0.8816 (m-80) cc_final: 0.8526 (m-80)
REVERT: I   22 LYS cc_start: 0.9374 (mttm) cc_final: 0.9081 (mmtt)
REVERT: I   24 GLN cc_start: 0.8125 (mt0) cc_final: 0.7785 (tm-30)
REVERT: I   49 TYR cc_start: 0.8682 (p90) cc_final: 0.8399 (p90)
REVERT: I   53 ASN cc_start: 0.8023 (t0) cc_final: 0.7525 (t0)
REVERT: I   72 ILE cc_start: 0.9207 (pt) cc_final: 0.8976 (mp)
REVERT: I   79 GLU cc_start: 0.8875 (tp30) cc_final: 0.8298 (tm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 118
  average time/residue: 0.0630
  time to fit residues: 9.5474
Evaluate side-chains
  127 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   31 ASN
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
I  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.089194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.076100 restraints weight = 14135.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.078460 restraints weight = 7186.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.080101 restraints weight = 4670.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.081245 restraints weight = 3457.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.082055 restraints weight = 2773.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4646  Z= 0.231
  Angle     :  0.755  16.471   6344  Z= 0.362
  Chirality :  0.042   0.150    703
  Planarity :  0.005   0.034    802
  Dihedral  :  6.189  61.321    647
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 25.51 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -2.09 (0.34), residues: 583
  helix: -1.06 (1.45), residues: 15
  sheet: -0.75 (0.35), residues: 218
  loop : -1.89 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  79 
 TYR   0.010   0.001   TYR J  86 
 PHE   0.020   0.002   PHE E 108 
 TRP   0.011   0.002   TRP C 163 
 HIS   0.003   0.001   HIS I 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 4637)
  covalent geometry    : angle       0.75337 ( 6326)
  SS BOND              : bond        0.00604 (    9)
  SS BOND              : angle       1.19194 (   18)
  hydrogen bonds       : bond        0.03348 (  112)
  hydrogen bonds       : angle       5.35769 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  104 TYR cc_start: 0.8944 (m-80) cc_final: 0.8644 (m-80)
REVERT: I   22 LYS cc_start: 0.9366 (mttm) cc_final: 0.9105 (mmtt)
REVERT: I   24 GLN cc_start: 0.8124 (mt0) cc_final: 0.7859 (tm-30)
REVERT: I   49 TYR cc_start: 0.8869 (p90) cc_final: 0.8612 (p90)
REVERT: I   53 ASN cc_start: 0.8123 (t0) cc_final: 0.7618 (t0)
REVERT: I   72 ILE cc_start: 0.9209 (pt) cc_final: 0.8972 (mp)
  outliers start: 18
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0619
  time to fit residues: 9.1763
Evaluate side-chains
  125 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 8 optimal weight:    0.4980
   chunk 45 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
I  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.078768 restraints weight = 13891.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.081196 restraints weight = 7048.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.082888 restraints weight = 4576.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.084049 restraints weight = 3369.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.084863 restraints weight = 2691.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4646  Z= 0.135
  Angle     :  0.731  15.579   6344  Z= 0.349
  Chirality :  0.042   0.160    703
  Planarity :  0.004   0.040    802
  Dihedral  :  5.998  62.444    647
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 26.12 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -1.89 (0.34), residues: 583
  helix: -1.10 (1.44), residues: 15
  sheet: -0.42 (0.37), residues: 202
  loop : -1.84 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  79 
 TYR   0.008   0.001   TYR I  87 
 PHE   0.017   0.001   PHE E 108 
 TRP   0.007   0.001   TRP E  46 
 HIS   0.003   0.001   HIS C 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4637)
  covalent geometry    : angle       0.72916 ( 6326)
  SS BOND              : bond        0.00423 (    9)
  SS BOND              : angle       1.28950 (   18)
  hydrogen bonds       : bond        0.03022 (  112)
  hydrogen bonds       : angle       5.20480 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: C  106 GLU cc_start: 0.8577 (pm20) cc_final: 0.8371 (pm20)
REVERT: E    5 GLU cc_start: 0.7100 (pm20) cc_final: 0.6856 (pm20)
REVERT: E   33 MET cc_start: 0.8856 (mmt) cc_final: 0.8473 (mmm)
REVERT: E  104 TYR cc_start: 0.8877 (m-80) cc_final: 0.8594 (m-80)
REVERT: I   22 LYS cc_start: 0.9369 (mttm) cc_final: 0.9098 (mmtt)
REVERT: I   24 GLN cc_start: 0.8149 (mt0) cc_final: 0.7811 (tm-30)
REVERT: I   49 TYR cc_start: 0.8788 (p90) cc_final: 0.8519 (p90)
REVERT: I   53 ASN cc_start: 0.8092 (t0) cc_final: 0.7582 (t0)
REVERT: I   72 ILE cc_start: 0.9202 (pt) cc_final: 0.8955 (mp)
REVERT: I   79 GLU cc_start: 0.8885 (tp30) cc_final: 0.8379 (tm-30)
  outliers start: 17
  outliers final: 17
  residues processed: 122
  average time/residue: 0.0616
  time to fit residues: 9.6036
Evaluate side-chains
  129 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   56 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 41 optimal weight:    0.0050
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:    0.1980
   chunk 52 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
E 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.091842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.078582 restraints weight = 14208.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.081002 restraints weight = 7355.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.082710 restraints weight = 4827.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.083833 restraints weight = 3584.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.084684 restraints weight = 2892.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4646  Z= 0.141
  Angle     :  0.710  15.282   6344  Z= 0.341
  Chirality :  0.042   0.149    703
  Planarity :  0.005   0.038    802
  Dihedral  :  5.956  63.024    647
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 25.10 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -1.88 (0.34), residues: 583
  helix: -1.38 (1.37), residues: 16
  sheet: -0.52 (0.36), residues: 207
  loop : -1.75 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  79 
 TYR   0.007   0.001   TYR J  36 
 PHE   0.016   0.001   PHE E 108 
 TRP   0.008   0.001   TRP E  61 
 HIS   0.002   0.001   HIS C 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4637)
  covalent geometry    : angle       0.70774 ( 6326)
  SS BOND              : bond        0.00419 (    9)
  SS BOND              : angle       1.23537 (   18)
  hydrogen bonds       : bond        0.02926 (  112)
  hydrogen bonds       : angle       5.11954 (  330)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: E   33 MET cc_start: 0.8855 (mmt) cc_final: 0.8479 (mmm)
REVERT: E  104 TYR cc_start: 0.8840 (m-80) cc_final: 0.8587 (m-80)
REVERT: I   22 LYS cc_start: 0.9345 (mttm) cc_final: 0.9081 (mmtt)
REVERT: I   24 GLN cc_start: 0.8134 (mt0) cc_final: 0.7891 (tm-30)
REVERT: I   49 TYR cc_start: 0.8781 (p90) cc_final: 0.8506 (p90)
REVERT: I   53 ASN cc_start: 0.8088 (t0) cc_final: 0.7567 (t0)
REVERT: I   72 ILE cc_start: 0.9185 (pt) cc_final: 0.8943 (mp)
REVERT: I   79 GLU cc_start: 0.8910 (tp30) cc_final: 0.8513 (tm-30)
  outliers start: 21
  outliers final: 20
  residues processed: 121
  average time/residue: 0.0606
  time to fit residues: 9.4487
Evaluate side-chains
  129 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain E residue    1 GLN
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue  101 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   83 LEU
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   74 THR
Chi-restraints excluded: chain I residue  106 THR
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   22 LYS
Chi-restraints excluded: chain J residue   26 SER
Chi-restraints excluded: chain J residue   48 ILE
Chi-restraints excluded: chain J residue   56 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0670
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0000
   chunk 57 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.4522

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

Flipped N/Q/H residues before XYZ refinement:
E 101 ASN
J  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.092722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.079421 restraints weight = 14357.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.081901 restraints weight = 7434.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.083577 restraints weight = 4835.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.084794 restraints weight = 3598.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.085625 restraints weight = 2868.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4646  Z= 0.120
  Angle     :  0.715  14.770   6344  Z= 0.345
  Chirality :  0.042   0.140    703
  Planarity :  0.005   0.039    802
  Dihedral  :  5.863  63.997    647
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 25.92 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -1.77 (0.34), residues: 583
  helix: -1.43 (1.39), residues: 16
  sheet: -0.26 (0.38), residues: 194
  loop : -1.76 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  79 
 TYR   0.009   0.001   TYR I  87 
 PHE   0.016   0.001   PHE E 108 
 TRP   0.008   0.001   TRP E  46 
 HIS   0.002   0.001   HIS C 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4637)
  covalent geometry    : angle       0.71432 ( 6326)
  SS BOND              : bond        0.00375 (    9)
  SS BOND              : angle       1.04983 (   18)
  hydrogen bonds       : bond        0.02834 (  112)
  hydrogen bonds       : angle       5.06224 (  330)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 965.68 seconds
wall clock time: 17 minutes 18.72 seconds (1038.72 seconds total)