Starting phenix.real_space_refine
on Tue Mar  3 13:10:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p2p_13171/03_2026/7p2p_13171_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p2p_13171/03_2026/7p2p_13171.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2026/7p2p_13171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2026/7p2p_13171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2026/7p2p_13171_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2026/7p2p_13171_neut.cif"
  }
  resolution = 4.9
  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=   0.002
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      23      5.16       5
     C    3109      2.51       5
     N     785      2.21       5
     O     866      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4783
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1189
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 6, 'TRANS': 141}
    Chain: "B"
      Number of atoms: 1426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1426
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 7, 'TRANS': 171}
    Chain: "C"
      Number of atoms: 1411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1411
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 6, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 696
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 6, 'TRANS': 79}
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.23, per 1000 atoms: 0.26
  Number of scatterers: 4783
  At special positions: 0
  Unit cell: (79.38, 84.24, 131.22, 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      23     16.00
     O     866      8.00
     N     785      7.00
     C    3109      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 141 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 318.9 milliseconds
  

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 8 sheets defined
      38.0% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 43
    Processing helix  chain 'A' and resid 148 through 158
      removed outlier: 4.210A  pdb=" N   VAL A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 30
    Processing helix  chain 'C' and resid 53 through 72
    Processing helix  chain 'C' and resid 79 through 104
    Processing helix  chain 'C' and resid 110 through 136
      removed outlier: 3.894A  pdb=" N   LEU C 114 " --> pdb=" O   SER C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 207
      removed outlier: 3.559A  pdb=" N   ALA C 207 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 204 through 207'
    Processing helix  chain 'C' and resid 208 through 224
      removed outlier: 4.018A  pdb=" N   ILE C 212 " --> pdb=" O   TYR C 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 110
    Processing helix  chain 'D' and resid 111 through 131
      removed outlier: 4.352A  pdb=" N   THR D 115 " --> pdb=" O   GLN D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 140
    Processing helix  chain 'D' and resid 141 through 144
      removed outlier: 4.021A  pdb=" N   TRP D 144 " --> pdb=" O   PRO D 141 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 141 through 144'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 87
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101
      removed outlier: 4.151A  pdb=" N   ILE A 101 " --> pdb=" O   GLN B 102 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN B 102 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111
      removed outlier: 3.535A  pdb=" N   PHE A 111 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.078A  pdb=" N   LEU B  48 " --> pdb=" O   THR B  67 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   THR B  67 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASN B  50 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   PHE B  65 " --> pdb=" O   ASN B  50 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLY B  64 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   PHE B 129 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71
    Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 90
      removed outlier: 4.321A  pdb=" N   GLN B  84 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL B 151 " --> pdb=" O   GLN B  84 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR B  88 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 147 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   LEU B 146 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   GLY B 164 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   TRP B 148 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLY B 162 " --> pdb=" O   TRP B 148 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   VAL B 150 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   VAL B 160 " --> pdb=" O   VAL B 150 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77
      removed outlier: 4.313A  pdb=" N   VAL C 142 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   LEU C 159 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   VAL C 142 " --> pdb=" O   TRP C 157 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   TRP C 157 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)

    218 hydrogen bonds defined for protein.
    621 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: 0.51

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 816
        1.33 -     1.45: 1298
        1.45 -     1.57: 2744
        1.57 -     1.69: 1
        1.69 -     1.81: 41
  Bond restraints: 4900
  Sorted by residual:
  bond pdb=" N   LEU D 131 "
       pdb=" CA  LEU D 131 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.04e-02 9.25e+03 9.86e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.37e+00
  bond pdb=" N   LEU A  69 "
       pdb=" CA  LEU A  69 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.34e+00
  bond pdb=" N   ILE D 136 "
       pdb=" CA  ILE D 136 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.21e+00
  bond pdb=" C   PRO D 135 "
       pdb=" O   PRO D 135 "
    ideal  model  delta    sigma   weight residual
    1.237  1.205  0.032 1.26e-02 6.30e+03 6.63e+00
  ... (remaining 4895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 6279
        2.07 -     4.14: 270
        4.14 -     6.21: 48
        6.21 -     8.28: 24
        8.28 -    10.35: 13
  Bond angle restraints: 6634
  Sorted by residual:
  angle pdb=" N   PRO D 141 "
        pdb=" CA  PRO D 141 "
        pdb=" C   PRO D 141 "
      ideal   model   delta    sigma   weight residual
     113.57  106.87    6.70 1.31e+00 5.83e-01 2.62e+01
  angle pdb=" C   LYS B 121 "
        pdb=" N   ASP B 122 "
        pdb=" CA  ASP B 122 "
      ideal   model   delta    sigma   weight residual
     121.54  131.13   -9.59 1.91e+00 2.74e-01 2.52e+01
  angle pdb=" C   LYS B  49 "
        pdb=" N   ASN B  50 "
        pdb=" CA  ASN B  50 "
      ideal   model   delta    sigma   weight residual
     121.54  130.80   -9.26 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   GLY B 133 "
        pdb=" N   ASN B 134 "
        pdb=" CA  ASN B 134 "
      ideal   model   delta    sigma   weight residual
     121.54  130.78   -9.24 1.91e+00 2.74e-01 2.34e+01
  angle pdb=" C   CYS B  26 "
        pdb=" N   PHE B  27 "
        pdb=" CA  PHE B  27 "
      ideal   model   delta    sigma   weight residual
     121.66  113.71    7.95 1.76e+00 3.23e-01 2.04e+01
  ... (remaining 6629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.45: 2808
       21.45 -    42.90: 140
       42.90 -    64.35: 8
       64.35 -    85.80: 8
       85.80 -   107.25: 4
  Dihedral angle restraints: 2968
    sinusoidal: 1262
      harmonic: 1706
  Sorted by residual:
  dihedral pdb=" CA  LYS C 111 "
           pdb=" C   LYS C 111 "
           pdb=" N   PRO C 112 "
           pdb=" CA  PRO C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  LEU D  75 "
           pdb=" C   LEU D  75 "
           pdb=" N   PRO D  76 "
           pdb=" CA  PRO D  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.61   21.39     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  PRO D 133 "
           pdb=" C   PRO D 133 "
           pdb=" N   TRP D 134 "
           pdb=" CA  TRP D 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.57  -20.43     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 2965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 707
       0.122 -    0.244: 47
       0.244 -    0.366: 2
       0.366 -    0.488: 0
       0.488 -    0.610: 1
  Chirality restraints: 757
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 141 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.79   -0.61 2.00e-01 2.50e+01 9.31e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  PHE A  68 "
            pdb=" N   PHE A  68 "
            pdb=" C   PHE A  68 "
            pdb=" CB  PHE A  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 754 not shown)

  Planarity restraints: 821
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  22 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.51e+00
        pdb=" C   VAL A  22 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   VAL A  22 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A  23 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 216 "    0.013 2.00e-02 2.50e+03   1.71e-02 4.37e+00
        pdb=" CG  HIS C 216 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 216 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 216 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 216 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 216 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  24 "    0.012 2.00e-02 2.50e+03   1.55e-02 4.20e+00
        pdb=" CG  PHE B  24 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  24 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  24 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  24 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  24 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  24 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 818 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1464
        2.84 -     3.35: 4304
        3.35 -     3.87: 7635
        3.87 -     4.38: 7919
        4.38 -     4.90: 13585
  Nonbonded interactions: 34907
  Sorted by model distance:
  nonbonded pdb=" O   THR A  43 "
            pdb=" ND2 ASN A  71 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" O   ILE A  87 "
            pdb=" N   GLU A  91 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   SER D 126 "
            pdb=" OG1 THR D 130 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   TRP C  51 "
            pdb=" OG1 THR D  77 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OG  SER B  90 "
            pdb=" O   THR B 145 "
     model   vdw
     2.353 3.040
  ... (remaining 34902 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.120
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
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      :  0.005   0.054   4905  Z= 0.292
  Angle     :  1.132  14.597   6649  Z= 0.570
  Chirality :  0.067   0.610    757
  Planarity :  0.007   0.046    820
  Dihedral  : 13.150 107.252   1868
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  8.06 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.94 (0.28), residues: 579
  helix: -1.72 (0.27), residues: 208
  sheet: -1.10 (0.63), residues: 57
  loop : -3.72 (0.28), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 185 
 TYR   0.018   0.002   TYR B 174 
 PHE   0.036   0.004   PHE B  24 
 TRP   0.013   0.001   TRP B  80 
 HIS   0.021   0.002   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 4900)
  covalent geometry    : angle       1.10399 ( 6634)
  hydrogen bonds       : bond        0.06956 (  218)
  hydrogen bonds       : angle       6.51319 (  621)
  link_ALPHA1-3        : bond        0.00513 (    1)
  link_ALPHA1-3        : angle       1.36385 (    3)
  link_ALPHA1-6        : bond        0.00272 (    1)
  link_ALPHA1-6        : angle       1.28915 (    3)
  link_BETA1-4         : bond        0.02037 (    2)
  link_BETA1-4         : angle       4.96832 (    6)
  link_NAG-ASN         : bond        0.01791 (    1)
  link_NAG-ASN         : angle       9.58246 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 TYR cc_start: 0.8498 (m-80) cc_final: 0.8257 (m-80)
REVERT: A   24 ASN cc_start: 0.8489 (p0) cc_final: 0.8286 (p0)
REVERT: A   29 VAL cc_start: 0.9273 (m) cc_final: 0.8913 (p)
REVERT: A   40 MET cc_start: 0.7844 (mmm) cc_final: 0.7537 (mmm)
REVERT: A   41 VAL cc_start: 0.8947 (t) cc_final: 0.8732 (p)
REVERT: A   67 LEU cc_start: 0.8969 (mm) cc_final: 0.8700 (mm)
REVERT: A  126 TYR cc_start: 0.6041 (m-80) cc_final: 0.4929 (m-80)
REVERT: A  135 LYS cc_start: 0.8748 (pttt) cc_final: 0.8206 (tptt)
REVERT: A  137 ASP cc_start: 0.7849 (m-30) cc_final: 0.7593 (p0)
REVERT: A  143 ARG cc_start: 0.7333 (mmm160) cc_final: 0.6114 (ptt180)
REVERT: A  156 MET cc_start: 0.8235 (tpt) cc_final: 0.7819 (tpt)
REVERT: B   70 ILE cc_start: 0.8739 (pp) cc_final: 0.8454 (mm)
REVERT: B  174 TYR cc_start: 0.7391 (t80) cc_final: 0.6566 (t80)
REVERT: C   69 LEU cc_start: 0.8353 (tm) cc_final: 0.7844 (pp)
REVERT: C  129 THR cc_start: 0.8495 (m) cc_final: 0.8292 (p)
REVERT: D   90 MET cc_start: 0.4131 (mmt) cc_final: 0.3529 (tpt)
REVERT: D  116 VAL cc_start: 0.7631 (t) cc_final: 0.7387 (t)
REVERT: D  149 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8261 (mm-30)
REVERT: D  150 SER cc_start: 0.8327 (m) cc_final: 0.7949 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 197
  average time/residue: 0.1077
  time to fit residues: 25.1016
Evaluate side-chains
  110 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
A 118 ASN
A 128 GLN
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.106157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.096180 restraints weight = 35291.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.097680 restraints weight = 24107.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.098771 restraints weight = 17651.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.099494 restraints weight = 13690.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.100099 restraints weight = 11187.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4905  Z= 0.153
  Angle     :  0.783  12.506   6649  Z= 0.389
  Chirality :  0.051   0.419    757
  Planarity :  0.006   0.051    820
  Dihedral  :  9.833  69.946    732
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.32), residues: 579
  helix:  0.02 (0.34), residues: 211
  sheet: -0.72 (0.68), residues: 58
  loop : -3.48 (0.29), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 112 
 TYR   0.024   0.002   TYR D 117 
 PHE   0.026   0.002   PHE C  94 
 TRP   0.012   0.001   TRP C  51 
 HIS   0.015   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4900)
  covalent geometry    : angle       0.75409 ( 6634)
  hydrogen bonds       : bond        0.04012 (  218)
  hydrogen bonds       : angle       5.37267 (  621)
  link_ALPHA1-3        : bond        0.01153 (    1)
  link_ALPHA1-3        : angle       2.73218 (    3)
  link_ALPHA1-6        : bond        0.00338 (    1)
  link_ALPHA1-6        : angle       1.62479 (    3)
  link_BETA1-4         : bond        0.00896 (    2)
  link_BETA1-4         : angle       3.53305 (    6)
  link_NAG-ASN         : bond        0.01586 (    1)
  link_NAG-ASN         : angle       8.12724 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8500 (t80) cc_final: 0.8284 (t80)
REVERT: A  135 LYS cc_start: 0.8956 (pttt) cc_final: 0.8150 (tptp)
REVERT: A  137 ASP cc_start: 0.7894 (m-30) cc_final: 0.7271 (p0)
REVERT: A  143 ARG cc_start: 0.7447 (mmm160) cc_final: 0.6130 (ptt180)
REVERT: A  156 MET cc_start: 0.8005 (tpt) cc_final: 0.7700 (tpt)
REVERT: B   69 ASP cc_start: 0.7612 (m-30) cc_final: 0.7286 (m-30)
REVERT: B   70 ILE cc_start: 0.8815 (pt) cc_final: 0.8041 (mp)
REVERT: C  165 ARG cc_start: 0.8397 (tpm170) cc_final: 0.8182 (tpm170)
REVERT: D   86 LEU cc_start: 0.7924 (mm) cc_final: 0.7677 (tp)
REVERT: D   90 MET cc_start: 0.4560 (mmt) cc_final: 0.3909 (tpt)
REVERT: D  103 PHE cc_start: 0.8725 (p90) cc_final: 0.8523 (p90)
REVERT: D  114 TRP cc_start: 0.7336 (m100) cc_final: 0.7129 (m100)
REVERT: D  116 VAL cc_start: 0.8397 (t) cc_final: 0.7769 (t)
REVERT: D  149 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8229 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0759
  time to fit residues: 13.2128
Evaluate side-chains
  106 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 4 optimal weight:    0.1980
   chunk 43 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    0.2980
   chunk 14 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.105928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.096078 restraints weight = 34674.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.097520 restraints weight = 23784.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.098587 restraints weight = 17488.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.099362 restraints weight = 13598.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.099948 restraints weight = 11038.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4905  Z= 0.128
  Angle     :  0.753  11.940   6649  Z= 0.365
  Chirality :  0.050   0.385    757
  Planarity :  0.005   0.040    820
  Dihedral  :  9.271  63.990    732
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.33), residues: 579
  helix:  0.49 (0.35), residues: 212
  sheet: -0.46 (0.69), residues: 58
  loop : -3.26 (0.30), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 112 
 TYR   0.025   0.002   TYR D 117 
 PHE   0.029   0.002   PHE B  12 
 TRP   0.009   0.001   TRP D 114 
 HIS   0.016   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4900)
  covalent geometry    : angle       0.72708 ( 6634)
  hydrogen bonds       : bond        0.03713 (  218)
  hydrogen bonds       : angle       5.07859 (  621)
  link_ALPHA1-3        : bond        0.01236 (    1)
  link_ALPHA1-3        : angle       2.38086 (    3)
  link_ALPHA1-6        : bond        0.01118 (    1)
  link_ALPHA1-6        : angle       1.52080 (    3)
  link_BETA1-4         : bond        0.00914 (    2)
  link_BETA1-4         : angle       3.21792 (    6)
  link_NAG-ASN         : bond        0.01380 (    1)
  link_NAG-ASN         : angle       7.70404 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8420 (t80) cc_final: 0.8213 (t80)
REVERT: A   67 LEU cc_start: 0.8736 (mm) cc_final: 0.8502 (mm)
REVERT: A   75 ASP cc_start: 0.5583 (p0) cc_final: 0.5155 (p0)
REVERT: A   83 VAL cc_start: 0.8865 (t) cc_final: 0.8548 (t)
REVERT: A  135 LYS cc_start: 0.8981 (pttt) cc_final: 0.8190 (tptp)
REVERT: A  137 ASP cc_start: 0.8195 (m-30) cc_final: 0.7982 (p0)
REVERT: A  143 ARG cc_start: 0.7512 (mmm160) cc_final: 0.6167 (ptt180)
REVERT: A  156 MET cc_start: 0.7865 (tpt) cc_final: 0.7566 (tpt)
REVERT: B   69 ASP cc_start: 0.7741 (m-30) cc_final: 0.7322 (m-30)
REVERT: C   89 THR cc_start: 0.8891 (p) cc_final: 0.8629 (p)
REVERT: C  165 ARG cc_start: 0.8389 (tpm170) cc_final: 0.8189 (tpm170)
REVERT: D   90 MET cc_start: 0.4721 (mmt) cc_final: 0.4059 (tpt)
REVERT: D  149 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8245 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0735
  time to fit residues: 12.6997
Evaluate side-chains
  105 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0980
   chunk 12 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0070
   chunk 22 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.2204

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN
B  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.102270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.092438 restraints weight = 34966.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.093862 restraints weight = 23818.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.094903 restraints weight = 17524.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.095641 restraints weight = 13635.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.096231 restraints weight = 11101.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4905  Z= 0.154
  Angle     :  0.756  11.090   6649  Z= 0.374
  Chirality :  0.049   0.355    757
  Planarity :  0.005   0.039    820
  Dihedral  :  8.804  56.795    732
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.76 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.34), residues: 579
  helix:  0.66 (0.36), residues: 213
  sheet: -0.96 (0.67), residues: 67
  loop : -3.13 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 141 
 TYR   0.028   0.002   TYR D 117 
 PHE   0.012   0.002   PHE B  78 
 TRP   0.012   0.001   TRP C  51 
 HIS   0.016   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4900)
  covalent geometry    : angle       0.73393 ( 6634)
  hydrogen bonds       : bond        0.03996 (  218)
  hydrogen bonds       : angle       5.07180 (  621)
  link_ALPHA1-3        : bond        0.00934 (    1)
  link_ALPHA1-3        : angle       2.71229 (    3)
  link_ALPHA1-6        : bond        0.01130 (    1)
  link_ALPHA1-6        : angle       1.43857 (    3)
  link_BETA1-4         : bond        0.00987 (    2)
  link_BETA1-4         : angle       2.96826 (    6)
  link_NAG-ASN         : bond        0.01214 (    1)
  link_NAG-ASN         : angle       7.05375 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.5525 (p0) cc_final: 0.5302 (p0)
REVERT: A  135 LYS cc_start: 0.9006 (pttt) cc_final: 0.8179 (tptp)
REVERT: A  137 ASP cc_start: 0.8371 (m-30) cc_final: 0.8046 (p0)
REVERT: A  143 ARG cc_start: 0.7852 (mmm160) cc_final: 0.6316 (ptt180)
REVERT: A  156 MET cc_start: 0.7911 (tpt) cc_final: 0.7568 (tpt)
REVERT: B   68 PHE cc_start: 0.8313 (p90) cc_final: 0.8038 (p90)
REVERT: B   69 ASP cc_start: 0.7993 (m-30) cc_final: 0.7657 (m-30)
REVERT: B   70 ILE cc_start: 0.8925 (mt) cc_final: 0.7972 (mp)
REVERT: C   84 ARG cc_start: 0.8758 (mmp80) cc_final: 0.7984 (mmp80)
REVERT: C   89 THR cc_start: 0.8958 (p) cc_final: 0.8741 (p)
REVERT: D   90 MET cc_start: 0.4748 (mmt) cc_final: 0.4055 (tpt)
REVERT: D  116 VAL cc_start: 0.8218 (t) cc_final: 0.7775 (t)
REVERT: D  149 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8324 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0766
  time to fit residues: 12.6482
Evaluate side-chains
  103 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.079600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.063955 restraints weight = 28308.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.065389 restraints weight = 22348.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.066502 restraints weight = 18609.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.067241 restraints weight = 16029.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.067980 restraints weight = 14347.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4905  Z= 0.204
  Angle     :  0.829  10.546   6649  Z= 0.413
  Chirality :  0.050   0.319    757
  Planarity :  0.005   0.041    820
  Dihedral  :  8.951  58.668    732
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 18.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.33), residues: 579
  helix:  0.28 (0.34), residues: 215
  sheet: -0.38 (0.71), residues: 61
  loop : -3.28 (0.31), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  86 
 TYR   0.031   0.003   TYR D 117 
 PHE   0.038   0.003   PHE B  12 
 TRP   0.018   0.002   TRP C  51 
 HIS   0.013   0.002   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 4900)
  covalent geometry    : angle       0.81152 ( 6634)
  hydrogen bonds       : bond        0.04251 (  218)
  hydrogen bonds       : angle       5.26107 (  621)
  link_ALPHA1-3        : bond        0.00203 (    1)
  link_ALPHA1-3        : angle       2.59447 (    3)
  link_ALPHA1-6        : bond        0.00612 (    1)
  link_ALPHA1-6        : angle       1.52385 (    3)
  link_BETA1-4         : bond        0.01370 (    2)
  link_BETA1-4         : angle       2.77819 (    6)
  link_NAG-ASN         : bond        0.01063 (    1)
  link_NAG-ASN         : angle       6.56501 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.9337 (t) cc_final: 0.9032 (t)
REVERT: A  135 LYS cc_start: 0.9048 (pttt) cc_final: 0.8085 (tptp)
REVERT: A  137 ASP cc_start: 0.8350 (m-30) cc_final: 0.7938 (p0)
REVERT: A  143 ARG cc_start: 0.7970 (mmm160) cc_final: 0.6469 (ptt180)
REVERT: A  156 MET cc_start: 0.7964 (tpt) cc_final: 0.7631 (tpt)
REVERT: B   68 PHE cc_start: 0.8602 (p90) cc_final: 0.8259 (p90)
REVERT: B   69 ASP cc_start: 0.8314 (m-30) cc_final: 0.8044 (m-30)
REVERT: B   70 ILE cc_start: 0.8967 (mt) cc_final: 0.8050 (mp)
REVERT: C   88 CYS cc_start: 0.9075 (m) cc_final: 0.8750 (p)
REVERT: C  182 LYS cc_start: 0.8076 (mppt) cc_final: 0.7783 (tptp)
REVERT: D   90 MET cc_start: 0.4798 (mmt) cc_final: 0.4331 (tpt)
REVERT: D  116 VAL cc_start: 0.7946 (t) cc_final: 0.7716 (t)
REVERT: D  136 ILE cc_start: 0.4360 (pt) cc_final: 0.3954 (pt)
REVERT: D  149 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8660 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0733
  time to fit residues: 11.6980
Evaluate side-chains
  102 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0770
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    1.9344

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.098402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.088779 restraints weight = 35613.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.090180 restraints weight = 24261.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.091180 restraints weight = 17891.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.091945 restraints weight = 13969.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.092358 restraints weight = 11355.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.5791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4905  Z= 0.144
  Angle     :  0.777  10.563   6649  Z= 0.381
  Chirality :  0.049   0.338    757
  Planarity :  0.004   0.036    820
  Dihedral  :  8.530  57.897    732
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.65 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.34), residues: 579
  helix:  0.72 (0.35), residues: 210
  sheet: -1.18 (0.60), residues: 75
  loop : -3.08 (0.32), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  86 
 TYR   0.027   0.002   TYR D 117 
 PHE   0.013   0.002   PHE D 103 
 TRP   0.009   0.001   TRP C  51 
 HIS   0.016   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4900)
  covalent geometry    : angle       0.75736 ( 6634)
  hydrogen bonds       : bond        0.04160 (  218)
  hydrogen bonds       : angle       5.07626 (  621)
  link_ALPHA1-3        : bond        0.00853 (    1)
  link_ALPHA1-3        : angle       2.59648 (    3)
  link_ALPHA1-6        : bond        0.00976 (    1)
  link_ALPHA1-6        : angle       1.40887 (    3)
  link_BETA1-4         : bond        0.00950 (    2)
  link_BETA1-4         : angle       2.73359 (    6)
  link_NAG-ASN         : bond        0.01194 (    1)
  link_NAG-ASN         : angle       6.71403 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.6896 (p0) cc_final: 0.6595 (p0)
REVERT: A  135 LYS cc_start: 0.8908 (pttt) cc_final: 0.8174 (tptp)
REVERT: A  137 ASP cc_start: 0.8523 (m-30) cc_final: 0.7213 (p0)
REVERT: A  143 ARG cc_start: 0.7849 (mmm160) cc_final: 0.6391 (ptt180)
REVERT: A  156 MET cc_start: 0.7961 (tpt) cc_final: 0.7623 (tpt)
REVERT: B   68 PHE cc_start: 0.8788 (p90) cc_final: 0.8363 (p90)
REVERT: B   69 ASP cc_start: 0.8351 (m-30) cc_final: 0.8115 (m-30)
REVERT: B   70 ILE cc_start: 0.8936 (mt) cc_final: 0.8058 (mp)
REVERT: B   88 TYR cc_start: 0.8608 (p90) cc_final: 0.8338 (p90)
REVERT: C   84 ARG cc_start: 0.8721 (mmp80) cc_final: 0.8393 (mmp80)
REVERT: C   88 CYS cc_start: 0.8969 (m) cc_final: 0.8693 (p)
REVERT: C  165 ARG cc_start: 0.8970 (ttp-110) cc_final: 0.8619 (tpp-160)
REVERT: D   86 LEU cc_start: 0.7465 (tp) cc_final: 0.6925 (mm)
REVERT: D   90 MET cc_start: 0.4792 (mmt) cc_final: 0.4171 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0737
  time to fit residues: 12.1556
Evaluate side-chains
  105 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 21 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 43 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.9722

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.081731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.065730 restraints weight = 27866.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.067273 restraints weight = 21738.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.068482 restraints weight = 17911.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.069357 restraints weight = 15314.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.070091 restraints weight = 13567.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.5870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4905  Z= 0.132
  Angle     :  0.777  10.650   6649  Z= 0.383
  Chirality :  0.050   0.347    757
  Planarity :  0.005   0.049    820
  Dihedral  :  8.168  54.684    732
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.34), residues: 579
  helix:  0.85 (0.36), residues: 210
  sheet: -0.92 (0.57), residues: 83
  loop : -3.10 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  86 
 TYR   0.029   0.001   TYR D 117 
 PHE   0.036   0.002   PHE B  12 
 TRP   0.007   0.001   TRP C  51 
 HIS   0.017   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4900)
  covalent geometry    : angle       0.75771 ( 6634)
  hydrogen bonds       : bond        0.04109 (  218)
  hydrogen bonds       : angle       5.07988 (  621)
  link_ALPHA1-3        : bond        0.00906 (    1)
  link_ALPHA1-3        : angle       2.34161 (    3)
  link_ALPHA1-6        : bond        0.01081 (    1)
  link_ALPHA1-6        : angle       1.36446 (    3)
  link_BETA1-4         : bond        0.01048 (    2)
  link_BETA1-4         : angle       2.71053 (    6)
  link_NAG-ASN         : bond        0.01230 (    1)
  link_NAG-ASN         : angle       6.77539 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.8831 (mmm) cc_final: 0.8050 (mmm)
REVERT: A   75 ASP cc_start: 0.6848 (p0) cc_final: 0.6581 (p0)
REVERT: A   99 LEU cc_start: 0.9457 (tt) cc_final: 0.9233 (mm)
REVERT: A  135 LYS cc_start: 0.8992 (pttt) cc_final: 0.8087 (tptp)
REVERT: A  143 ARG cc_start: 0.7930 (mmm160) cc_final: 0.6438 (ptt180)
REVERT: A  156 MET cc_start: 0.7952 (tpt) cc_final: 0.7642 (tpt)
REVERT: B   68 PHE cc_start: 0.8520 (p90) cc_final: 0.8275 (p90)
REVERT: B   70 ILE cc_start: 0.8873 (mt) cc_final: 0.7993 (mt)
REVERT: B   88 TYR cc_start: 0.8518 (p90) cc_final: 0.8288 (p90)
REVERT: C   84 ARG cc_start: 0.8683 (mmp80) cc_final: 0.8041 (mmp80)
REVERT: C   88 CYS cc_start: 0.8980 (m) cc_final: 0.8673 (p)
REVERT: C  165 ARG cc_start: 0.9033 (ttp-110) cc_final: 0.8664 (tpp-160)
REVERT: D   86 LEU cc_start: 0.7592 (tp) cc_final: 0.7141 (mm)
REVERT: D   90 MET cc_start: 0.4930 (mmt) cc_final: 0.4297 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0751
  time to fit residues: 11.7096
Evaluate side-chains
  97 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.077404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.062268 restraints weight = 28579.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.063805 restraints weight = 21850.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.064957 restraints weight = 17779.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.065930 restraints weight = 15195.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.066677 restraints weight = 13232.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.6440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4905  Z= 0.193
  Angle     :  0.824  10.209   6649  Z= 0.411
  Chirality :  0.050   0.323    757
  Planarity :  0.005   0.044    820
  Dihedral  :  8.320  58.301    732
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.33), residues: 579
  helix:  0.54 (0.35), residues: 209
  sheet: -1.07 (0.57), residues: 83
  loop : -3.23 (0.32), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  86 
 TYR   0.029   0.002   TYR D 117 
 PHE   0.039   0.003   PHE D  91 
 TRP   0.014   0.001   TRP C  51 
 HIS   0.017   0.002   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4900)
  covalent geometry    : angle       0.80675 ( 6634)
  hydrogen bonds       : bond        0.04328 (  218)
  hydrogen bonds       : angle       5.32986 (  621)
  link_ALPHA1-3        : bond        0.00713 (    1)
  link_ALPHA1-3        : angle       2.87758 (    3)
  link_ALPHA1-6        : bond        0.00991 (    1)
  link_ALPHA1-6        : angle       1.40231 (    3)
  link_BETA1-4         : bond        0.00969 (    2)
  link_BETA1-4         : angle       2.58992 (    6)
  link_NAG-ASN         : bond        0.01148 (    1)
  link_NAG-ASN         : angle       6.36883 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.9443 (tt) cc_final: 0.9227 (mm)
REVERT: A  135 LYS cc_start: 0.8986 (pttt) cc_final: 0.8131 (tptp)
REVERT: A  143 ARG cc_start: 0.8110 (mmm160) cc_final: 0.6678 (ptt180)
REVERT: A  156 MET cc_start: 0.7952 (tpt) cc_final: 0.7616 (tpt)
REVERT: B   68 PHE cc_start: 0.8532 (p90) cc_final: 0.8093 (p90)
REVERT: B   69 ASP cc_start: 0.8110 (m-30) cc_final: 0.7899 (m-30)
REVERT: B   70 ILE cc_start: 0.8949 (mt) cc_final: 0.8019 (mp)
REVERT: C   84 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8138 (mmp80)
REVERT: C   88 CYS cc_start: 0.9072 (m) cc_final: 0.8756 (p)
REVERT: D   86 LEU cc_start: 0.7532 (tp) cc_final: 0.7009 (mm)
REVERT: D   90 MET cc_start: 0.5115 (mmt) cc_final: 0.4468 (tpt)
REVERT: D  116 VAL cc_start: 0.7945 (t) cc_final: 0.7671 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0679
  time to fit residues: 10.1446
Evaluate side-chains
  92 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0060
   chunk 25 optimal weight:    0.0060
   chunk 39 optimal weight:    0.0870
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.080486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.065506 restraints weight = 29954.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.067075 restraints weight = 22923.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.068262 restraints weight = 18582.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.069154 restraints weight = 15754.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.069910 restraints weight = 13834.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.6305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4905  Z= 0.134
  Angle     :  0.802  10.445   6649  Z= 0.391
  Chirality :  0.050   0.348    757
  Planarity :  0.005   0.045    820
  Dihedral  :  7.780  54.230    732
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.34), residues: 579
  helix:  0.69 (0.36), residues: 209
  sheet: -1.02 (0.62), residues: 74
  loop : -3.15 (0.31), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  86 
 TYR   0.029   0.001   TYR D 117 
 PHE   0.029   0.002   PHE B  12 
 TRP   0.006   0.001   TRP C 157 
 HIS   0.019   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4900)
  covalent geometry    : angle       0.78426 ( 6634)
  hydrogen bonds       : bond        0.04201 (  218)
  hydrogen bonds       : angle       5.11965 (  621)
  link_ALPHA1-3        : bond        0.01095 (    1)
  link_ALPHA1-3        : angle       2.14089 (    3)
  link_ALPHA1-6        : bond        0.01042 (    1)
  link_ALPHA1-6        : angle       1.27938 (    3)
  link_BETA1-4         : bond        0.01071 (    2)
  link_BETA1-4         : angle       2.66619 (    6)
  link_NAG-ASN         : bond        0.01252 (    1)
  link_NAG-ASN         : angle       6.67566 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.8623 (mmm) cc_final: 0.7934 (mmm)
REVERT: A   75 ASP cc_start: 0.6673 (p0) cc_final: 0.6437 (p0)
REVERT: A  135 LYS cc_start: 0.8920 (pttt) cc_final: 0.7970 (tptp)
REVERT: A  143 ARG cc_start: 0.7934 (mmm160) cc_final: 0.6591 (ptt180)
REVERT: A  156 MET cc_start: 0.8054 (tpt) cc_final: 0.7731 (tpt)
REVERT: B   68 PHE cc_start: 0.8057 (p90) cc_final: 0.7791 (p90)
REVERT: B   70 ILE cc_start: 0.8928 (mt) cc_final: 0.7978 (mt)
REVERT: C   84 ARG cc_start: 0.8605 (mmp80) cc_final: 0.8105 (mmp80)
REVERT: D   86 LEU cc_start: 0.7563 (tp) cc_final: 0.7049 (mm)
REVERT: D   90 MET cc_start: 0.5226 (mmt) cc_final: 0.4565 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0731
  time to fit residues: 11.6870
Evaluate side-chains
  100 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0570
   overall best weight:    2.4104

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.079681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.063785 restraints weight = 27657.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.065396 restraints weight = 21084.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.066624 restraints weight = 17140.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.067523 restraints weight = 14528.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.068219 restraints weight = 12774.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.6619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4905  Z= 0.163
  Angle     :  0.804  10.189   6649  Z= 0.399
  Chirality :  0.050   0.335    757
  Planarity :  0.005   0.054    820
  Dihedral  :  7.720  53.834    732
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.34), residues: 579
  helix:  0.64 (0.35), residues: 209
  sheet: -0.82 (0.58), residues: 83
  loop : -3.19 (0.32), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  90 
 TYR   0.049   0.003   TYR C 121 
 PHE   0.029   0.002   PHE D  91 
 TRP   0.011   0.001   TRP C  51 
 HIS   0.019   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 4900)
  covalent geometry    : angle       0.78728 ( 6634)
  hydrogen bonds       : bond        0.04277 (  218)
  hydrogen bonds       : angle       5.20817 (  621)
  link_ALPHA1-3        : bond        0.00716 (    1)
  link_ALPHA1-3        : angle       2.54144 (    3)
  link_ALPHA1-6        : bond        0.00934 (    1)
  link_ALPHA1-6        : angle       1.31378 (    3)
  link_BETA1-4         : bond        0.01000 (    2)
  link_BETA1-4         : angle       2.58803 (    6)
  link_NAG-ASN         : bond        0.01176 (    1)
  link_NAG-ASN         : angle       6.38534 (    3)

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

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.8564 (mmm) cc_final: 0.7332 (mmm)
REVERT: A   75 ASP cc_start: 0.7193 (p0) cc_final: 0.6914 (p0)
REVERT: A  135 LYS cc_start: 0.8893 (pttt) cc_final: 0.8112 (tptp)
REVERT: A  143 ARG cc_start: 0.8083 (mmm160) cc_final: 0.6670 (ptt180)
REVERT: A  156 MET cc_start: 0.8045 (tpt) cc_final: 0.7711 (tpt)
REVERT: B   68 PHE cc_start: 0.8539 (p90) cc_final: 0.8173 (p90)
REVERT: B   70 ILE cc_start: 0.8991 (mt) cc_final: 0.8120 (mt)
REVERT: B   98 ASN cc_start: 0.7956 (m-40) cc_final: 0.7745 (m-40)
REVERT: C   84 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8101 (mmp80)
REVERT: C   88 CYS cc_start: 0.8999 (m) cc_final: 0.8696 (p)
REVERT: C  185 ARG cc_start: 0.6934 (tmm160) cc_final: 0.6128 (mtp180)
REVERT: D   86 LEU cc_start: 0.7608 (tp) cc_final: 0.7161 (mm)
REVERT: D   90 MET cc_start: 0.5211 (mmt) cc_final: 0.4610 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0758
  time to fit residues: 11.2545
Evaluate side-chains
  103 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    1.6026

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.078497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.063695 restraints weight = 28663.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.065293 restraints weight = 21496.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.066509 restraints weight = 17242.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.067411 restraints weight = 14459.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.068137 restraints weight = 12562.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.6715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4905  Z= 0.141
  Angle     :  0.785  10.191   6649  Z= 0.389
  Chirality :  0.050   0.338    757
  Planarity :  0.005   0.055    820
  Dihedral  :  7.549  53.574    732
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.34), residues: 579
  helix:  0.65 (0.35), residues: 209
  sheet: -0.74 (0.63), residues: 74
  loop : -3.14 (0.31), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  90 
 TYR   0.029   0.002   TYR C 121 
 PHE   0.029   0.002   PHE B  12 
 TRP   0.008   0.001   TRP C 157 
 HIS   0.019   0.001   HIS C 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4900)
  covalent geometry    : angle       0.76848 ( 6634)
  hydrogen bonds       : bond        0.04304 (  218)
  hydrogen bonds       : angle       5.13480 (  621)
  link_ALPHA1-3        : bond        0.00930 (    1)
  link_ALPHA1-3        : angle       2.35846 (    3)
  link_ALPHA1-6        : bond        0.01137 (    1)
  link_ALPHA1-6        : angle       1.25459 (    3)
  link_BETA1-4         : bond        0.01054 (    2)
  link_BETA1-4         : angle       2.54571 (    6)
  link_NAG-ASN         : bond        0.01189 (    1)
  link_NAG-ASN         : angle       6.41230 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 884.86 seconds
wall clock time: 16 minutes 0.96 seconds (960.96 seconds total)