Starting phenix.real_space_refine
on Wed Sep 17 05:55:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jqt_61741/09_2025/9jqt_61741.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jqt_61741/09_2025/9jqt_61741.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jqt_61741/09_2025/9jqt_61741.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jqt_61741/09_2025/9jqt_61741.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jqt_61741/09_2025/9jqt_61741.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jqt_61741/09_2025/9jqt_61741.cif"
  }
  resolution = 2.7
  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=   0.014
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    3581      2.51       5
     N     963      2.21       5
     O    1102      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5669
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1599
          Classifications: {'peptide': 188}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 177}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1557
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 193}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1603
          Classifications: {'peptide': 208}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 194}
    Chain: "D"
      Number of atoms: 910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 910
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
  Time building chain proxies: 1.51, per 1000 atoms: 0.27
  Number of scatterers: 5669
  At special positions: 0
  Unit cell: (80.864, 85.918, 113.354, 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    1102      8.00
     N     963      7.00
     C    3581      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 182 " - pdb=" SG  CYS A 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 133 " - pdb=" SG  CYS C 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  98 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 225.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 18 sheets defined
      8.3% alpha, 49.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 79
      removed outlier: 3.615A  pdb=" N   SER A  78 " --> pdb=" O   ASN A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 122
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   THR B  91 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 191 through 193
      No H-bonds generated for 'chain 'B' and resid 191 through 193'
    Processing helix  chain 'B' and resid 205 through 208
    Processing helix  chain 'C' and resid 78 through 82
      removed outlier: 3.647A  pdb=" N   PHE C  82 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 127
    Processing helix  chain 'C' and resid 182 through 188
      removed outlier: 3.871A  pdb=" N   HIS C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 34
      removed outlier: 4.175A  pdb=" N   ARG D  33 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108
      removed outlier: 6.601A  pdb=" N   LEU A 106 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE A 153 " --> pdb=" O   CYS A  62 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   VAL A  64 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101
    Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 163
      removed outlier: 4.428A  pdb=" N   LEU A 160 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASN A 173 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU A 162 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLU A 171 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.530A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.530A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 128
      removed outlier: 5.927A  pdb=" N   TYR B 180 " --> pdb=" O   ASP B 148 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 128
      removed outlier: 5.927A  pdb=" N   TYR B 180 " --> pdb=" O   ASP B 148 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 158
    Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.015A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   TRP C  34 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.015A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR C  96 " --> pdb=" O   GLN C  89 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 113 through 117
      removed outlier: 5.626A  pdb=" N   TYR C 172 " --> pdb=" O   ASN C 137 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 152 through 154
      removed outlier: 4.648A  pdb=" N   TRP C 147 " --> pdb=" O   GLN C 154 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 7 through 9
    Processing sheet with id=AB8, first strand: chain 'D' and resid 60 through 62
      removed outlier: 6.672A  pdb=" N   TRP D  38 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL D  52 " --> pdb=" O   MET D  36 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   MET D  36 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA D  35 " --> pdb=" O   ASP D 101 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   TYR D 112 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 60 through 62
      removed outlier: 6.672A  pdb=" N   TRP D  38 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL D  52 " --> pdb=" O   MET D  36 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   MET D  36 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA D  35 " --> pdb=" O   ASP D 101 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    627 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: 0.91

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1822
        1.34 -     1.46: 1422
        1.46 -     1.58: 2541
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 5815
  Sorted by residual:
  bond pdb=" N   VAL A 223 "
       pdb=" CA  VAL A 223 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.18e-02 7.18e+03 1.00e+01
  bond pdb=" N   GLY D 116 "
       pdb=" CA  GLY D 116 "
    ideal  model  delta    sigma   weight residual
    1.446  1.476 -0.030 1.02e-02 9.61e+03 8.91e+00
  bond pdb=" N   VAL B 146 "
       pdb=" CA  VAL B 146 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.10e-02 8.26e+03 8.85e+00
  bond pdb=" N   VAL B 125 "
       pdb=" CA  VAL B 125 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.24e-02 6.50e+03 8.62e+00
  bond pdb=" N   VAL A 187 "
       pdb=" CA  VAL A 187 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.52e+00
  ... (remaining 5810 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 7431
        1.35 -     2.70: 387
        2.70 -     4.05: 75
        4.05 -     5.40: 10
        5.40 -     6.76: 7
  Bond angle restraints: 7910
  Sorted by residual:
  angle pdb=" CA  GLY D 116 "
        pdb=" C   GLY D 116 "
        pdb=" O   GLY D 116 "
      ideal   model   delta    sigma   weight residual
     122.23  118.37    3.86 6.90e-01 2.10e+00 3.13e+01
  angle pdb=" CA  GLY B  49 "
        pdb=" C   GLY B  49 "
        pdb=" O   GLY B  49 "
      ideal   model   delta    sigma   weight residual
     121.60  118.12    3.48 9.70e-01 1.06e+00 1.28e+01
  angle pdb=" N   TYR B 106 "
        pdb=" CA  TYR B 106 "
        pdb=" CB  TYR B 106 "
      ideal   model   delta    sigma   weight residual
     110.69  104.95    5.74 1.61e+00 3.86e-01 1.27e+01
  angle pdb=" CA  ASP B  52 "
        pdb=" CB  ASP B  52 "
        pdb=" CG  ASP B  52 "
      ideal   model   delta    sigma   weight residual
     112.60  116.13   -3.53 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" N   PRO A 229 "
        pdb=" CA  PRO A 229 "
        pdb=" CB  PRO A 229 "
      ideal   model   delta    sigma   weight residual
     102.60   99.00    3.60 1.10e+00 8.26e-01 1.07e+01
  ... (remaining 7905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3162
       17.94 -    35.88: 229
       35.88 -    53.82: 56
       53.82 -    71.77: 9
       71.77 -    89.71: 4
  Dihedral angle restraints: 3460
    sinusoidal: 1357
      harmonic: 2103
  Sorted by residual:
  dihedral pdb=" CB  CYS B 144 "
           pdb=" SG  CYS B 144 "
           pdb=" SG  CYS B 200 "
           pdb=" CB  CYS B 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.27   38.73     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" CA  ASN A 228 "
           pdb=" C   ASN A 228 "
           pdb=" N   PRO A 229 "
           pdb=" CA  PRO A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -20.52   20.52     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  87 "
           pdb=" CB  CYS C  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.50   29.50     1      1.00e+01 1.00e-02 1.24e+01
  ... (remaining 3457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 711
       0.060 -    0.120: 129
       0.120 -    0.179: 19
       0.179 -    0.239: 2
       0.239 -    0.299: 2
  Chirality restraints: 863
  Sorted by residual:
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  VAL C 145 "
            pdb=" N   VAL C 145 "
            pdb=" C   VAL C 145 "
            pdb=" CB  VAL C 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  VAL B 146 "
            pdb=" N   VAL B 146 "
            pdb=" C   VAL B 146 "
            pdb=" CB  VAL B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 860 not shown)

  Planarity restraints: 1014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  78 "   -0.037 5.00e-02 4.00e+02   5.63e-02 5.06e+00
        pdb=" N   PRO C  79 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C  79 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C  79 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  50 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   THR C  50 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   THR C  50 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER C  51 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  61 "    0.028 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO B  62 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B  62 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  62 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1011 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 507
        2.75 -     3.29: 5054
        3.29 -     3.82: 9534
        3.82 -     4.36: 12193
        4.36 -     4.90: 20589
  Nonbonded interactions: 47877
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 102 "
            pdb=" OD1 ASP B 105 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD1 ASN A 150 "
            pdb=" OG  SER A 233 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP B  73 "
            pdb=" OG  SER B  75 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NH1 ARG D  40 "
            pdb=" OD1 ASP D  92 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   PRO A 157 "
            pdb=" OG  SER A 241 "
     model   vdw
     2.309 3.040
  ... (remaining 47872 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 individual isotropic
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:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.310
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5878
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   0.037   5822  Z= 0.318
  Angle     :  0.718   6.756   7924  Z= 0.449
  Chirality :  0.050   0.299    863
  Planarity :  0.005   0.063   1014
  Dihedral  : 13.514  89.707   2085
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 12.60 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.32), residues: 706
  helix:  0.65 (1.11), residues: 21
  sheet:  0.47 (0.28), residues: 323
  loop :  0.34 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  24 
 TYR   0.010   0.001   TYR C  48 
 PHE   0.014   0.002   PHE C 138 
 TRP   0.011   0.001   TRP B  47 
 HIS   0.006   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 5815)
  covalent geometry    : angle       0.71712 ( 7910)
  SS BOND              : bond        0.00475 (    7)
  SS BOND              : angle       1.18742 (   14)
  hydrogen bonds       : bond        0.12968 (  229)
  hydrogen bonds       : angle       7.39875 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.7565 (mttt) cc_final: 0.7243 (mptm)
REVERT: B   30 GLU cc_start: 0.6940 (pt0) cc_final: 0.6120 (pm20)
REVERT: B   59 ASN cc_start: 0.7210 (m-40) cc_final: 0.6879 (m110)
REVERT: C  168 LYS cc_start: 0.6680 (mttt) cc_final: 0.6369 (ttpp)
  outliers start: 2
  outliers final: 1
  residues processed: 97
  average time/residue: 0.5620
  time to fit residues: 57.0232
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 201 ASN
C  93 ASN
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.187299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.131527 restraints weight = 5547.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.45
r_work: 0.3465 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5822  Z= 0.198
  Angle     :  0.575   8.773   7924  Z= 0.300
  Chirality :  0.043   0.161    863
  Planarity :  0.005   0.052   1014
  Dihedral  :  4.640  16.959    779
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.76 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.32), residues: 706
  helix:  0.84 (1.05), residues: 21
  sheet:  0.41 (0.27), residues: 343
  loop :  0.45 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  49 
 TYR   0.010   0.002   TYR C  48 
 PHE   0.019   0.002   PHE D  49 
 TRP   0.011   0.001   TRP B  47 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 5815)
  covalent geometry    : angle       0.57474 ( 7910)
  SS BOND              : bond        0.00310 (    7)
  SS BOND              : angle       0.90380 (   14)
  hydrogen bonds       : bond        0.03798 (  229)
  hydrogen bonds       : angle       5.84398 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8526 (t0)
REVERT: A  101 LYS cc_start: 0.8162 (mttt) cc_final: 0.7872 (mptm)
REVERT: B   19 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8349 (tttt)
REVERT: B   30 GLU cc_start: 0.7669 (pt0) cc_final: 0.6985 (pm20)
REVERT: B   59 ASN cc_start: 0.8287 (m-40) cc_final: 0.8040 (m110)
REVERT: C  168 LYS cc_start: 0.7497 (mttt) cc_final: 0.7123 (ttpp)
REVERT: D   92 ASP cc_start: 0.7532 (m-30) cc_final: 0.7246 (m-30)
  outliers start: 20
  outliers final: 8
  residues processed: 101
  average time/residue: 0.6622
  time to fit residues: 69.5238
Evaluate side-chains
  92 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0770
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.8540

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.190397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.134717 restraints weight = 5360.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.44
r_work: 0.3497 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5822  Z= 0.147
  Angle     :  0.527   7.319   7924  Z= 0.274
  Chirality :  0.042   0.152    863
  Planarity :  0.005   0.054   1014
  Dihedral  :  4.442  15.858    778
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.17 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.32), residues: 706
  helix:  1.06 (1.06), residues: 21
  sheet:  0.47 (0.27), residues: 343
  loop :  0.41 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  24 
 TYR   0.010   0.001   TYR C  85 
 PHE   0.017   0.002   PHE D  49 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5815)
  covalent geometry    : angle       0.52678 ( 7910)
  SS BOND              : bond        0.00269 (    7)
  SS BOND              : angle       0.76295 (   14)
  hydrogen bonds       : bond        0.03396 (  229)
  hydrogen bonds       : angle       5.60375 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8486 (t0)
REVERT: A  101 LYS cc_start: 0.8122 (mttt) cc_final: 0.7786 (mptm)
REVERT: A  149 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7405 (pt0)
REVERT: B   19 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8280 (tttt)
REVERT: B   30 GLU cc_start: 0.7593 (pt0) cc_final: 0.6889 (pm20)
REVERT: B   59 ASN cc_start: 0.8250 (m-40) cc_final: 0.8032 (m110)
REVERT: B  210 LYS cc_start: 0.7634 (tttt) cc_final: 0.7054 (tptm)
REVERT: D   92 ASP cc_start: 0.7516 (m-30) cc_final: 0.7243 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 94
  average time/residue: 0.6264
  time to fit residues: 61.3454
Evaluate side-chains
  93 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 11 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.4164

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

Flipped N/Q/H residues before XYZ refinement:
A  88 HIS
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.187754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.130900 restraints weight = 5408.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.46
r_work: 0.3452 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   5822  Z= 0.212
  Angle     :  0.578   9.051   7924  Z= 0.299
  Chirality :  0.044   0.163    863
  Planarity :  0.005   0.055   1014
  Dihedral  :  4.707  17.524    778
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 14.02 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.31), residues: 706
  helix:  0.97 (1.07), residues: 21
  sheet:  0.48 (0.27), residues: 345
  loop :  0.24 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  24 
 TYR   0.011   0.002   TYR C 139 
 PHE   0.021   0.002   PHE D  49 
 TRP   0.010   0.001   TRP B  47 
 HIS   0.004   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 5815)
  covalent geometry    : angle       0.57720 ( 7910)
  SS BOND              : bond        0.00381 (    7)
  SS BOND              : angle       0.87436 (   14)
  hydrogen bonds       : bond        0.03725 (  229)
  hydrogen bonds       : angle       5.78427 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (t0)
REVERT: A  101 LYS cc_start: 0.8195 (mttt) cc_final: 0.7859 (mptm)
REVERT: A  149 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7474 (pt0)
REVERT: B   19 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8330 (tttt)
REVERT: B   30 GLU cc_start: 0.7644 (pt0) cc_final: 0.6964 (pm20)
REVERT: B   59 ASN cc_start: 0.8315 (m-40) cc_final: 0.8055 (m110)
REVERT: B  155 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7499 (t)
REVERT: B  210 LYS cc_start: 0.7675 (tttt) cc_final: 0.7018 (tptm)
REVERT: C   80 GLU cc_start: 0.8413 (pm20) cc_final: 0.7966 (pm20)
REVERT: C  168 LYS cc_start: 0.7783 (ttmt) cc_final: 0.6914 (ttpp)
REVERT: D   92 ASP cc_start: 0.7586 (m-30) cc_final: 0.7360 (m-30)
  outliers start: 27
  outliers final: 10
  residues processed: 103
  average time/residue: 0.5787
  time to fit residues: 62.0947
Evaluate side-chains
  99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.189250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.132598 restraints weight = 5487.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.48
r_work: 0.3474 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5822  Z= 0.168
  Angle     :  0.544   8.241   7924  Z= 0.281
  Chirality :  0.042   0.154    863
  Planarity :  0.005   0.056   1014
  Dihedral  :  4.545  16.393    778
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.28 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.32), residues: 706
  helix:  1.11 (1.08), residues: 21
  sheet:  0.48 (0.27), residues: 345
  loop :  0.31 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  24 
 TYR   0.010   0.002   TYR C  85 
 PHE   0.018   0.002   PHE D  49 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 5815)
  covalent geometry    : angle       0.54396 ( 7910)
  SS BOND              : bond        0.00327 (    7)
  SS BOND              : angle       0.72155 (   14)
  hydrogen bonds       : bond        0.03420 (  229)
  hydrogen bonds       : angle       5.61633 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8512 (t0)
REVERT: A  101 LYS cc_start: 0.8178 (mttt) cc_final: 0.7809 (mptm)
REVERT: A  149 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7448 (pt0)
REVERT: B   19 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8310 (tttt)
REVERT: B   30 GLU cc_start: 0.7613 (pt0) cc_final: 0.6921 (pm20)
REVERT: B   59 ASN cc_start: 0.8263 (m-40) cc_final: 0.8020 (m110)
REVERT: B  210 LYS cc_start: 0.7675 (tttt) cc_final: 0.7009 (tptm)
REVERT: C   80 GLU cc_start: 0.8281 (pm20) cc_final: 0.7776 (pm20)
REVERT: C  168 LYS cc_start: 0.7757 (ttmt) cc_final: 0.6876 (ttpp)
  outliers start: 22
  outliers final: 11
  residues processed: 98
  average time/residue: 0.6087
  time to fit residues: 62.1178
Evaluate side-chains
  94 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.191975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136119 restraints weight = 5408.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.45
r_work: 0.3504 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5822  Z= 0.123
  Angle     :  0.501   7.396   7924  Z= 0.259
  Chirality :  0.041   0.147    863
  Planarity :  0.005   0.057   1014
  Dihedral  :  4.326  14.982    778
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.43 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.32), residues: 706
  helix:  1.42 (1.12), residues: 21
  sheet:  0.44 (0.27), residues: 348
  loop :  0.44 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  24 
 TYR   0.009   0.001   TYR A 189 
 PHE   0.014   0.002   PHE D  49 
 TRP   0.007   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5815)
  covalent geometry    : angle       0.50040 ( 7910)
  SS BOND              : bond        0.00263 (    7)
  SS BOND              : angle       0.57121 (   14)
  hydrogen bonds       : bond        0.03109 (  229)
  hydrogen bonds       : angle       5.35747 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8460 (t0)
REVERT: A  101 LYS cc_start: 0.8145 (mttt) cc_final: 0.7799 (mptm)
REVERT: A  149 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7440 (pt0)
REVERT: B   30 GLU cc_start: 0.7564 (pt0) cc_final: 0.6886 (pm20)
REVERT: B   59 ASN cc_start: 0.8246 (m-40) cc_final: 0.7996 (m110)
REVERT: B  210 LYS cc_start: 0.7666 (tttt) cc_final: 0.7033 (tptm)
REVERT: C   80 GLU cc_start: 0.8287 (pm20) cc_final: 0.7782 (pm20)
REVERT: C  122 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6470 (mt-10)
REVERT: C  168 LYS cc_start: 0.7642 (ttmt) cc_final: 0.6768 (ttpp)
REVERT: D   85 MET cc_start: 0.6786 (mtt) cc_final: 0.6359 (mtt)
  outliers start: 22
  outliers final: 13
  residues processed: 95
  average time/residue: 0.5666
  time to fit residues: 56.0588
Evaluate side-chains
  98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0870
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.192334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136183 restraints weight = 5428.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.46
r_work: 0.3513 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5822  Z= 0.125
  Angle     :  0.501   7.341   7924  Z= 0.259
  Chirality :  0.041   0.148    863
  Planarity :  0.005   0.057   1014
  Dihedral  :  4.282  14.665    778
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.75 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.32), residues: 706
  helix:  1.55 (1.14), residues: 21
  sheet:  0.42 (0.27), residues: 348
  loop :  0.47 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  24 
 TYR   0.009   0.001   TYR D  97 
 PHE   0.014   0.002   PHE D  49 
 TRP   0.007   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5815)
  covalent geometry    : angle       0.50060 ( 7910)
  SS BOND              : bond        0.00241 (    7)
  SS BOND              : angle       0.70978 (   14)
  hydrogen bonds       : bond        0.03093 (  229)
  hydrogen bonds       : angle       5.30291 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8443 (t0)
REVERT: A  101 LYS cc_start: 0.8170 (mttt) cc_final: 0.7835 (mptm)
REVERT: A  149 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7444 (pt0)
REVERT: B   19 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (tttt)
REVERT: B   30 GLU cc_start: 0.7534 (pt0) cc_final: 0.6878 (pm20)
REVERT: B   59 ASN cc_start: 0.8278 (m-40) cc_final: 0.8034 (m110)
REVERT: B  210 LYS cc_start: 0.7668 (tttt) cc_final: 0.7068 (tptm)
REVERT: C   80 GLU cc_start: 0.8344 (pm20) cc_final: 0.7856 (pm20)
REVERT: C  122 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6471 (mt-10)
REVERT: D   85 MET cc_start: 0.6777 (mtt) cc_final: 0.6378 (mtt)
  outliers start: 19
  outliers final: 11
  residues processed: 94
  average time/residue: 0.6197
  time to fit residues: 60.6267
Evaluate side-chains
  94 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0070
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.192776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137262 restraints weight = 5399.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.46
r_work: 0.3560 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5822  Z= 0.106
  Angle     :  0.480   7.147   7924  Z= 0.249
  Chirality :  0.041   0.143    863
  Planarity :  0.004   0.058   1014
  Dihedral  :  4.147  13.699    778
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.06 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.32), residues: 706
  helix:  1.73 (1.18), residues: 21
  sheet:  0.54 (0.27), residues: 343
  loop :  0.53 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  24 
 TYR   0.010   0.001   TYR D  97 
 PHE   0.013   0.001   PHE D  49 
 TRP   0.006   0.001   TRP A  90 
 HIS   0.002   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5815)
  covalent geometry    : angle       0.47978 ( 7910)
  SS BOND              : bond        0.00314 (    7)
  SS BOND              : angle       0.68919 (   14)
  hydrogen bonds       : bond        0.02910 (  229)
  hydrogen bonds       : angle       5.14820 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8418 (t0)
REVERT: A  101 LYS cc_start: 0.8191 (mttt) cc_final: 0.7782 (mptm)
REVERT: A  149 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7394 (pt0)
REVERT: B   19 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8283 (tttt)
REVERT: B   30 GLU cc_start: 0.7465 (pt0) cc_final: 0.6823 (pm20)
REVERT: B   59 ASN cc_start: 0.8270 (m-40) cc_final: 0.8052 (m110)
REVERT: B  210 LYS cc_start: 0.7612 (tttt) cc_final: 0.7018 (tptm)
REVERT: C   80 GLU cc_start: 0.8332 (pm20) cc_final: 0.7841 (pm20)
REVERT: C  122 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6468 (mt-10)
REVERT: D   85 MET cc_start: 0.6730 (mtt) cc_final: 0.6370 (mtt)
  outliers start: 18
  outliers final: 10
  residues processed: 97
  average time/residue: 0.6034
  time to fit residues: 60.9144
Evaluate side-chains
  93 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.192432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.136006 restraints weight = 5413.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.47
r_work: 0.3517 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5822  Z= 0.129
  Angle     :  0.503   7.264   7924  Z= 0.260
  Chirality :  0.041   0.149    863
  Planarity :  0.005   0.056   1014
  Dihedral  :  4.251  14.276    778
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.69 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.32), residues: 706
  helix:  1.73 (1.19), residues: 21
  sheet:  0.55 (0.27), residues: 343
  loop :  0.54 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  24 
 TYR   0.009   0.001   TYR C  85 
 PHE   0.014   0.002   PHE D  49 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5815)
  covalent geometry    : angle       0.50214 ( 7910)
  SS BOND              : bond        0.00310 (    7)
  SS BOND              : angle       0.73416 (   14)
  hydrogen bonds       : bond        0.03076 (  229)
  hydrogen bonds       : angle       5.23490 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8437 (t0)
REVERT: A  101 LYS cc_start: 0.8201 (mttt) cc_final: 0.7818 (mptm)
REVERT: A  133 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.5654 (mp-120)
REVERT: A  149 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7443 (pt0)
REVERT: B   19 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8307 (tttt)
REVERT: B   30 GLU cc_start: 0.7440 (pt0) cc_final: 0.6834 (pm20)
REVERT: B   59 ASN cc_start: 0.8316 (m-40) cc_final: 0.8080 (m110)
REVERT: B  210 LYS cc_start: 0.7656 (tttt) cc_final: 0.7069 (tptm)
REVERT: C   80 GLU cc_start: 0.8354 (pm20) cc_final: 0.7887 (pm20)
REVERT: C  122 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6473 (mt-10)
REVERT: D   40 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7687 (ptt180)
REVERT: D   85 MET cc_start: 0.6814 (mtt) cc_final: 0.6434 (mtt)
  outliers start: 19
  outliers final: 10
  residues processed: 90
  average time/residue: 0.6078
  time to fit residues: 56.8772
Evaluate side-chains
  90 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  133 GLN
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0050
   chunk 44 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.192556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.136197 restraints weight = 5439.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.48
r_work: 0.3519 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5822  Z= 0.130
  Angle     :  0.505   7.252   7924  Z= 0.260
  Chirality :  0.041   0.149    863
  Planarity :  0.005   0.056   1014
  Dihedral  :  4.267  14.295    778
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.85 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.32), residues: 706
  helix:  1.79 (1.21), residues: 21
  sheet:  0.57 (0.27), residues: 343
  loop :  0.55 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  24 
 TYR   0.009   0.001   TYR D  97 
 PHE   0.015   0.002   PHE D  49 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5815)
  covalent geometry    : angle       0.50413 ( 7910)
  SS BOND              : bond        0.00296 (    7)
  SS BOND              : angle       0.71093 (   14)
  hydrogen bonds       : bond        0.03075 (  229)
  hydrogen bonds       : angle       5.24987 (  627)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8440 (t0)
REVERT: A  101 LYS cc_start: 0.8191 (mttt) cc_final: 0.7857 (mptm)
REVERT: A  133 GLN cc_start: 0.6410 (mm-40) cc_final: 0.5724 (mp-120)
REVERT: A  149 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7447 (pt0)
REVERT: B   19 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8301 (tttt)
REVERT: B   30 GLU cc_start: 0.7424 (pt0) cc_final: 0.6832 (pm20)
REVERT: B   59 ASN cc_start: 0.8321 (m-40) cc_final: 0.8098 (m110)
REVERT: B  210 LYS cc_start: 0.7642 (tttt) cc_final: 0.7046 (tptm)
REVERT: C   80 GLU cc_start: 0.8377 (pm20) cc_final: 0.7902 (pm20)
REVERT: C  122 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6482 (mt-10)
REVERT: D   40 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7714 (ptt180)
REVERT: D   85 MET cc_start: 0.6752 (mtt) cc_final: 0.6365 (mtt)
  outliers start: 16
  outliers final: 10
  residues processed: 86
  average time/residue: 0.6392
  time to fit residues: 57.3314
Evaluate side-chains
  88 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.189926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133558 restraints weight = 5369.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.42
r_work: 0.3479 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   5822  Z= 0.201
  Angle     :  0.569   8.237   7924  Z= 0.293
  Chirality :  0.043   0.160    863
  Planarity :  0.005   0.073   1014
  Dihedral  :  4.599  16.026    778
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.38 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.32), residues: 706
  helix:  1.63 (1.19), residues: 21
  sheet:  0.43 (0.27), residues: 350
  loop :  0.39 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  24 
 TYR   0.012   0.002   TYR C  48 
 PHE   0.020   0.002   PHE D  49 
 TRP   0.010   0.001   TRP B  47 
 HIS   0.004   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 5815)
  covalent geometry    : angle       0.56776 ( 7910)
  SS BOND              : bond        0.00412 (    7)
  SS BOND              : angle       0.99086 (   14)
  hydrogen bonds       : bond        0.03531 (  229)
  hydrogen bonds       : angle       5.57719 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2832.10 seconds
wall clock time: 48 minutes 54.13 seconds (2934.13 seconds total)