Starting phenix.real_space_refine
on Wed Sep 17 09:43:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fx8_50843/09_2025/9fx8_50843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fx8_50843/09_2025/9fx8_50843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fx8_50843/09_2025/9fx8_50843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fx8_50843/09_2025/9fx8_50843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fx8_50843/09_2025/9fx8_50843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fx8_50843/09_2025/9fx8_50843.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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    4860      2.51       5
     N    1369      2.21       5
     O    1486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 7738
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1541
          Classifications: {'peptide': 198}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 183}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 5170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5170
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 24, 'TRANS': 640}
          Chain breaks: 7
    Chain: "I"
      Number of atoms: 1027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1027
          Classifications: {'peptide': 137}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 4
  Time building chain proxies: 1.74, per 1000 atoms: 0.22
  Number of scatterers: 7738
  At special positions: 0
  Unit cell: (93.84, 78.54, 128.52, 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    1486      8.00
     N    1369      7.00
     C    4860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 810 " - pdb=" SG  CYS D 832 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  24 " - pdb=" SG  CYS I  64 " 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: 0.69
  Conformation dependent library (CDL) restraints added in 523.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1812

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 15 sheets defined
      4.7% alpha, 30.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'C' and resid 127 through 131
    Processing helix  chain 'D' and resid 210 through 212
      No H-bonds generated for 'chain 'D' and resid 210 through 212'
    Processing helix  chain 'D' and resid 242 through 245
    Processing helix  chain 'D' and resid 360 through 362
      No H-bonds generated for 'chain 'D' and resid 360 through 362'
    Processing helix  chain 'D' and resid 387 through 389
      No H-bonds generated for 'chain 'D' and resid 387 through 389'
    Processing helix  chain 'D' and resid 558 through 560
      No H-bonds generated for 'chain 'D' and resid 558 through 560'
    Processing helix  chain 'D' and resid 567 through 571
      removed outlier: 3.598A  pdb=" N   HIS D 571 " --> pdb=" O   GLN D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 716 through 720
    Processing helix  chain 'D' and resid 817 through 822
    Processing helix  chain 'I' and resid 30 through 32
      No H-bonds generated for 'chain 'I' and resid 30 through 32'
    Processing helix  chain 'I' and resid 65 through 71
      removed outlier: 3.767A  pdb=" N   ARG I  71 " --> pdb=" O   VAL I  67 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4
    Processing sheet with id=AA2, first strand: chain 'C' and resid 8 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 8 through 12
    current: chain 'C' and resid 54 through 58
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 54 through 58
    current: chain 'C' and resid 102 through 116
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 34 through 36
    current: chain 'I' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'C' and resid 132 through 135
      removed outlier: 3.575A  pdb=" N   SER C 173 " --> pdb=" O   LEU C 142 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY C 171 " --> pdb=" O   ASN C 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 157
      removed outlier: 3.925A  pdb=" N   ARG C 160 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 160 through 161
    current: chain 'C' and resid 200 through 201
    Processing sheet with id=AA5, first strand: chain 'D' and resid 139 through 151
      removed outlier: 3.532A  pdb=" N   ALA D 139 " --> pdb=" O   ASN D 171 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER D 147 " --> pdb=" O   TYR D 163 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASP D 179 " --> pdb=" O   SER D 168 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   ARG D 176 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU D 205 " --> pdb=" O   ARG D 176 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ARG D 178 " --> pdb=" O   THR D 203 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   THR D 203 " --> pdb=" O   ARG D 178 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER D 184 " --> pdb=" O   LYS D 197 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LYS D 197 " --> pdb=" O   SER D 184 " (cutoff:3.500A)
      removed outlier: 16.192A  pdb=" N   ILE D 201 " --> pdb=" O   TYR D 222 " (cutoff:3.500A)
      removed outlier: 10.529A  pdb=" N   TYR D 222 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   THR D 203 " --> pdb=" O   ASP D 220 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU D 218 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 232 through 234
    current: chain 'D' and resid 332 through 334
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 332 through 334
    current: chain 'D' and resid 364 through 372
      removed outlier: 4.011A  pdb=" N   ALA D 377 " --> pdb=" O   GLN D 370 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TYR D 375 " --> pdb=" O   ALA D 372 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN D 398 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER D 407 " --> pdb=" O   LEU D 403 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 407 through 409
    current: chain 'D' and resid 430 through 437
      removed outlier: 5.366A  pdb=" N   ARG D 481 " --> pdb=" O   SER D 437 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER D 496 " --> pdb=" O   LEU D 492 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 496 through 500
    current: chain 'D' and resid 531 through 537
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 586 through 589
    current: chain 'D' and resid 603 through 604
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 603 through 604
    current: chain 'D' and resid 635 through 636
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 649 through 652
    current: chain 'D' and resid 662 through 666
    Processing sheet with id=AA6, first strand: chain 'D' and resid 259 through 260
      removed outlier: 3.702A  pdb=" N   ALA D 260 " --> pdb=" O   GLY D 283 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY D 283 " --> pdb=" O   ALA D 260 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 280
      removed outlier: 5.325A  pdb=" N   ASP D 274 " --> pdb=" O   GLN D 270 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   GLN D 270 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   TYR D 276 " --> pdb=" O   ILE D 268 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 622 through 624
    Processing sheet with id=AA9, first strand: chain 'D' and resid 699 through 702
      removed outlier: 3.761A  pdb=" N   VAL D 674 " --> pdb=" O   LEU D 702 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 713 through 714
    Processing sheet with id=AB2, first strand: chain 'D' and resid 724 through 726
    Processing sheet with id=AB3, first strand: chain 'D' and resid 751 through 756
      removed outlier: 5.358A  pdb=" N   ILE D 751 " --> pdb=" O   GLY D 791 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY D 791 " --> pdb=" O   ILE D 751 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 758 through 759
    Processing sheet with id=AB5, first strand: chain 'D' and resid 778 through 780
    Processing sheet with id=AB6, first strand: chain 'I' and resid 25 through 28
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 55 through 62
    current: chain 'I' and resid 98 through 106
      removed outlier: 5.833A  pdb=" N   ASN I  99 " --> pdb=" O   THR I 140 " (cutoff:3.500A)

    173 hydrogen bonds defined for protein.
    450 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2592
        1.34 -     1.46: 1506
        1.46 -     1.57: 3758
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 7898
  Sorted by residual:
  bond pdb=" N   VAL I  55 "
       pdb=" CA  VAL I  55 "
    ideal  model  delta    sigma   weight residual
    1.454  1.462 -0.007 7.70e-03 1.69e+04 8.54e-01
  bond pdb=" C   VAL D 280 "
       pdb=" O   VAL D 280 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.008 8.90e-03 1.26e+04 7.84e-01
  bond pdb=" CG  PRO C  52 "
       pdb=" CD  PRO C  52 "
    ideal  model  delta    sigma   weight residual
    1.512  1.492  0.020 2.70e-02 1.37e+03 5.64e-01
  bond pdb=" CA  LEU D 359 "
       pdb=" C   LEU D 359 "
    ideal  model  delta    sigma   weight residual
    1.517  1.524 -0.007 1.02e-02 9.61e+03 4.88e-01
  bond pdb=" CB  ASN D 171 "
       pdb=" CG  ASN D 171 "
    ideal  model  delta    sigma   weight residual
    1.516  1.499  0.017 2.50e-02 1.60e+03 4.78e-01
  ... (remaining 7893 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.86: 10144
        0.86 -     1.72: 486
        1.72 -     2.59: 54
        2.59 -     3.45: 41
        3.45 -     4.31: 5
  Bond angle restraints: 10730
  Sorted by residual:
  angle pdb=" N   VAL D 280 "
        pdb=" CA  VAL D 280 "
        pdb=" C   VAL D 280 "
      ideal   model   delta    sigma   weight residual
     107.61  110.50   -2.89 1.19e+00 7.06e-01 5.89e+00
  angle pdb=" C   ASN D 760 "
        pdb=" N   ASN D 761 "
        pdb=" CA  ASN D 761 "
      ideal   model   delta    sigma   weight residual
     121.54  125.49   -3.95 1.91e+00 2.74e-01 4.28e+00
  angle pdb=" C   THR D 279 "
        pdb=" N   VAL D 280 "
        pdb=" CA  VAL D 280 "
      ideal   model   delta    sigma   weight residual
     123.33  121.78    1.55 8.70e-01 1.32e+00 3.15e+00
  angle pdb=" N   VAL D 280 "
        pdb=" CA  VAL D 280 "
        pdb=" CB  VAL D 280 "
      ideal   model   delta    sigma   weight residual
     112.37  110.62    1.75 1.06e+00 8.90e-01 2.72e+00
  angle pdb=" N   ILE D 201 "
        pdb=" CA  ILE D 201 "
        pdb=" C   ILE D 201 "
      ideal   model   delta    sigma   weight residual
     109.34  112.45   -3.11 2.08e+00 2.31e-01 2.23e+00
  ... (remaining 10725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4295
       17.62 -    35.24: 311
       35.24 -    52.86: 30
       52.86 -    70.49: 17
       70.49 -    88.11: 3
  Dihedral angle restraints: 4656
    sinusoidal: 1810
      harmonic: 2846
  Sorted by residual:
  dihedral pdb=" CB  CYS D 810 "
           pdb=" SG  CYS D 810 "
           pdb=" SG  CYS D 832 "
           pdb=" CB  CYS D 832 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.36   60.36     1      1.00e+01 1.00e-02 4.85e+01
  dihedral pdb=" CG  ARG I 138 "
           pdb=" CD  ARG I 138 "
           pdb=" NE  ARG I 138 "
           pdb=" CZ  ARG I 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.94  -43.94     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CG  ARG D 742 "
           pdb=" CD  ARG D 742 "
           pdb=" NE  ARG D 742 "
           pdb=" CZ  ARG D 742 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.00  -41.00     2      1.50e+01 4.44e-03 9.18e+00
  ... (remaining 4653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 700
       0.027 -    0.055: 302
       0.055 -    0.082: 87
       0.082 -    0.110: 75
       0.110 -    0.137: 20
  Chirality restraints: 1184
  Sorted by residual:
  chirality pdb=" CA  VAL D 320 "
            pdb=" N   VAL D 320 "
            pdb=" C   VAL D 320 "
            pdb=" CB  VAL D 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  ILE D 128 "
            pdb=" N   ILE D 128 "
            pdb=" C   ILE D 128 "
            pdb=" CB  ILE D 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE D 637 "
            pdb=" N   ILE D 637 "
            pdb=" C   ILE D 637 "
            pdb=" CB  ILE D 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  ... (remaining 1181 not shown)

  Planarity restraints: 1405
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 320 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO D 321 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO D 321 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 321 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 359 "    0.020 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO D 360 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO D 360 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 360 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 197 "    0.019 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO C 198 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 198 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 198 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1402 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1971
        2.80 -     3.33: 6398
        3.33 -     3.85: 11956
        3.85 -     4.38: 13399
        4.38 -     4.90: 24492
  Nonbonded interactions: 58216
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 672 "
            pdb=" O   ALA D 705 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASN D 186 "
            pdb=" OG  SER D 188 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OD2 ASP D 395 "
            pdb=" NH2 ARG D 415 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" OG  SER D 575 "
            pdb=" O   GLY D 591 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OG  SER C 136 "
            pdb=" OG  SER C 139 "
     model   vdw
     2.341 3.040
  ... (remaining 58211 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:             1.730
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.780
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7900  Z= 0.146
  Angle     :  0.449   4.309  10734  Z= 0.238
  Chirality :  0.041   0.137   1184
  Planarity :  0.003   0.034   1405
  Dihedral  : 12.092  88.107   2838
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.27), residues: 970
  helix: -1.68 (2.00), residues: 6
  sheet: -1.39 (0.23), residues: 505
  loop : -0.39 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 339 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.012   0.002   PHE D 416 
 TRP   0.013   0.001   TRP D 530 
 HIS   0.003   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7898)
  covalent geometry    : angle       0.44868 (10730)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.53276 (    4)
  hydrogen bonds       : bond        0.25771 (  173)
  hydrogen bonds       : angle      11.83367 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   72 ASN cc_start: 0.7860 (m-40) cc_final: 0.7541 (t0)
REVERT: C  130 LYS cc_start: 0.8490 (mttm) cc_final: 0.8166 (mptt)
REVERT: C  154 GLU cc_start: 0.8896 (tt0) cc_final: 0.8688 (tt0)
REVERT: D  300 GLN cc_start: 0.7478 (tt0) cc_final: 0.7113 (tm-30)
REVERT: D  382 ILE cc_start: 0.8685 (tt) cc_final: 0.8262 (pt)
REVERT: D  529 ASN cc_start: 0.7779 (t0) cc_final: 0.7463 (t0)
REVERT: D  546 ASP cc_start: 0.8065 (t0) cc_final: 0.7674 (t70)
REVERT: D  687 GLU cc_start: 0.7845 (tp30) cc_final: 0.7632 (tp30)
REVERT: D  728 ASN cc_start: 0.8325 (m-40) cc_final: 0.7786 (p0)
REVERT: D  730 VAL cc_start: 0.9566 (t) cc_final: 0.9274 (m)
REVERT: D  821 GLN cc_start: 0.7818 (mt0) cc_final: 0.7538 (tm-30)
REVERT: I   22 GLU cc_start: 0.8405 (pt0) cc_final: 0.8106 (pt0)
REVERT: I   33 MET cc_start: 0.8192 (mmt) cc_final: 0.7154 (mtt)
REVERT: I  121 TRP cc_start: 0.6210 (m-90) cc_final: 0.5853 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0919
  time to fit residues: 15.8987
Evaluate side-chains
  90 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.161127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133053 restraints weight = 8406.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.131490 restraints weight = 11825.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133263 restraints weight = 11512.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.133025 restraints weight = 8038.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.133274 restraints weight = 7849.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7900  Z= 0.183
  Angle     :  0.521   5.432  10734  Z= 0.280
  Chirality :  0.043   0.148   1184
  Planarity :  0.004   0.041   1405
  Dihedral  :  3.753  31.876   1085
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.61 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.27), residues: 970
  helix: -2.93 (1.31), residues: 6
  sheet: -1.36 (0.23), residues: 510
  loop : -0.36 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 494 
 TYR   0.017   0.001   TYR I 159 
 PHE   0.011   0.002   PHE D 416 
 TRP   0.007   0.001   TRP D 204 
 HIS   0.003   0.001   HIS D 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7898)
  covalent geometry    : angle       0.52111 (10730)
  SS BOND              : bond        0.00299 (    2)
  SS BOND              : angle       0.63923 (    4)
  hydrogen bonds       : bond        0.04075 (  173)
  hydrogen bonds       : angle       7.80608 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   45 ASP cc_start: 0.7834 (t0) cc_final: 0.7529 (m-30)
REVERT: D  213 ARG cc_start: 0.8038 (mpt180) cc_final: 0.7836 (ttm-80)
REVERT: D  529 ASN cc_start: 0.7546 (t0) cc_final: 0.7301 (t0)
REVERT: D  546 ASP cc_start: 0.7955 (t0) cc_final: 0.7678 (t70)
REVERT: D  578 MET cc_start: 0.6640 (tpt) cc_final: 0.6216 (tpt)
REVERT: D  728 ASN cc_start: 0.8115 (m-40) cc_final: 0.7693 (p0)
REVERT: D  730 VAL cc_start: 0.9412 (t) cc_final: 0.9055 (m)
REVERT: I   33 MET cc_start: 0.8263 (mmt) cc_final: 0.7581 (mtt)
  outliers start: 8
  outliers final: 3
  residues processed: 96
  average time/residue: 0.0894
  time to fit residues: 11.9089
Evaluate side-chains
  83 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  637 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0570
   overall best weight:    1.7504

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

Flipped N/Q/H residues before XYZ refinement:
C  72 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 ASN
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 554 ASN
I  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.160620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.138044 restraints weight = 8502.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135523 restraints weight = 14597.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.136533 restraints weight = 14390.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.135984 restraints weight = 10335.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.136130 restraints weight = 10941.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   7900  Z= 0.240
  Angle     :  0.565   4.984  10734  Z= 0.306
  Chirality :  0.045   0.159   1184
  Planarity :  0.005   0.046   1405
  Dihedral  :  4.120  31.654   1085
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.67 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.27), residues: 970
  helix: -4.28 (0.71), residues: 6
  sheet: -1.45 (0.23), residues: 512
  loop : -0.52 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 215 
 TYR   0.017   0.002   TYR I 159 
 PHE   0.017   0.002   PHE D 350 
 TRP   0.009   0.001   TRP D 204 
 HIS   0.005   0.001   HIS D 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 7898)
  covalent geometry    : angle       0.56521 (10730)
  SS BOND              : bond        0.00352 (    2)
  SS BOND              : angle       0.72604 (    4)
  hydrogen bonds       : bond        0.03566 (  173)
  hydrogen bonds       : angle       7.09962 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 ASN cc_start: 0.8761 (p0) cc_final: 0.8533 (p0)
REVERT: C   45 ASP cc_start: 0.7762 (t0) cc_final: 0.7435 (m-30)
REVERT: D  529 ASN cc_start: 0.7504 (t0) cc_final: 0.7217 (t0)
REVERT: D  546 ASP cc_start: 0.7906 (t0) cc_final: 0.7679 (t70)
REVERT: D  650 TYR cc_start: 0.7847 (p90) cc_final: 0.7473 (p90)
REVERT: D  728 ASN cc_start: 0.8067 (m-40) cc_final: 0.7651 (p0)
REVERT: D  730 VAL cc_start: 0.9329 (t) cc_final: 0.8962 (m)
REVERT: I   33 MET cc_start: 0.8245 (mmt) cc_final: 0.7648 (mtt)
  outliers start: 16
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0920
  time to fit residues: 12.8229
Evaluate side-chains
  96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  226 ASP
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  386 MET
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  783 ASP
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 90 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
C  86 ASN
C 138 ASN
D 196 ASN
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.163439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.142780 restraints weight = 8478.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.141363 restraints weight = 13115.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.138400 restraints weight = 12451.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.134959 restraints weight = 11557.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.135924 restraints weight = 9884.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7900  Z= 0.128
  Angle     :  0.473   4.232  10734  Z= 0.254
  Chirality :  0.043   0.149   1184
  Planarity :  0.004   0.047   1405
  Dihedral  :  3.744  27.428   1085
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.12 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.26), residues: 970
  helix: -4.43 (0.61), residues: 6
  sheet: -1.37 (0.23), residues: 510
  loop : -0.46 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 213 
 TYR   0.012   0.001   TYR D 366 
 PHE   0.009   0.001   PHE D 416 
 TRP   0.007   0.001   TRP D 204 
 HIS   0.002   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7898)
  covalent geometry    : angle       0.47335 (10730)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.52230 (    4)
  hydrogen bonds       : bond        0.02908 (  173)
  hydrogen bonds       : angle       6.52906 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: C   45 ASP cc_start: 0.7816 (t0) cc_final: 0.7525 (m-30)
REVERT: D  728 ASN cc_start: 0.8045 (m-40) cc_final: 0.7643 (p0)
REVERT: D  730 VAL cc_start: 0.9364 (t) cc_final: 0.9026 (m)
REVERT: D  755 MET cc_start: 0.8693 (mtm) cc_final: 0.8347 (mtm)
REVERT: I   33 MET cc_start: 0.8338 (mmt) cc_final: 0.7581 (mtt)
  outliers start: 16
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0818
  time to fit residues: 11.1629
Evaluate side-chains
  85 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  196 ASN
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain I residue   22 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 86 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0970
   chunk 5 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
D 196 ASN
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.164264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.143389 restraints weight = 8404.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142036 restraints weight = 12529.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.141999 restraints weight = 12387.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.141418 restraints weight = 9797.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.141621 restraints weight = 9479.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7900  Z= 0.110
  Angle     :  0.460   4.302  10734  Z= 0.246
  Chirality :  0.042   0.146   1184
  Planarity :  0.004   0.045   1405
  Dihedral  :  3.565  24.481   1085
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.00 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.27), residues: 970
  helix: -4.41 (0.64), residues: 6
  sheet: -1.28 (0.23), residues: 515
  loop : -0.40 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 138 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.009   0.001   PHE D 442 
 TRP   0.006   0.001   TRP D 204 
 HIS   0.002   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7898)
  covalent geometry    : angle       0.46038 (10730)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.46992 (    4)
  hydrogen bonds       : bond        0.02721 (  173)
  hydrogen bonds       : angle       6.18913 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.288 
Fit side-chains
REVERT: C   45 ASP cc_start: 0.7769 (t0) cc_final: 0.7500 (m-30)
REVERT: C  160 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7715 (ptp-110)
REVERT: D  728 ASN cc_start: 0.7944 (m-40) cc_final: 0.7558 (p0)
REVERT: D  730 VAL cc_start: 0.9380 (t) cc_final: 0.9039 (m)
REVERT: D  744 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6893 (pt0)
REVERT: I   33 MET cc_start: 0.8240 (mmt) cc_final: 0.7643 (mtt)
REVERT: I  121 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.6504 (m-90)
  outliers start: 19
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0814
  time to fit residues: 11.1683
Evaluate side-chains
  94 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  396 MET
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  672 THR
Chi-restraints excluded: chain D residue  744 GLU
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Chi-restraints excluded: chain I residue  121 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 73 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
C 138 ASN
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 559 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.159794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.138497 restraints weight = 8519.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136893 restraints weight = 12525.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.137191 restraints weight = 11923.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.136504 restraints weight = 9480.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.136800 restraints weight = 9091.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7900  Z= 0.181
  Angle     :  0.503   4.414  10734  Z= 0.271
  Chirality :  0.043   0.153   1184
  Planarity :  0.004   0.046   1405
  Dihedral  :  3.726  24.366   1085
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.73 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.26), residues: 970
  helix: -4.58 (0.55), residues: 6
  sheet: -1.38 (0.23), residues: 515
  loop : -0.44 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I 138 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.012   0.002   PHE D 350 
 TRP   0.007   0.001   TRP D 204 
 HIS   0.003   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 7898)
  covalent geometry    : angle       0.50273 (10730)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.62350 (    4)
  hydrogen bonds       : bond        0.02809 (  173)
  hydrogen bonds       : angle       6.23749 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.258 
Fit side-chains
REVERT: C   45 ASP cc_start: 0.7772 (t0) cc_final: 0.7485 (m-30)
REVERT: D  650 TYR cc_start: 0.7741 (p90) cc_final: 0.7368 (p90)
REVERT: D  728 ASN cc_start: 0.7967 (m-40) cc_final: 0.7575 (p0)
REVERT: D  730 VAL cc_start: 0.9373 (t) cc_final: 0.9021 (m)
REVERT: I   33 MET cc_start: 0.8293 (mmt) cc_final: 0.7668 (mtt)
REVERT: I  121 TRP cc_start: 0.7225 (OUTLIER) cc_final: 0.6538 (m-90)
  outliers start: 21
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0808
  time to fit residues: 11.5282
Evaluate side-chains
  90 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  578 MET
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  672 THR
Chi-restraints excluded: chain D residue  744 GLU
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Chi-restraints excluded: chain I residue  121 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0470
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3884

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

Flipped N/Q/H residues before XYZ refinement:
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 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 = 0.3768 r_free = 0.3768 target = 0.158755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.137679 restraints weight = 8523.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.136084 restraints weight = 13529.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.135934 restraints weight = 13356.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.134729 restraints weight = 11484.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.135112 restraints weight = 10803.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7900  Z= 0.194
  Angle     :  0.522   6.665  10734  Z= 0.281
  Chirality :  0.044   0.154   1184
  Planarity :  0.004   0.047   1405
  Dihedral  :  3.837  24.683   1085
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.21 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.26), residues: 970
  helix: -4.65 (0.51), residues: 6
  sheet: -1.43 (0.23), residues: 510
  loop : -0.58 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 215 
 TYR   0.012   0.001   TYR D 366 
 PHE   0.012   0.002   PHE D 745 
 TRP   0.008   0.001   TRP D 204 
 HIS   0.003   0.001   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 7898)
  covalent geometry    : angle       0.52228 (10730)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.70153 (    4)
  hydrogen bonds       : bond        0.02817 (  173)
  hydrogen bonds       : angle       6.23376 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.330 
Fit side-chains
REVERT: C   45 ASP cc_start: 0.7784 (t0) cc_final: 0.7475 (m-30)
REVERT: D  650 TYR cc_start: 0.7668 (p90) cc_final: 0.7300 (p90)
REVERT: D  728 ASN cc_start: 0.7966 (m-40) cc_final: 0.7575 (p0)
REVERT: D  730 VAL cc_start: 0.9385 (t) cc_final: 0.9019 (m)
REVERT: I   33 MET cc_start: 0.8340 (mmt) cc_final: 0.7729 (mtt)
REVERT: I  121 TRP cc_start: 0.7247 (OUTLIER) cc_final: 0.6515 (m-90)
  outliers start: 21
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0857
  time to fit residues: 12.3071
Evaluate side-chains
  96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  578 MET
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  672 THR
Chi-restraints excluded: chain D residue  744 GLU
Chi-restraints excluded: chain D residue  757 LEU
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Chi-restraints excluded: chain I residue  121 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0470
   chunk 96 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    0.4980
   chunk 32 optimal weight:    8.9990
   overall best weight:    1.0882

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

Flipped N/Q/H residues before XYZ refinement:
C  77 GLN
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 583 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.159605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.136790 restraints weight = 8496.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.135091 restraints weight = 12634.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134708 restraints weight = 12433.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.134152 restraints weight = 11174.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.134531 restraints weight = 10056.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7900  Z= 0.162
  Angle     :  0.511   6.373  10734  Z= 0.275
  Chirality :  0.043   0.151   1184
  Planarity :  0.004   0.046   1405
  Dihedral  :  3.780  23.520   1085
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.18 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.26), residues: 970
  helix: -4.66 (0.49), residues: 6
  sheet: -1.37 (0.23), residues: 508
  loop : -0.56 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 494 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.010   0.001   PHE D 745 
 TRP   0.007   0.001   TRP D 204 
 HIS   0.003   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7898)
  covalent geometry    : angle       0.51115 (10730)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.61513 (    4)
  hydrogen bonds       : bond        0.02763 (  173)
  hydrogen bonds       : angle       6.15921 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C   45 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7502 (m-30)
REVERT: D  687 GLU cc_start: 0.7712 (tp30) cc_final: 0.7394 (tp30)
REVERT: D  728 ASN cc_start: 0.7993 (m-40) cc_final: 0.7594 (p0)
REVERT: D  730 VAL cc_start: 0.9416 (t) cc_final: 0.9057 (m)
REVERT: I   33 MET cc_start: 0.8365 (mmt) cc_final: 0.7746 (mtt)
REVERT: I  121 TRP cc_start: 0.6982 (OUTLIER) cc_final: 0.6295 (m-90)
  outliers start: 20
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0857
  time to fit residues: 11.2755
Evaluate side-chains
  92 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  578 MET
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  672 THR
Chi-restraints excluded: chain D residue  744 GLU
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Chi-restraints excluded: chain I residue  121 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 53 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 711 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.159796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135778 restraints weight = 8436.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.133642 restraints weight = 13239.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135292 restraints weight = 12915.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.134418 restraints weight = 9211.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.135288 restraints weight = 9114.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7900  Z= 0.162
  Angle     :  0.513   6.235  10734  Z= 0.275
  Chirality :  0.043   0.150   1184
  Planarity :  0.004   0.046   1405
  Dihedral  :  3.750  22.752   1085
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.55 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.26), residues: 970
  helix: -4.68 (0.48), residues: 6
  sheet: -1.38 (0.23), residues: 509
  loop : -0.58 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 494 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.010   0.002   PHE D 745 
 TRP   0.008   0.001   TRP D 204 
 HIS   0.003   0.001   HIS D 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7898)
  covalent geometry    : angle       0.51256 (10730)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.61132 (    4)
  hydrogen bonds       : bond        0.02720 (  173)
  hydrogen bonds       : angle       6.08756 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C   45 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7517 (m-30)
REVERT: D  728 ASN cc_start: 0.7988 (m-40) cc_final: 0.7608 (p0)
REVERT: D  730 VAL cc_start: 0.9433 (t) cc_final: 0.9060 (m)
REVERT: I   33 MET cc_start: 0.8393 (mmt) cc_final: 0.7749 (mtt)
REVERT: I  121 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.6251 (m-90)
  outliers start: 19
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0874
  time to fit residues: 11.1919
Evaluate side-chains
  91 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  578 MET
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  672 THR
Chi-restraints excluded: chain D residue  711 ASN
Chi-restraints excluded: chain D residue  744 GLU
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Chi-restraints excluded: chain I residue  121 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 72 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0470
   chunk 50 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 96 optimal weight:    5.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 583 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.161432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137980 restraints weight = 8394.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136676 restraints weight = 12162.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.136642 restraints weight = 12313.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.135345 restraints weight = 11134.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.136756 restraints weight = 9792.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7900  Z= 0.112
  Angle     :  0.493   6.452  10734  Z= 0.264
  Chirality :  0.043   0.146   1184
  Planarity :  0.004   0.046   1405
  Dihedral  :  3.634  21.249   1085
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.91 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.27), residues: 970
  helix:  None (None), residues: 0
  sheet: -1.35 (0.23), residues: 519
  loop : -0.37 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 494 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.023   0.001   PHE D 380 
 TRP   0.006   0.001   TRP D 204 
 HIS   0.002   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7898)
  covalent geometry    : angle       0.49330 (10730)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       0.51200 (    4)
  hydrogen bonds       : bond        0.02639 (  173)
  hydrogen bonds       : angle       5.91353 (  450)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.292 
Fit side-chains
REVERT: C   45 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7469 (m-30)
REVERT: D  728 ASN cc_start: 0.7967 (m-40) cc_final: 0.7602 (p0)
REVERT: D  730 VAL cc_start: 0.9400 (t) cc_final: 0.9022 (m)
REVERT: I   33 MET cc_start: 0.8302 (mmt) cc_final: 0.7679 (mtt)
REVERT: I  121 TRP cc_start: 0.6862 (OUTLIER) cc_final: 0.6188 (m-90)
  outliers start: 18
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0858
  time to fit residues: 11.2171
Evaluate side-chains
  94 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  295 ASN
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  396 MET
Chi-restraints excluded: chain D residue  578 MET
Chi-restraints excluded: chain D residue  583 ASN
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  637 ILE
Chi-restraints excluded: chain D residue  672 THR
Chi-restraints excluded: chain D residue  744 GLU
Chi-restraints excluded: chain I residue   22 GLU
Chi-restraints excluded: chain I residue   79 VAL
Chi-restraints excluded: chain I residue  121 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0010
   chunk 59 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 93 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 412 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 = 0.3794 r_free = 0.3794 target = 0.161386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137757 restraints weight = 8350.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.135570 restraints weight = 13244.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.135427 restraints weight = 12651.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.134194 restraints weight = 9768.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.134511 restraints weight = 9174.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.202   7900  Z= 0.250
  Angle     :  0.900  59.198  10734  Z= 0.548
  Chirality :  0.045   0.491   1184
  Planarity :  0.004   0.046   1405
  Dihedral  :  3.641  21.233   1085
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.91 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.26), residues: 970
  helix:  None (None), residues: 0
  sheet: -1.33 (0.23), residues: 518
  loop : -0.39 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 494 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.015   0.001   PHE D 380 
 TRP   0.006   0.001   TRP D 204 
 HIS   0.002   0.001   HIS I  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 7898)
  covalent geometry    : angle       0.90043 (10730)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.50910 (    4)
  hydrogen bonds       : bond        0.02639 (  173)
  hydrogen bonds       : angle       5.91248 (  450)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1317.89 seconds
wall clock time: 23 minutes 33.08 seconds (1413.08 seconds total)