Starting phenix.real_space_refine
on Sun May 11 20:31:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kej_37160/05_2025/8kej_37160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kej_37160/05_2025/8kej_37160.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kej_37160/05_2025/8kej_37160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kej_37160/05_2025/8kej_37160.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kej_37160/05_2025/8kej_37160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kej_37160/05_2025/8kej_37160.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.031
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      35      5.16       5
     C    5332      2.51       5
     N    1394      2.21       5
     O    1616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8377
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 1638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1638
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1653
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 12, 'TRANS': 200}
    Chain: "A"
      Number of atoms: 5086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 644, 5086
          Classifications: {'peptide': 644}
          Link IDs: {'PTRANS': 33, 'TRANS': 610}
          Chain breaks: 2
  Time building chain proxies: 5.02, per 1000 atoms: 0.60
  Number of scatterers: 8377
  At special positions: 0
  Unit cell: (93.2, 115.568, 157.508, 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      35     16.00
     O    1616      8.00
     N    1394      7.00
     C    5332      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 132 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " 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: 2.01
  Conformation dependent library (CDL) restraints added in 988.7 milliseconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2006

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 22 sheets defined
      4.1% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'H' and resid 134 through 138
      removed outlier: 4.126A  pdb=" N   THR H 138 " --> pdb=" O   SER H 135 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 163 through 165
      No H-bonds generated for 'chain 'H' and resid 163 through 165'
    Processing helix  chain 'H' and resid 194 through 196
      No H-bonds generated for 'chain 'H' and resid 194 through 196'
    Processing helix  chain 'L' and resid 123 through 129
      removed outlier: 3.659A  pdb=" N   SER L 129 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 191
      removed outlier: 3.695A  pdb=" N   HIS L 191 " --> pdb=" O   ASP L 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 3.690A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
      removed outlier: 3.604A  pdb=" N   LEU H  83 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.840A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET H  34 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL H  50 " --> pdb=" O   THR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 131
    Processing sheet with id=AA4, first strand: chain 'H' and resid 160 through 161
    Processing sheet with id=AA5, first strand: chain 'H' and resid 176 through 177
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.568A  pdb=" N   LEU L  13 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 20 through 22
      removed outlier: 3.797A  pdb=" N   LEU L  21 " --> pdb=" O   LEU L  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 49
      removed outlier: 5.583A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120
      removed outlier: 5.979A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 155 through 157
      removed outlier: 4.349A  pdb=" N   TRP L 150 " --> pdb=" O   GLN L 157 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS L 147 " --> pdb=" O   THR L 199 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR L 199 " --> pdb=" O   LYS L 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 29 through 31
      removed outlier: 3.832A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 49 through 56
      removed outlier: 4.213A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 72
      removed outlier: 3.609A  pdb=" N   VAL A  71 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 90 through 91
      removed outlier: 3.669A  pdb=" N   ARG A 190 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 90 through 91
      removed outlier: 3.949A  pdb=" N   GLU A 191 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LYS A 206 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A 193 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLU A 224 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 166 through 170
      removed outlier: 3.536A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ILE A 129 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   TRP A 105 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.609A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AC1, first strand: chain 'A' and resid 541 through 543
      removed outlier: 3.794A  pdb=" N   LEU A 546 " --> pdb=" O   PHE A 543 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 551 through 554
    Processing sheet with id=AC3, first strand: chain 'A' and resid 594 through 598
    Processing sheet with id=AC4, first strand: chain 'A' and resid 654 through 655
      removed outlier: 5.964A  pdb=" N   GLU A 654 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   THR A 696 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 691 " --> pdb=" O   GLN A 675 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLN A 675 " --> pdb=" O   SER A 691 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)

    182 hydrogen bonds defined for protein.
    471 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: 2.34

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2594
        1.34 -     1.45: 1450
        1.45 -     1.57: 4501
        1.57 -     1.69: 0
        1.69 -     1.81: 43
  Bond restraints: 8588
  Sorted by residual:
  bond pdb=" N   GLU L 145 "
       pdb=" CA  GLU L 145 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 9.10e-03 1.21e+04 9.65e+00
  bond pdb=" N   VAL A 595 "
       pdb=" CA  VAL A 595 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 1.10e-02 8.26e+03 9.42e+00
  bond pdb=" N   ASN L 139 "
       pdb=" CA  ASN L 139 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.23e-02 6.61e+03 8.76e+00
  bond pdb=" N   LEU A 585 "
       pdb=" CA  LEU A 585 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.035 1.25e-02 6.40e+03 7.65e+00
  bond pdb=" N   ARG L 144 "
       pdb=" CA  ARG L 144 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.96e+00
  ... (remaining 8583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 10981
        1.24 -     2.49: 542
        2.49 -     3.73: 137
        3.73 -     4.98: 22
        4.98 -     6.22: 7
  Bond angle restraints: 11689
  Sorted by residual:
  angle pdb=" CA  PHE L 141 "
        pdb=" CB  PHE L 141 "
        pdb=" CG  PHE L 141 "
      ideal   model   delta    sigma   weight residual
     113.80  117.84   -4.04 1.00e+00 1.00e+00 1.64e+01
  angle pdb=" N   GLU L 145 "
        pdb=" CA  GLU L 145 "
        pdb=" C   GLU L 145 "
      ideal   model   delta    sigma   weight residual
     112.99  106.78    6.21 1.61e+00 3.86e-01 1.49e+01
  angle pdb=" C   TYR L 142 "
        pdb=" N   PRO L 143 "
        pdb=" CA  PRO L 143 "
      ideal   model   delta    sigma   weight residual
     119.84  124.53   -4.69 1.25e+00 6.40e-01 1.41e+01
  angle pdb=" C   PHE H 102 "
        pdb=" N   ILE H 103 "
        pdb=" CA  ILE H 103 "
      ideal   model   delta    sigma   weight residual
     120.43  123.97   -3.54 9.60e-01 1.09e+00 1.36e+01
  angle pdb=" CA  TYR L 142 "
        pdb=" C   TYR L 142 "
        pdb=" O   TYR L 142 "
      ideal   model   delta    sigma   weight residual
     120.87  116.94    3.93 1.10e+00 8.26e-01 1.28e+01
  ... (remaining 11684 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 4840
       17.31 -    34.63: 212
       34.63 -    51.94: 39
       51.94 -    69.25: 9
       69.25 -    86.56: 1
  Dihedral angle restraints: 5101
    sinusoidal: 1970
      harmonic: 3131
  Sorted by residual:
  dihedral pdb=" CA  PRO A 589 "
           pdb=" C   PRO A 589 "
           pdb=" N   CYS A 590 "
           pdb=" CA  CYS A 590 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.63  -24.37     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CB  GLU A 281 "
           pdb=" CG  GLU A 281 "
           pdb=" CD  GLU A 281 "
           pdb=" OE1 GLU A 281 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.56  -86.56     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CG  ARG L 144 "
           pdb=" CD  ARG L 144 "
           pdb=" NE  ARG L 144 "
           pdb=" CZ  ARG L 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.73  -43.27     2      1.50e+01 4.44e-03 1.00e+01
  ... (remaining 5098 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1087
       0.055 -    0.110: 197
       0.110 -    0.165: 15
       0.165 -    0.220: 2
       0.220 -    0.275: 1
  Chirality restraints: 1302
  Sorted by residual:
  chirality pdb=" CA  LEU A 585 "
            pdb=" N   LEU A 585 "
            pdb=" C   LEU A 585 "
            pdb=" CB  LEU A 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  GLU L 145 "
            pdb=" N   GLU L 145 "
            pdb=" C   GLU L 145 "
            pdb=" CB  GLU L 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CA  LYS L 147 "
            pdb=" N   LYS L 147 "
            pdb=" C   LYS L 147 "
            pdb=" CB  LYS L 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 1299 not shown)

  Planarity restraints: 1507
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 520 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO A 521 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 521 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 521 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.019 5.00e-02 4.00e+02   2.89e-02 1.33e+00
        pdb=" N   PRO A 463 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 329 "   -0.019 5.00e-02 4.00e+02   2.81e-02 1.27e+00
        pdb=" N   PRO A 330 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 330 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 330 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1504 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1685
        2.78 -     3.31: 7447
        3.31 -     3.84: 13495
        3.84 -     4.37: 15093
        4.37 -     4.90: 26493
  Nonbonded interactions: 64213
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L 107 "
            pdb=" OH  TYR L 175 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR A 430 "
            pdb=" O   PHE A 515 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR L  32 "
            pdb=" OD1 ASP A 428 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   VAL H 149 "
            pdb=" OG  SER H 184 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   TYR L 188 "
            pdb=" OH  TYR L 194 "
     model   vdw
     2.299 3.040
  ... (remaining 64208 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.410
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5604
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   0.046   8600  Z= 0.195
  Angle     :  0.653   6.219  11713  Z= 0.417
  Chirality :  0.042   0.275   1302
  Planarity :  0.003   0.033   1507
  Dihedral  :  9.634  86.563   3059
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.70 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  :  7.35 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.21), residues: 1065
  helix: -2.47 (0.70), residues: 31
  sheet: -2.40 (0.25), residues: 322
  loop : -3.20 (0.19), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A 353 
 HIS   0.001   0.000   HIS L  90 
 PHE   0.018   0.001   PHE L 141 
 TYR   0.007   0.001   TYR L 142 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28674 (  180)
  hydrogen bonds       : angle      11.18339 (  471)
  SS BOND              : bond        0.00125 (   12)
  SS BOND              : angle       0.34960 (   24)
  covalent geometry    : bond        0.00295 ( 8588)
  covalent geometry    : angle       0.65302 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 228
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   59 THR cc_start: 0.8256 (m) cc_final: 0.7505 (p)
REVERT: H   85 SER cc_start: 0.7685 (t) cc_final: 0.7411 (p)
REVERT: H   91 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (p)
REVERT: H  117 LEU cc_start: 0.8193 (tp) cc_final: 0.7982 (tp)
REVERT: H  176 VAL cc_start: 0.7815 (t) cc_final: 0.7526 (p)
REVERT: H  200 THR cc_start: 0.8462 (m) cc_final: 0.8140 (t)
REVERT: H  201 TYR cc_start: 0.6469 (m-80) cc_final: 0.6173 (m-80)
REVERT: L  120 PHE cc_start: 0.7454 (m-80) cc_final: 0.7248 (m-80)
REVERT: L  164 SER cc_start: 0.8213 (t) cc_final: 0.7648 (p)
REVERT: L  171 LYS cc_start: 0.8395 (mttt) cc_final: 0.8190 (mttt)
REVERT: L  178 SER cc_start: 0.8267 (t) cc_final: 0.8028 (p)
REVERT: A   57 LEU cc_start: 0.7331 (tp) cc_final: 0.7046 (tp)
REVERT: A  203 ILE cc_start: 0.6012 (mt) cc_final: 0.5713 (mm)
REVERT: A  357 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.7279 (ptm-80)
REVERT: A  359 SER cc_start: 0.7902 (p) cc_final: 0.7655 (p)
REVERT: A  436 TRP cc_start: 0.7417 (p90) cc_final: 0.6776 (p90)
REVERT: A  448 ASN cc_start: 0.6863 (m110) cc_final: 0.6514 (m-40)
REVERT: A  460 LYS cc_start: 0.7776 (mptm) cc_final: 0.7525 (mptm)
REVERT: A  510 VAL cc_start: 0.8205 (t) cc_final: 0.7817 (m)
REVERT: A  511 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7488 (m)
REVERT: A  524 VAL cc_start: 0.5265 (OUTLIER) cc_final: 0.4634 (t)
REVERT: A  585 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5278 (pp)
REVERT: A  592 PHE cc_start: 0.0518 (OUTLIER) cc_final: -0.0528 (m-80)
  outliers start: 54
  outliers final: 19
  residues processed: 267
  average time/residue: 0.2190
  time to fit residues: 78.3331
Evaluate side-chains
  227 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   33 TYR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  677 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0370
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    0.0010
   overall best weight:    0.7866

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

Flipped N/Q/H residues before XYZ refinement:
H 114 GLN
H 171 HIS
L  38 GLN
L  42 GLN
L 102 GLN
L 168 GLN
A  53 GLN
A 173 GLN
A 354 ASN
A 409 GLN
A 414 GLN
A 422 ASN
A 450 ASN
A 487 ASN
A 613 GLN
A 675 GLN
A 677 GLN
A 690 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.218450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.184226 restraints weight = 18342.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.189666 restraints weight = 9623.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.193109 restraints weight = 5761.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5754
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8600  Z= 0.147
  Angle     :  0.609  10.588  11713  Z= 0.312
  Chirality :  0.045   0.168   1302
  Planarity :  0.005   0.055   1507
  Dihedral  :  7.084  87.745   1217
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 12.46 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.22), residues: 1065
  helix: -1.49 (0.87), residues: 25
  sheet: -1.76 (0.27), residues: 318
  loop : -2.84 (0.20), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  94 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.017   0.001   PHE A 377 
 TYR   0.017   0.001   TYR A 265 
 ARG   0.003   0.000   ARG L  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04536 (  180)
  hydrogen bonds       : angle       7.73295 (  471)
  SS BOND              : bond        0.00492 (   12)
  SS BOND              : angle       1.24657 (   24)
  covalent geometry    : bond        0.00339 ( 8588)
  covalent geometry    : angle       0.60667 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 217
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7770 (mp) cc_final: 0.7024 (tt)
REVERT: H   29 PHE cc_start: 0.8010 (t80) cc_final: 0.7810 (t80)
REVERT: H   68 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8051 (t)
REVERT: H   85 SER cc_start: 0.7734 (t) cc_final: 0.7298 (p)
REVERT: H  103 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.6141 (mt)
REVERT: H  117 LEU cc_start: 0.8204 (tp) cc_final: 0.7989 (tp)
REVERT: H  148 LEU cc_start: 0.8093 (tt) cc_final: 0.7861 (tt)
REVERT: H  160 SER cc_start: 0.8011 (p) cc_final: 0.7721 (t)
REVERT: H  176 VAL cc_start: 0.7688 (t) cc_final: 0.7250 (p)
REVERT: H  189 VAL cc_start: 0.8654 (t) cc_final: 0.8263 (p)
REVERT: H  200 THR cc_start: 0.8519 (m) cc_final: 0.8172 (t)
REVERT: H  201 TYR cc_start: 0.6454 (m-80) cc_final: 0.6160 (m-80)
REVERT: L   11 LEU cc_start: 0.7595 (tp) cc_final: 0.7355 (mm)
REVERT: L   14 SER cc_start: 0.8131 (t) cc_final: 0.7915 (m)
REVERT: L   46 LEU cc_start: 0.8044 (tp) cc_final: 0.7727 (tp)
REVERT: L   82 ASP cc_start: 0.8199 (m-30) cc_final: 0.7989 (m-30)
REVERT: L   83 PHE cc_start: 0.7536 (m-80) cc_final: 0.7147 (m-80)
REVERT: L   97 MET cc_start: 0.6241 (mtm) cc_final: 0.5729 (mtm)
REVERT: L  164 SER cc_start: 0.8396 (t) cc_final: 0.7979 (p)
REVERT: L  171 LYS cc_start: 0.8481 (mttt) cc_final: 0.8263 (mttt)
REVERT: L  178 SER cc_start: 0.8297 (t) cc_final: 0.7412 (m)
REVERT: A   57 LEU cc_start: 0.7395 (tp) cc_final: 0.7104 (tp)
REVERT: A   59 PHE cc_start: 0.7176 (m-10) cc_final: 0.6972 (m-10)
REVERT: A  147 LYS cc_start: 0.4538 (mmmt) cc_final: 0.4328 (mmmt)
REVERT: A  269 TYR cc_start: 0.7557 (m-80) cc_final: 0.7319 (m-80)
REVERT: A  298 GLU cc_start: 0.7283 (tt0) cc_final: 0.7082 (tt0)
REVERT: A  310 LYS cc_start: 0.7364 (mtmt) cc_final: 0.6832 (ptpp)
REVERT: A  357 ARG cc_start: 0.7536 (ptm-80) cc_final: 0.7274 (ptm-80)
REVERT: A  378 LYS cc_start: 0.8039 (ptpp) cc_final: 0.7577 (pttm)
REVERT: A  382 VAL cc_start: 0.5914 (OUTLIER) cc_final: 0.4985 (p)
REVERT: A  436 TRP cc_start: 0.7233 (p90) cc_final: 0.6793 (p90)
REVERT: A  448 ASN cc_start: 0.6987 (m110) cc_final: 0.6615 (m-40)
REVERT: A  460 LYS cc_start: 0.8164 (mptm) cc_final: 0.7713 (mptm)
REVERT: A  510 VAL cc_start: 0.8179 (t) cc_final: 0.7943 (m)
REVERT: A  542 ASN cc_start: 0.6932 (t0) cc_final: 0.6694 (t0)
REVERT: A  592 PHE cc_start: 0.1047 (OUTLIER) cc_final: -0.0479 (m-10)
REVERT: A  697 MET cc_start: -0.4682 (ptp) cc_final: -0.5686 (ptt)
  outliers start: 44
  outliers final: 27
  residues processed: 251
  average time/residue: 0.2193
  time to fit residues: 74.7330
Evaluate side-chains
  232 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 201
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  328 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0670
   chunk 94 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0970
   chunk 83 optimal weight:    0.6980
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.5516

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.217773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.183249 restraints weight = 18525.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.188778 restraints weight = 9728.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.192333 restraints weight = 5840.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8600  Z= 0.117
  Angle     :  0.571  10.230  11713  Z= 0.292
  Chirality :  0.045   0.176   1302
  Planarity :  0.004   0.051   1507
  Dihedral  :  6.869  87.794   1206
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 14.91 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.23), residues: 1065
  helix: -1.78 (0.80), residues: 26
  sheet: -1.49 (0.28), residues: 336
  loop : -2.67 (0.21), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP L 150 
 HIS   0.002   0.001   HIS H 207 
 PHE   0.018   0.001   PHE A 136 
 TYR   0.013   0.001   TYR A 265 
 ARG   0.004   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  180)
  hydrogen bonds       : angle       7.06233 (  471)
  SS BOND              : bond        0.00397 (   12)
  SS BOND              : angle       1.15949 (   24)
  covalent geometry    : bond        0.00273 ( 8588)
  covalent geometry    : angle       0.56905 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7806 (mp) cc_final: 0.6892 (tt)
REVERT: H   29 PHE cc_start: 0.8021 (t80) cc_final: 0.7806 (t80)
REVERT: H   58 VAL cc_start: 0.8271 (m) cc_final: 0.7962 (p)
REVERT: H   85 SER cc_start: 0.7646 (t) cc_final: 0.7174 (p)
REVERT: H  148 LEU cc_start: 0.8030 (tt) cc_final: 0.7821 (tt)
REVERT: H  160 SER cc_start: 0.8011 (p) cc_final: 0.7755 (t)
REVERT: H  176 VAL cc_start: 0.7697 (t) cc_final: 0.7277 (p)
REVERT: H  189 VAL cc_start: 0.8583 (t) cc_final: 0.8204 (p)
REVERT: H  200 THR cc_start: 0.8527 (m) cc_final: 0.8169 (t)
REVERT: H  201 TYR cc_start: 0.6464 (m-80) cc_final: 0.6172 (m-80)
REVERT: L   14 SER cc_start: 0.8126 (t) cc_final: 0.7914 (m)
REVERT: L   46 LEU cc_start: 0.8102 (tp) cc_final: 0.7790 (tp)
REVERT: L   83 PHE cc_start: 0.7583 (m-80) cc_final: 0.7197 (m-80)
REVERT: L   97 MET cc_start: 0.6266 (mtm) cc_final: 0.5855 (mtm)
REVERT: L  164 SER cc_start: 0.8425 (t) cc_final: 0.8068 (p)
REVERT: L  178 SER cc_start: 0.8294 (t) cc_final: 0.7335 (m)
REVERT: A   57 LEU cc_start: 0.7461 (tp) cc_final: 0.7113 (tp)
REVERT: A   59 PHE cc_start: 0.7183 (m-10) cc_final: 0.6951 (m-10)
REVERT: A  269 TYR cc_start: 0.7644 (m-80) cc_final: 0.7372 (m-80)
REVERT: A  298 GLU cc_start: 0.7355 (tt0) cc_final: 0.7114 (tt0)
REVERT: A  310 LYS cc_start: 0.7432 (mtmt) cc_final: 0.7158 (mtpt)
REVERT: A  357 ARG cc_start: 0.7620 (ptm-80) cc_final: 0.7294 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7261 (m-80) cc_final: 0.7057 (m-10)
REVERT: A  382 VAL cc_start: 0.5947 (OUTLIER) cc_final: 0.5000 (p)
REVERT: A  394 ASN cc_start: 0.6315 (t0) cc_final: 0.5565 (t0)
REVERT: A  406 GLU cc_start: 0.7544 (pt0) cc_final: 0.7158 (pt0)
REVERT: A  424 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7804 (ttmm)
REVERT: A  436 TRP cc_start: 0.7248 (p90) cc_final: 0.6787 (p90)
REVERT: A  448 ASN cc_start: 0.7028 (m110) cc_final: 0.6640 (m-40)
REVERT: A  460 LYS cc_start: 0.8231 (mptm) cc_final: 0.7760 (mptm)
REVERT: A  465 GLU cc_start: 0.6969 (tt0) cc_final: 0.6378 (tt0)
REVERT: A  510 VAL cc_start: 0.8130 (t) cc_final: 0.7918 (m)
REVERT: A  539 VAL cc_start: 0.7675 (t) cc_final: 0.7418 (p)
REVERT: A  542 ASN cc_start: 0.6927 (t0) cc_final: 0.6688 (t0)
REVERT: A  592 PHE cc_start: 0.1114 (OUTLIER) cc_final: -0.0503 (m-10)
REVERT: A  697 MET cc_start: -0.4835 (ptp) cc_final: -0.5723 (ptt)
  outliers start: 40
  outliers final: 30
  residues processed: 227
  average time/residue: 0.2043
  time to fit residues: 62.5037
Evaluate side-chains
  229 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  328 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 0 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   chunk 67 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0060
   chunk 89 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
H 107 ASN
H 171 HIS
A 314 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.217276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.184168 restraints weight = 18423.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.189304 restraints weight = 9904.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.192530 restraints weight = 6014.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5798
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8600  Z= 0.107
  Angle     :  0.552   9.049  11713  Z= 0.280
  Chirality :  0.044   0.166   1302
  Planarity :  0.004   0.053   1507
  Dihedral  :  6.835  87.730   1205
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 15.87 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.24), residues: 1065
  helix: -1.16 (0.90), residues: 26
  sheet: -1.30 (0.28), residues: 339
  loop : -2.54 (0.21), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP L 150 
 HIS   0.003   0.001   HIS L 200 
 PHE   0.023   0.001   PHE A 374 
 TYR   0.014   0.001   TYR H  60 
 ARG   0.004   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03017 (  180)
  hydrogen bonds       : angle       6.51022 (  471)
  SS BOND              : bond        0.00365 (   12)
  SS BOND              : angle       1.16458 (   24)
  covalent geometry    : bond        0.00247 ( 8588)
  covalent geometry    : angle       0.55024 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 197
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7782 (mp) cc_final: 0.7142 (tt)
REVERT: H   29 PHE cc_start: 0.7974 (t80) cc_final: 0.7766 (t80)
REVERT: H   34 MET cc_start: 0.7433 (mmm) cc_final: 0.7093 (mmm)
REVERT: H   36 TRP cc_start: 0.7218 (t-100) cc_final: 0.6759 (m-90)
REVERT: H   68 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (t)
REVERT: H   85 SER cc_start: 0.7491 (t) cc_final: 0.7044 (p)
REVERT: H  160 SER cc_start: 0.7956 (p) cc_final: 0.7692 (t)
REVERT: H  176 VAL cc_start: 0.7841 (t) cc_final: 0.7444 (p)
REVERT: H  189 VAL cc_start: 0.8472 (t) cc_final: 0.8123 (p)
REVERT: H  200 THR cc_start: 0.8478 (m) cc_final: 0.8150 (t)
REVERT: H  201 TYR cc_start: 0.6360 (m-80) cc_final: 0.6097 (m-80)
REVERT: L   46 LEU cc_start: 0.8153 (tp) cc_final: 0.7891 (tp)
REVERT: L   83 PHE cc_start: 0.7430 (m-80) cc_final: 0.7089 (m-80)
REVERT: L   97 MET cc_start: 0.6192 (mtm) cc_final: 0.5943 (mtm)
REVERT: L  164 SER cc_start: 0.8488 (t) cc_final: 0.8203 (p)
REVERT: L  168 GLN cc_start: 0.7815 (tt0) cc_final: 0.7315 (mt0)
REVERT: L  178 SER cc_start: 0.8295 (t) cc_final: 0.7415 (m)
REVERT: A  269 TYR cc_start: 0.7564 (m-80) cc_final: 0.7289 (m-80)
REVERT: A  298 GLU cc_start: 0.7279 (tt0) cc_final: 0.7043 (tt0)
REVERT: A  310 LYS cc_start: 0.7402 (mtmt) cc_final: 0.7150 (mtpt)
REVERT: A  357 ARG cc_start: 0.7604 (ptm-80) cc_final: 0.7172 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7166 (m-80) cc_final: 0.6954 (m-10)
REVERT: A  378 LYS cc_start: 0.7982 (ptpp) cc_final: 0.7715 (pttm)
REVERT: A  382 VAL cc_start: 0.5980 (OUTLIER) cc_final: 0.5013 (p)
REVERT: A  394 ASN cc_start: 0.6306 (t0) cc_final: 0.5548 (t0)
REVERT: A  406 GLU cc_start: 0.7479 (pt0) cc_final: 0.7226 (pt0)
REVERT: A  424 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7706 (ttmm)
REVERT: A  436 TRP cc_start: 0.7248 (p90) cc_final: 0.6749 (p90)
REVERT: A  448 ASN cc_start: 0.7011 (m110) cc_final: 0.6669 (m-40)
REVERT: A  460 LYS cc_start: 0.8234 (mptm) cc_final: 0.7830 (mptm)
REVERT: A  465 GLU cc_start: 0.6929 (tt0) cc_final: 0.6360 (tt0)
REVERT: A  539 VAL cc_start: 0.7707 (t) cc_final: 0.7459 (p)
REVERT: A  542 ASN cc_start: 0.6932 (t0) cc_final: 0.6688 (t0)
REVERT: A  592 PHE cc_start: 0.1070 (OUTLIER) cc_final: -0.0732 (m-80)
REVERT: A  697 MET cc_start: -0.4947 (ptp) cc_final: -0.5754 (ptt)
  outliers start: 41
  outliers final: 31
  residues processed: 222
  average time/residue: 0.2168
  time to fit residues: 64.7761
Evaluate side-chains
  225 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  328 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 97 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0770
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.217351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.183842 restraints weight = 18428.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.189259 restraints weight = 9723.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.192649 restraints weight = 5843.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5794
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8600  Z= 0.099
  Angle     :  0.559   9.321  11713  Z= 0.277
  Chirality :  0.044   0.197   1302
  Planarity :  0.004   0.053   1507
  Dihedral  :  6.789  87.746   1205
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 16.61 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.24), residues: 1065
  helix: -0.70 (0.95), residues: 26
  sheet: -0.94 (0.30), residues: 308
  loop : -2.44 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP L 150 
 HIS   0.002   0.000   HIS H 207 
 PHE   0.016   0.001   PHE A  60 
 TYR   0.011   0.001   TYR A 265 
 ARG   0.004   0.000   ARG L 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02719 (  180)
  hydrogen bonds       : angle       6.13363 (  471)
  SS BOND              : bond        0.00341 (   12)
  SS BOND              : angle       1.06093 (   24)
  covalent geometry    : bond        0.00237 ( 8588)
  covalent geometry    : angle       0.55775 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 203
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7811 (mp) cc_final: 0.7119 (tt)
REVERT: H   36 TRP cc_start: 0.7139 (t-100) cc_final: 0.6850 (m-90)
REVERT: H   58 VAL cc_start: 0.8123 (m) cc_final: 0.7765 (p)
REVERT: H   60 TYR cc_start: 0.8906 (m-80) cc_final: 0.8693 (m-80)
REVERT: H   68 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8314 (t)
REVERT: H   85 SER cc_start: 0.7457 (t) cc_final: 0.7018 (p)
REVERT: H  117 LEU cc_start: 0.8217 (tp) cc_final: 0.7987 (tp)
REVERT: H  160 SER cc_start: 0.7992 (p) cc_final: 0.7703 (t)
REVERT: H  172 THR cc_start: 0.8480 (m) cc_final: 0.7890 (p)
REVERT: H  176 VAL cc_start: 0.7814 (t) cc_final: 0.7407 (p)
REVERT: H  200 THR cc_start: 0.8508 (m) cc_final: 0.8174 (t)
REVERT: H  201 TYR cc_start: 0.6394 (m-80) cc_final: 0.6112 (m-80)
REVERT: L   46 LEU cc_start: 0.8154 (tp) cc_final: 0.7887 (tp)
REVERT: L   83 PHE cc_start: 0.7463 (m-80) cc_final: 0.7114 (m-80)
REVERT: L   97 MET cc_start: 0.6274 (mtm) cc_final: 0.5927 (mtm)
REVERT: L  164 SER cc_start: 0.8401 (t) cc_final: 0.8109 (p)
REVERT: L  168 GLN cc_start: 0.7860 (tt0) cc_final: 0.7363 (mt0)
REVERT: L  178 SER cc_start: 0.8306 (t) cc_final: 0.7475 (m)
REVERT: A  269 TYR cc_start: 0.7683 (m-80) cc_final: 0.7459 (m-80)
REVERT: A  298 GLU cc_start: 0.7316 (tt0) cc_final: 0.7091 (tt0)
REVERT: A  310 LYS cc_start: 0.7455 (mtmt) cc_final: 0.6602 (ptmt)
REVERT: A  357 ARG cc_start: 0.7645 (ptm-80) cc_final: 0.7306 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7233 (m-80) cc_final: 0.7022 (m-10)
REVERT: A  378 LYS cc_start: 0.8028 (ptpp) cc_final: 0.7642 (pttm)
REVERT: A  382 VAL cc_start: 0.6011 (OUTLIER) cc_final: 0.5075 (p)
REVERT: A  406 GLU cc_start: 0.7525 (pt0) cc_final: 0.7204 (pt0)
REVERT: A  424 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7597 (ttmm)
REVERT: A  436 TRP cc_start: 0.7266 (p90) cc_final: 0.6711 (p90)
REVERT: A  448 ASN cc_start: 0.7015 (m110) cc_final: 0.6630 (m-40)
REVERT: A  460 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7722 (mptm)
REVERT: A  465 GLU cc_start: 0.6998 (tt0) cc_final: 0.6369 (tt0)
REVERT: A  518 LEU cc_start: 0.8655 (mp) cc_final: 0.8324 (mp)
REVERT: A  539 VAL cc_start: 0.7708 (t) cc_final: 0.7441 (p)
REVERT: A  542 ASN cc_start: 0.6925 (t0) cc_final: 0.6696 (t0)
REVERT: A  592 PHE cc_start: 0.1190 (OUTLIER) cc_final: -0.0753 (m-80)
REVERT: A  697 MET cc_start: -0.4805 (ptp) cc_final: -0.5526 (ptt)
  outliers start: 48
  outliers final: 32
  residues processed: 236
  average time/residue: 0.2141
  time to fit residues: 68.1023
Evaluate side-chains
  235 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  328 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:    0.3980
   chunk 14 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0270
   chunk 71 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.9640

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS
A  70 HIS
A 188 ASN
A 207 HIS
A 448 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.212087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.178218 restraints weight = 17971.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.183459 restraints weight = 9612.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.186954 restraints weight = 5903.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5927
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8600  Z= 0.155
  Angle     :  0.615   9.013  11713  Z= 0.315
  Chirality :  0.045   0.158   1302
  Planarity :  0.004   0.054   1507
  Dihedral  :  7.098  87.916   1205
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 16.08 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.24), residues: 1065
  helix: -1.69 (0.79), residues: 32
  sheet: -1.00 (0.30), residues: 314
  loop : -2.31 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L 150 
 HIS   0.006   0.001   HIS A  70 
 PHE   0.020   0.002   PHE A 374 
 TYR   0.017   0.002   TYR A 265 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03115 (  180)
  hydrogen bonds       : angle       6.18291 (  471)
  SS BOND              : bond        0.00435 (   12)
  SS BOND              : angle       1.29955 (   24)
  covalent geometry    : bond        0.00352 ( 8588)
  covalent geometry    : angle       0.61241 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 208
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLN cc_start: 0.6777 (tt0) cc_final: 0.6325 (tt0)
REVERT: H   59 THR cc_start: 0.8661 (t) cc_final: 0.8440 (t)
REVERT: H   85 SER cc_start: 0.7423 (t) cc_final: 0.6971 (p)
REVERT: H  116 THR cc_start: 0.7655 (m) cc_final: 0.7095 (p)
REVERT: H  117 LEU cc_start: 0.8295 (tp) cc_final: 0.8013 (tp)
REVERT: H  176 VAL cc_start: 0.7868 (t) cc_final: 0.7486 (p)
REVERT: H  189 VAL cc_start: 0.8711 (t) cc_final: 0.8279 (p)
REVERT: H  200 THR cc_start: 0.8635 (m) cc_final: 0.8291 (t)
REVERT: H  201 TYR cc_start: 0.6300 (m-80) cc_final: 0.6043 (m-80)
REVERT: L   27 GLN cc_start: 0.7752 (tt0) cc_final: 0.7522 (tt0)
REVERT: L   46 LEU cc_start: 0.8198 (tp) cc_final: 0.7972 (tp)
REVERT: L   61 ARG cc_start: 0.7534 (ptt-90) cc_final: 0.7161 (ptt-90)
REVERT: L   79 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6618 (mm-30)
REVERT: L   83 PHE cc_start: 0.7484 (m-80) cc_final: 0.7155 (m-80)
REVERT: L   97 MET cc_start: 0.6261 (mtm) cc_final: 0.5931 (mtm)
REVERT: L  164 SER cc_start: 0.8393 (t) cc_final: 0.8101 (p)
REVERT: L  178 SER cc_start: 0.8352 (t) cc_final: 0.7525 (m)
REVERT: A  298 GLU cc_start: 0.7406 (tt0) cc_final: 0.7108 (tt0)
REVERT: A  345 THR cc_start: 0.7253 (p) cc_final: 0.6988 (t)
REVERT: A  353 TRP cc_start: 0.8152 (p-90) cc_final: 0.7544 (p-90)
REVERT: A  357 ARG cc_start: 0.7605 (ptm-80) cc_final: 0.6985 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7287 (m-80) cc_final: 0.7084 (m-10)
REVERT: A  378 LYS cc_start: 0.8119 (ptpp) cc_final: 0.7852 (ptpp)
REVERT: A  382 VAL cc_start: 0.6224 (OUTLIER) cc_final: 0.5322 (p)
REVERT: A  392 PHE cc_start: 0.7445 (m-10) cc_final: 0.7242 (m-10)
REVERT: A  394 ASN cc_start: 0.6775 (t0) cc_final: 0.5866 (t0)
REVERT: A  406 GLU cc_start: 0.7415 (pt0) cc_final: 0.7174 (pt0)
REVERT: A  424 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7759 (ttmm)
REVERT: A  436 TRP cc_start: 0.7401 (p90) cc_final: 0.6817 (p90)
REVERT: A  448 ASN cc_start: 0.7191 (m-40) cc_final: 0.6936 (m-40)
REVERT: A  450 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7982 (p0)
REVERT: A  458 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8544 (ttmm)
REVERT: A  460 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7742 (mptm)
REVERT: A  465 GLU cc_start: 0.6921 (tt0) cc_final: 0.6375 (tt0)
REVERT: A  528 LYS cc_start: 0.4752 (OUTLIER) cc_final: 0.4532 (mmmt)
REVERT: A  539 VAL cc_start: 0.7957 (t) cc_final: 0.7734 (p)
REVERT: A  592 PHE cc_start: 0.1753 (OUTLIER) cc_final: -0.0439 (m-10)
REVERT: A  697 MET cc_start: -0.4472 (ptp) cc_final: -0.5524 (ptt)
  outliers start: 53
  outliers final: 37
  residues processed: 236
  average time/residue: 0.2103
  time to fit residues: 66.9155
Evaluate side-chains
  246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 204
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain L residue  177 LEU
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain L residue  201 GLN
Chi-restraints excluded: chain L residue  211 PHE
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  328 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  528 LYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0970
   chunk 37 optimal weight:    5.9990
   chunk 50 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS
L 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.213392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.179588 restraints weight = 18321.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.184896 restraints weight = 9758.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.188201 restraints weight = 5938.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5889
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8600  Z= 0.119
  Angle     :  0.590   8.227  11713  Z= 0.296
  Chirality :  0.045   0.262   1302
  Planarity :  0.004   0.058   1507
  Dihedral  :  6.968  87.430   1204
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 18.42 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.25), residues: 1065
  helix: -1.49 (0.83), residues: 32
  sheet: -0.93 (0.30), residues: 316
  loop : -2.24 (0.22), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP L 150 
 HIS   0.002   0.001   HIS L 191 
 PHE   0.018   0.001   PHE L 118 
 TYR   0.013   0.001   TYR A 612 
 ARG   0.002   0.000   ARG A 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02761 (  180)
  hydrogen bonds       : angle       5.94565 (  471)
  SS BOND              : bond        0.00318 (   12)
  SS BOND              : angle       1.28276 (   24)
  covalent geometry    : bond        0.00277 ( 8588)
  covalent geometry    : angle       0.58806 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 209
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7787 (mp) cc_final: 0.7262 (tt)
REVERT: H   85 SER cc_start: 0.7422 (t) cc_final: 0.6971 (p)
REVERT: H  117 LEU cc_start: 0.8310 (tp) cc_final: 0.8050 (tp)
REVERT: H  172 THR cc_start: 0.8454 (m) cc_final: 0.7885 (p)
REVERT: H  176 VAL cc_start: 0.7833 (t) cc_final: 0.7447 (p)
REVERT: H  189 VAL cc_start: 0.8620 (t) cc_final: 0.8260 (p)
REVERT: H  200 THR cc_start: 0.8626 (m) cc_final: 0.8292 (t)
REVERT: H  201 TYR cc_start: 0.6271 (m-80) cc_final: 0.6004 (m-80)
REVERT: L   14 SER cc_start: 0.8523 (m) cc_final: 0.8278 (t)
REVERT: L   27 GLN cc_start: 0.7762 (tt0) cc_final: 0.7521 (tt0)
REVERT: L   83 PHE cc_start: 0.7487 (m-80) cc_final: 0.7143 (m-80)
REVERT: L   97 MET cc_start: 0.6251 (mtm) cc_final: 0.5899 (mtm)
REVERT: L  164 SER cc_start: 0.8465 (t) cc_final: 0.8149 (p)
REVERT: L  168 GLN cc_start: 0.7886 (tt0) cc_final: 0.7198 (mt0)
REVERT: L  178 SER cc_start: 0.8321 (t) cc_final: 0.7520 (m)
REVERT: A  298 GLU cc_start: 0.7344 (tt0) cc_final: 0.7044 (tt0)
REVERT: A  345 THR cc_start: 0.7192 (p) cc_final: 0.6924 (t)
REVERT: A  353 TRP cc_start: 0.8122 (p-90) cc_final: 0.7519 (p-90)
REVERT: A  357 ARG cc_start: 0.7632 (ptm-80) cc_final: 0.7051 (ptm-80)
REVERT: A  375 PHE cc_start: 0.8167 (t80) cc_final: 0.7810 (t80)
REVERT: A  378 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7812 (ptpp)
REVERT: A  394 ASN cc_start: 0.6901 (t0) cc_final: 0.6125 (t0)
REVERT: A  406 GLU cc_start: 0.7512 (pt0) cc_final: 0.7218 (pt0)
REVERT: A  424 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7632 (ttmm)
REVERT: A  436 TRP cc_start: 0.7372 (p90) cc_final: 0.6798 (p90)
REVERT: A  448 ASN cc_start: 0.7139 (m-40) cc_final: 0.6813 (m-40)
REVERT: A  458 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8560 (ttmm)
REVERT: A  460 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7723 (mptm)
REVERT: A  465 GLU cc_start: 0.6950 (tt0) cc_final: 0.6335 (tt0)
REVERT: A  493 GLN cc_start: 0.6587 (tp40) cc_final: 0.6154 (tp40)
REVERT: A  539 VAL cc_start: 0.7845 (t) cc_final: 0.7599 (p)
REVERT: A  592 PHE cc_start: 0.1586 (OUTLIER) cc_final: -0.0666 (m-10)
REVERT: A  697 MET cc_start: -0.4646 (ptp) cc_final: -0.5546 (ptt)
  outliers start: 44
  outliers final: 37
  residues processed: 232
  average time/residue: 0.2108
  time to fit residues: 65.4825
Evaluate side-chains
  247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 208
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  213 LYS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  149 GLN
Chi-restraints excluded: chain L residue  177 LEU
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain L residue  211 PHE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  528 LYS
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0870
   chunk 95 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0270
   chunk 0 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H 171 HIS
L  89 GLN
L 149 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.212979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.179218 restraints weight = 18105.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184504 restraints weight = 9644.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.187825 restraints weight = 5864.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5908
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8600  Z= 0.117
  Angle     :  0.583   8.050  11713  Z= 0.295
  Chirality :  0.045   0.281   1302
  Planarity :  0.004   0.057   1507
  Dihedral  :  6.944  87.263   1204
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 18.64 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.25), residues: 1065
  helix: -1.23 (0.87), residues: 32
  sheet: -0.91 (0.30), residues: 309
  loop : -2.22 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP L 150 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.018   0.001   PHE L 118 
 TYR   0.043   0.001   TYR H  35 
 ARG   0.003   0.000   ARG L  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02715 (  180)
  hydrogen bonds       : angle       5.87180 (  471)
  SS BOND              : bond        0.00343 (   12)
  SS BOND              : angle       1.04878 (   24)
  covalent geometry    : bond        0.00280 ( 8588)
  covalent geometry    : angle       0.58169 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 207
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7755 (mp) cc_final: 0.7284 (tt)
REVERT: H   39 GLN cc_start: 0.7722 (tp40) cc_final: 0.7083 (tt0)
REVERT: H   85 SER cc_start: 0.7374 (t) cc_final: 0.6934 (p)
REVERT: H   96 CYS cc_start: 0.5162 (p) cc_final: 0.3753 (p)
REVERT: H  117 LEU cc_start: 0.8332 (tp) cc_final: 0.8063 (tp)
REVERT: H  176 VAL cc_start: 0.7871 (t) cc_final: 0.7486 (p)
REVERT: H  189 VAL cc_start: 0.8601 (t) cc_final: 0.8233 (p)
REVERT: H  200 THR cc_start: 0.8642 (m) cc_final: 0.8315 (t)
REVERT: H  201 TYR cc_start: 0.6201 (m-80) cc_final: 0.5955 (m-80)
REVERT: L    4 LEU cc_start: 0.7363 (mt) cc_final: 0.7110 (tp)
REVERT: L   14 SER cc_start: 0.8534 (m) cc_final: 0.8308 (t)
REVERT: L   27 GLN cc_start: 0.7780 (tt0) cc_final: 0.7547 (tt0)
REVERT: L   83 PHE cc_start: 0.7401 (m-80) cc_final: 0.7121 (m-80)
REVERT: L   97 MET cc_start: 0.6012 (mtm) cc_final: 0.5645 (mtm)
REVERT: L  164 SER cc_start: 0.8494 (t) cc_final: 0.8185 (p)
REVERT: L  168 GLN cc_start: 0.7903 (tt0) cc_final: 0.7326 (mt0)
REVERT: L  178 SER cc_start: 0.8323 (t) cc_final: 0.7568 (m)
REVERT: A  298 GLU cc_start: 0.7326 (tt0) cc_final: 0.7017 (tt0)
REVERT: A  345 THR cc_start: 0.7192 (p) cc_final: 0.6938 (t)
REVERT: A  353 TRP cc_start: 0.8117 (p-90) cc_final: 0.7503 (p-90)
REVERT: A  357 ARG cc_start: 0.7597 (ptm-80) cc_final: 0.7060 (ptm-80)
REVERT: A  378 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7787 (ptpp)
REVERT: A  394 ASN cc_start: 0.6834 (t0) cc_final: 0.6219 (t0)
REVERT: A  406 GLU cc_start: 0.7481 (pt0) cc_final: 0.7227 (pt0)
REVERT: A  424 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7634 (ttmm)
REVERT: A  436 TRP cc_start: 0.7391 (p90) cc_final: 0.6834 (p90)
REVERT: A  448 ASN cc_start: 0.7125 (m-40) cc_final: 0.6895 (m-40)
REVERT: A  458 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8562 (ttmm)
REVERT: A  460 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7749 (mptm)
REVERT: A  465 GLU cc_start: 0.6988 (tt0) cc_final: 0.6345 (tt0)
REVERT: A  493 GLN cc_start: 0.6525 (tp40) cc_final: 0.6137 (tp40)
REVERT: A  539 VAL cc_start: 0.7867 (t) cc_final: 0.7624 (p)
REVERT: A  592 PHE cc_start: 0.1505 (OUTLIER) cc_final: -0.0924 (m-10)
REVERT: A  697 MET cc_start: -0.4468 (ptp) cc_final: -0.5421 (ptt)
  outliers start: 42
  outliers final: 35
  residues processed: 227
  average time/residue: 0.2132
  time to fit residues: 65.2351
Evaluate side-chains
  240 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 203
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  213 LYS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain L residue  211 PHE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  528 LYS
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0270
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS
L 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.211027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.177741 restraints weight = 18318.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.183017 restraints weight = 9775.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.186280 restraints weight = 5969.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5955
moved from start:          0.4636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8600  Z= 0.144
  Angle     :  0.612   8.523  11713  Z= 0.311
  Chirality :  0.045   0.295   1302
  Planarity :  0.004   0.057   1507
  Dihedral  :  6.915  86.984   1199
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 18.32 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.24), residues: 1065
  helix: -1.94 (0.75), residues: 38
  sheet: -0.97 (0.30), residues: 305
  loop : -2.23 (0.22), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L 150 
 HIS   0.003   0.001   HIS L 191 
 PHE   0.017   0.002   PHE L 118 
 TYR   0.032   0.002   TYR H  35 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03009 (  180)
  hydrogen bonds       : angle       5.94532 (  471)
  SS BOND              : bond        0.00503 (   12)
  SS BOND              : angle       1.55966 (   24)
  covalent geometry    : bond        0.00331 ( 8588)
  covalent geometry    : angle       0.60812 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 209
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 GLN cc_start: 0.7739 (tp40) cc_final: 0.7098 (tt0)
REVERT: H   85 SER cc_start: 0.7382 (t) cc_final: 0.6936 (p)
REVERT: H  117 LEU cc_start: 0.8327 (tp) cc_final: 0.8033 (tp)
REVERT: H  172 THR cc_start: 0.8453 (m) cc_final: 0.7877 (p)
REVERT: H  176 VAL cc_start: 0.7905 (t) cc_final: 0.7528 (p)
REVERT: H  187 SER cc_start: 0.8239 (t) cc_final: 0.7895 (p)
REVERT: H  189 VAL cc_start: 0.8743 (t) cc_final: 0.8305 (p)
REVERT: H  200 THR cc_start: 0.8684 (m) cc_final: 0.8388 (t)
REVERT: L    4 LEU cc_start: 0.7539 (mt) cc_final: 0.7224 (tp)
REVERT: L   27 GLN cc_start: 0.7788 (tt0) cc_final: 0.7586 (tt0)
REVERT: L   35 TRP cc_start: 0.5760 (OUTLIER) cc_final: 0.5514 (m-90)
REVERT: L   83 PHE cc_start: 0.7471 (m-80) cc_final: 0.7172 (m-80)
REVERT: L   97 MET cc_start: 0.5965 (mtm) cc_final: 0.5512 (mtm)
REVERT: L  107 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6476 (mm-30)
REVERT: L  164 SER cc_start: 0.8484 (t) cc_final: 0.8151 (p)
REVERT: L  178 SER cc_start: 0.8319 (t) cc_final: 0.7571 (m)
REVERT: A  298 GLU cc_start: 0.7350 (tt0) cc_final: 0.7009 (tt0)
REVERT: A  345 THR cc_start: 0.7230 (p) cc_final: 0.6988 (t)
REVERT: A  353 TRP cc_start: 0.8096 (p-90) cc_final: 0.7482 (p-90)
REVERT: A  357 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.7070 (ptm-80)
REVERT: A  394 ASN cc_start: 0.6965 (t0) cc_final: 0.6341 (t0)
REVERT: A  406 GLU cc_start: 0.7509 (pt0) cc_final: 0.6290 (pt0)
REVERT: A  409 GLN cc_start: 0.7907 (mt0) cc_final: 0.7618 (mt0)
REVERT: A  436 TRP cc_start: 0.7481 (p90) cc_final: 0.6850 (p90)
REVERT: A  448 ASN cc_start: 0.7131 (m-40) cc_final: 0.6811 (m-40)
REVERT: A  460 LYS cc_start: 0.8200 (mptm) cc_final: 0.7766 (mptm)
REVERT: A  465 GLU cc_start: 0.6978 (tt0) cc_final: 0.6449 (tt0)
REVERT: A  531 THR cc_start: 0.6422 (OUTLIER) cc_final: 0.5863 (p)
REVERT: A  539 VAL cc_start: 0.7947 (t) cc_final: 0.7730 (p)
REVERT: A  592 PHE cc_start: 0.2561 (OUTLIER) cc_final: -0.0548 (m-10)
REVERT: A  697 MET cc_start: -0.4139 (ptp) cc_final: -0.4891 (ptt)
  outliers start: 45
  outliers final: 39
  residues processed: 231
  average time/residue: 0.2067
  time to fit residues: 64.4729
Evaluate side-chains
  245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 203
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  213 LYS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain L residue  201 GLN
Chi-restraints excluded: chain L residue  211 PHE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 105 optimal weight:    7.9990
   chunk 73 optimal weight:    0.0270
   chunk 5 optimal weight:    0.6980
   chunk 96 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.212303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.178731 restraints weight = 18295.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.184092 restraints weight = 9769.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.187425 restraints weight = 5976.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5932
moved from start:          0.4728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8600  Z= 0.116
  Angle     :  0.610   8.704  11713  Z= 0.308
  Chirality :  0.045   0.301   1302
  Planarity :  0.004   0.058   1507
  Dihedral  :  6.854  86.740   1199
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 19.17 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.25), residues: 1065
  helix: -1.97 (0.77), residues: 38
  sheet: -0.87 (0.30), residues: 301
  loop : -2.22 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP L 150 
 HIS   0.002   0.000   HIS L 191 
 PHE   0.053   0.002   PHE H  29 
 TYR   0.029   0.001   TYR H  35 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02792 (  180)
  hydrogen bonds       : angle       5.82044 (  471)
  SS BOND              : bond        0.00339 (   12)
  SS BOND              : angle       1.61507 (   24)
  covalent geometry    : bond        0.00274 ( 8588)
  covalent geometry    : angle       0.60669 (11689)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 206
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7792 (mp) cc_final: 0.7199 (tt)
REVERT: H   22 CYS cc_start: 0.5526 (t) cc_final: 0.3918 (t)
REVERT: H   39 GLN cc_start: 0.7630 (tp40) cc_final: 0.7163 (tt0)
REVERT: H   85 SER cc_start: 0.7347 (t) cc_final: 0.6904 (p)
REVERT: H  117 LEU cc_start: 0.8223 (tp) cc_final: 0.7963 (tp)
REVERT: H  172 THR cc_start: 0.8430 (m) cc_final: 0.7857 (p)
REVERT: H  176 VAL cc_start: 0.7839 (t) cc_final: 0.7482 (p)
REVERT: H  189 VAL cc_start: 0.8659 (t) cc_final: 0.8242 (p)
REVERT: H  200 THR cc_start: 0.8687 (m) cc_final: 0.8369 (t)
REVERT: H  201 TYR cc_start: 0.6183 (m-80) cc_final: 0.5930 (m-80)
REVERT: L    4 LEU cc_start: 0.7515 (mt) cc_final: 0.7231 (tp)
REVERT: L   14 SER cc_start: 0.8579 (m) cc_final: 0.8279 (t)
REVERT: L   35 TRP cc_start: 0.5858 (OUTLIER) cc_final: 0.5468 (m-90)
REVERT: L   83 PHE cc_start: 0.7462 (m-80) cc_final: 0.7169 (m-80)
REVERT: L   97 MET cc_start: 0.5976 (mtm) cc_final: 0.5529 (mtm)
REVERT: L  107 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6497 (mm-30)
REVERT: L  164 SER cc_start: 0.8532 (t) cc_final: 0.8162 (p)
REVERT: L  178 SER cc_start: 0.8336 (t) cc_final: 0.7558 (m)
REVERT: A  298 GLU cc_start: 0.7301 (tt0) cc_final: 0.7015 (tt0)
REVERT: A  319 ARG cc_start: 0.4417 (OUTLIER) cc_final: 0.3528 (mtm180)
REVERT: A  353 TRP cc_start: 0.8052 (p-90) cc_final: 0.7421 (p-90)
REVERT: A  406 GLU cc_start: 0.7486 (pt0) cc_final: 0.7201 (pt0)
REVERT: A  436 TRP cc_start: 0.7432 (p90) cc_final: 0.6826 (p90)
REVERT: A  448 ASN cc_start: 0.7124 (m-40) cc_final: 0.6787 (m-40)
REVERT: A  460 LYS cc_start: 0.8180 (mptm) cc_final: 0.7730 (mptm)
REVERT: A  465 GLU cc_start: 0.6970 (tt0) cc_final: 0.6434 (tt0)
REVERT: A  515 PHE cc_start: 0.7611 (m-10) cc_final: 0.7406 (m-10)
REVERT: A  531 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.5853 (p)
REVERT: A  539 VAL cc_start: 0.7820 (t) cc_final: 0.7580 (p)
REVERT: A  592 PHE cc_start: 0.2372 (OUTLIER) cc_final: -0.0290 (m-80)
  outliers start: 40
  outliers final: 36
  residues processed: 227
  average time/residue: 0.2289
  time to fit residues: 70.5964
Evaluate side-chains
  245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 205
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  213 LYS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   35 TRP
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  142 TYR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain L residue  201 GLN
Chi-restraints excluded: chain L residue  211 PHE
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  339 HIS
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  596 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    0.0030
   chunk 13 optimal weight:    0.0370
   chunk 101 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 104 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.2846

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.213359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.179839 restraints weight = 18410.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.185235 restraints weight = 9745.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.188617 restraints weight = 5903.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5900
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8600  Z= 0.108
  Angle     :  0.609   8.665  11713  Z= 0.307
  Chirality :  0.045   0.295   1302
  Planarity :  0.004   0.057   1507
  Dihedral  :  6.775  86.752   1199
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.38 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.25), residues: 1065
  helix: -1.18 (0.90), residues: 32
  sheet: -0.77 (0.31), residues: 303
  loop : -2.10 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP L 150 
 HIS   0.002   0.000   HIS L  90 
 PHE   0.054   0.002   PHE H  29 
 TYR   0.026   0.001   TYR H  35 
 ARG   0.005   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02633 (  180)
  hydrogen bonds       : angle       5.63279 (  471)
  SS BOND              : bond        0.00337 (   12)
  SS BOND              : angle       1.38029 (   24)
  covalent geometry    : bond        0.00256 ( 8588)
  covalent geometry    : angle       0.60648 (11689)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3282.71 seconds
wall clock time: 57 minutes 51.42 seconds (3471.42 seconds total)