Starting phenix.real_space_refine
on Fri Aug 22 22:46:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kej_37160/08_2025/8kej_37160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kej_37160/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kej_37160/08_2025/8kej_37160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kej_37160/08_2025/8kej_37160.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kej_37160/08_2025/8kej_37160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kej_37160/08_2025/8kej_37160.map"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.25, per 1000 atoms: 0.27
  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: 0.67
  Conformation dependent library (CDL) restraints added in 457.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.30
  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: 1.34

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     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:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.830
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.870
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 466 
 TYR   0.007   0.001   TYR L 142 
 PHE   0.018   0.001   PHE L 141 
 TRP   0.006   0.000   TRP A 353 
 HIS   0.001   0.000   HIS L  90 

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

*********************** 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  : 0.302 
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: 0.7280 (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: 0.5273 (pp)
REVERT: A  592 PHE cc_start: 0.0518 (OUTLIER) cc_final: -0.0529 (m-80)
  outliers start: 54
  outliers final: 19
  residues processed: 267
  average time/residue: 0.1030
  time to fit residues: 36.9863
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  : 0.307 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.3980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H 114 GLN
L  38 GLN
L  42 GLN
L 102 GLN
L 168 GLN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.219599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.185633 restraints weight = 18399.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.191013 restraints weight = 9645.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.194459 restraints weight = 5767.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.196666 restraints weight = 3786.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.198167 restraints weight = 2694.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5653
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8600  Z= 0.132
  Angle     :  0.605  10.214  11713  Z= 0.308
  Chirality :  0.045   0.154   1302
  Planarity :  0.005   0.052   1507
  Dihedral  :  7.021  87.587   1217
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 12.14 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.51 (0.23), residues: 1065
  helix: -1.50 (0.91), residues: 25
  sheet: -1.73 (0.27), residues: 318
  loop : -2.83 (0.20), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  87 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.015   0.001   PHE A  56 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.003   0.001   HIS L 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8588)
  covalent geometry    : angle       0.60279 (11689)
  SS BOND              : bond        0.00347 (   12)
  SS BOND              : angle       1.26428 (   24)
  hydrogen bonds       : bond        0.04210 (  180)
  hydrogen bonds       : angle       7.77635 (  471)

*********************** 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
  254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 212
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7743 (mp) cc_final: 0.7012 (tt)
REVERT: H   68 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.7922 (t)
REVERT: H   83 LEU cc_start: 0.8484 (tp) cc_final: 0.8064 (tp)
REVERT: H   85 SER cc_start: 0.7741 (t) cc_final: 0.7298 (p)
REVERT: H  103 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7570 (mt)
REVERT: H  160 SER cc_start: 0.7911 (p) cc_final: 0.7584 (t)
REVERT: H  176 VAL cc_start: 0.7680 (t) cc_final: 0.7259 (p)
REVERT: H  189 VAL cc_start: 0.8586 (t) cc_final: 0.8231 (p)
REVERT: H  200 THR cc_start: 0.8479 (m) cc_final: 0.8140 (t)
REVERT: H  201 TYR cc_start: 0.6340 (m-80) cc_final: 0.6076 (m-80)
REVERT: L   11 LEU cc_start: 0.7530 (tp) cc_final: 0.7301 (mm)
REVERT: L   14 SER cc_start: 0.8104 (t) cc_final: 0.7890 (m)
REVERT: L   46 LEU cc_start: 0.8013 (tp) cc_final: 0.7685 (tp)
REVERT: L   82 ASP cc_start: 0.8152 (m-30) cc_final: 0.7917 (m-30)
REVERT: L   83 PHE cc_start: 0.7474 (m-80) cc_final: 0.7097 (m-80)
REVERT: L   97 MET cc_start: 0.6176 (mtm) cc_final: 0.5676 (mtm)
REVERT: L  164 SER cc_start: 0.8311 (t) cc_final: 0.7905 (p)
REVERT: L  171 LYS cc_start: 0.8474 (mttt) cc_final: 0.8253 (mttt)
REVERT: L  178 SER cc_start: 0.8248 (t) cc_final: 0.7365 (m)
REVERT: A   57 LEU cc_start: 0.7381 (tp) cc_final: 0.7087 (tp)
REVERT: A   59 PHE cc_start: 0.7171 (m-10) cc_final: 0.6957 (m-10)
REVERT: A  269 TYR cc_start: 0.7586 (m-80) cc_final: 0.7349 (m-80)
REVERT: A  310 LYS cc_start: 0.7230 (mtmt) cc_final: 0.6681 (ptpp)
REVERT: A  332 ILE cc_start: 0.6379 (tt) cc_final: 0.5752 (pt)
REVERT: A  357 ARG cc_start: 0.7514 (ptm-80) cc_final: 0.7193 (ptm-80)
REVERT: A  378 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7638 (pttm)
REVERT: A  382 VAL cc_start: 0.5833 (OUTLIER) cc_final: 0.4878 (p)
REVERT: A  436 TRP cc_start: 0.7191 (p90) cc_final: 0.6741 (p90)
REVERT: A  448 ASN cc_start: 0.6894 (m110) cc_final: 0.6587 (m-40)
REVERT: A  460 LYS cc_start: 0.8134 (mptm) cc_final: 0.7705 (mptm)
REVERT: A  510 VAL cc_start: 0.8097 (t) cc_final: 0.7869 (m)
REVERT: A  524 VAL cc_start: 0.5495 (OUTLIER) cc_final: 0.4903 (t)
REVERT: A  542 ASN cc_start: 0.6886 (t0) cc_final: 0.6636 (t0)
REVERT: A  592 PHE cc_start: 0.0894 (OUTLIER) cc_final: -0.0453 (m-10)
REVERT: A  697 MET cc_start: -0.4597 (ptp) cc_final: -0.5752 (ptt)
  outliers start: 42
  outliers final: 27
  residues processed: 246
  average time/residue: 0.1008
  time to fit residues: 33.5128
Evaluate side-chains
  232 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 200
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   33 TYR
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  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  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  524 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 30 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
H  32 HIS
H 171 HIS
L  38 GLN
L 149 GLN
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
A 207 HIS
A 422 ASN
A 448 ASN
A 474 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.209231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.174455 restraints weight = 17923.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.179935 restraints weight = 9658.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.183395 restraints weight = 5922.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.185644 restraints weight = 3986.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.187207 restraints weight = 2910.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5931
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   8600  Z= 0.243
  Angle     :  0.726  10.273  11713  Z= 0.384
  Chirality :  0.049   0.188   1302
  Planarity :  0.006   0.063   1507
  Dihedral  :  7.803  88.303   1205
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.80 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 13.74 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (0.23), residues: 1065
  helix: -2.73 (0.63), residues: 31
  sheet: -1.54 (0.27), residues: 324
  loop : -2.75 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  24 
 TYR   0.026   0.002   TYR A 265 
 PHE   0.030   0.003   PHE A 377 
 TRP   0.031   0.003   TRP L 150 
 HIS   0.006   0.001   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 8588)
  covalent geometry    : angle       0.72288 (11689)
  SS BOND              : bond        0.01596 (   12)
  SS BOND              : angle       1.66190 (   24)
  hydrogen bonds       : bond        0.04549 (  180)
  hydrogen bonds       : angle       7.50511 (  471)

*********************** 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
  280 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 225
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7705 (mp) cc_final: 0.6687 (tt)
REVERT: H    6 GLN cc_start: 0.6869 (tt0) cc_final: 0.6612 (tt0)
REVERT: H   19 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7947 (tppt)
REVERT: H   29 PHE cc_start: 0.8225 (t80) cc_final: 0.7929 (t80)
REVERT: H   36 TRP cc_start: 0.7443 (t-100) cc_final: 0.6516 (m-90)
REVERT: H   43 GLN cc_start: 0.8038 (mp10) cc_final: 0.7811 (mp10)
REVERT: H   85 SER cc_start: 0.7796 (t) cc_final: 0.7306 (p)
REVERT: H  103 ILE cc_start: 0.8321 (mt) cc_final: 0.8110 (mt)
REVERT: H  116 THR cc_start: 0.7611 (m) cc_final: 0.6904 (p)
REVERT: H  172 THR cc_start: 0.8536 (m) cc_final: 0.8042 (p)
REVERT: H  176 VAL cc_start: 0.7904 (t) cc_final: 0.7487 (p)
REVERT: H  187 SER cc_start: 0.8364 (t) cc_final: 0.8077 (p)
REVERT: H  200 THR cc_start: 0.8670 (m) cc_final: 0.8339 (t)
REVERT: L   46 LEU cc_start: 0.8207 (tp) cc_final: 0.7887 (tp)
REVERT: L   62 PHE cc_start: 0.8700 (m-80) cc_final: 0.8241 (m-80)
REVERT: L   82 ASP cc_start: 0.8428 (m-30) cc_final: 0.8083 (m-30)
REVERT: L   83 PHE cc_start: 0.7608 (m-80) cc_final: 0.7277 (m-80)
REVERT: L   97 MET cc_start: 0.6370 (mtm) cc_final: 0.5891 (mtm)
REVERT: L  107 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6576 (mm-30)
REVERT: L  120 PHE cc_start: 0.7772 (m-80) cc_final: 0.7473 (m-80)
REVERT: L  138 LEU cc_start: 0.8441 (mp) cc_final: 0.8212 (mt)
REVERT: L  164 SER cc_start: 0.8363 (t) cc_final: 0.7929 (p)
REVERT: L  178 SER cc_start: 0.8354 (t) cc_final: 0.7503 (m)
REVERT: A   59 PHE cc_start: 0.7100 (m-10) cc_final: 0.6896 (m-10)
REVERT: A  345 THR cc_start: 0.7293 (p) cc_final: 0.7000 (t)
REVERT: A  353 TRP cc_start: 0.8235 (p-90) cc_final: 0.7669 (p-90)
REVERT: A  357 ARG cc_start: 0.7634 (ptm-80) cc_final: 0.7108 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7362 (m-80) cc_final: 0.7114 (m-10)
REVERT: A  382 VAL cc_start: 0.6192 (OUTLIER) cc_final: 0.5341 (p)
REVERT: A  394 ASN cc_start: 0.6593 (t0) cc_final: 0.5793 (t0)
REVERT: A  406 GLU cc_start: 0.7356 (pt0) cc_final: 0.7148 (pt0)
REVERT: A  424 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7661 (ttmm)
REVERT: A  436 TRP cc_start: 0.7476 (p90) cc_final: 0.6877 (p90)
REVERT: A  448 ASN cc_start: 0.7333 (m-40) cc_final: 0.7089 (m-40)
REVERT: A  460 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7831 (mptm)
REVERT: A  465 GLU cc_start: 0.6861 (tt0) cc_final: 0.6455 (tt0)
REVERT: A  510 VAL cc_start: 0.8274 (t) cc_final: 0.7930 (m)
REVERT: A  542 ASN cc_start: 0.6543 (t0) cc_final: 0.6328 (t0)
REVERT: A  592 PHE cc_start: 0.2058 (OUTLIER) cc_final: -0.0226 (m-10)
REVERT: A  697 MET cc_start: -0.4294 (ptp) cc_final: -0.5516 (ptt)
  outliers start: 55
  outliers final: 36
  residues processed: 261
  average time/residue: 0.1042
  time to fit residues: 36.5740
Evaluate side-chains
  253 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 213
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 H residue  168 SER
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  111 THR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  187 ASP
Chi-restraints excluded: chain A residue   67 HIS
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  176 LEU
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  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  424 LYS
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  470 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  549 THR
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 44 optimal weight:    0.0970
   chunk 5 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 77 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.9580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.210140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.175602 restraints weight = 18247.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.181154 restraints weight = 9704.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184632 restraints weight = 5900.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.186956 restraints weight = 3948.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.188317 restraints weight = 2841.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5900
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8600  Z= 0.152
  Angle     :  0.624   9.277  11713  Z= 0.318
  Chirality :  0.046   0.193   1302
  Planarity :  0.005   0.067   1507
  Dihedral  :  7.235  88.085   1198
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 15.87 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.11 (0.24), residues: 1065
  helix: -2.80 (0.65), residues: 38
  sheet: -1.22 (0.30), residues: 298
  loop : -2.57 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.016   0.001   TYR A 265 
 PHE   0.021   0.002   PHE A 392 
 TRP   0.013   0.001   TRP L 150 
 HIS   0.003   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8588)
  covalent geometry    : angle       0.62174 (11689)
  SS BOND              : bond        0.00490 (   12)
  SS BOND              : angle       1.38144 (   24)
  hydrogen bonds       : bond        0.03288 (  180)
  hydrogen bonds       : angle       6.85060 (  471)

*********************** 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
  285 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 220
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7823 (mp) cc_final: 0.7188 (tt)
REVERT: H    6 GLN cc_start: 0.6893 (tt0) cc_final: 0.6610 (tt0)
REVERT: H   19 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7974 (tppt)
REVERT: H   68 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8291 (t)
REVERT: H   85 SER cc_start: 0.7707 (t) cc_final: 0.7234 (p)
REVERT: H  103 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7961 (mt)
REVERT: H  116 THR cc_start: 0.7513 (m) cc_final: 0.6908 (p)
REVERT: H  172 THR cc_start: 0.8465 (m) cc_final: 0.8007 (p)
REVERT: H  176 VAL cc_start: 0.7861 (t) cc_final: 0.7442 (p)
REVERT: H  187 SER cc_start: 0.8274 (t) cc_final: 0.7976 (p)
REVERT: H  189 VAL cc_start: 0.8827 (t) cc_final: 0.8351 (p)
REVERT: H  200 THR cc_start: 0.8634 (m) cc_final: 0.8287 (t)
REVERT: H  201 TYR cc_start: 0.6229 (m-80) cc_final: 0.6008 (m-80)
REVERT: L   62 PHE cc_start: 0.8758 (m-80) cc_final: 0.8245 (m-80)
REVERT: L   82 ASP cc_start: 0.8404 (m-30) cc_final: 0.8055 (m-30)
REVERT: L  120 PHE cc_start: 0.7813 (m-80) cc_final: 0.7446 (m-80)
REVERT: L  164 SER cc_start: 0.8460 (t) cc_final: 0.8085 (p)
REVERT: L  178 SER cc_start: 0.8324 (t) cc_final: 0.7491 (m)
REVERT: A   59 PHE cc_start: 0.7034 (m-10) cc_final: 0.6716 (m-10)
REVERT: A  320 VAL cc_start: 0.5358 (m) cc_final: 0.4989 (t)
REVERT: A  345 THR cc_start: 0.7134 (p) cc_final: 0.6899 (t)
REVERT: A  353 TRP cc_start: 0.8208 (p-90) cc_final: 0.7650 (p-90)
REVERT: A  357 ARG cc_start: 0.7636 (ptm-80) cc_final: 0.7153 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7311 (m-80) cc_final: 0.7065 (m-10)
REVERT: A  394 ASN cc_start: 0.6549 (t0) cc_final: 0.5853 (t0)
REVERT: A  406 GLU cc_start: 0.7368 (pt0) cc_final: 0.7125 (pt0)
REVERT: A  424 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7430 (ttmm)
REVERT: A  436 TRP cc_start: 0.7453 (p90) cc_final: 0.6871 (p90)
REVERT: A  448 ASN cc_start: 0.7081 (m-40) cc_final: 0.6867 (m-40)
REVERT: A  460 LYS cc_start: 0.8231 (mptm) cc_final: 0.7762 (mptm)
REVERT: A  465 GLU cc_start: 0.6863 (tt0) cc_final: 0.6333 (tt0)
REVERT: A  510 VAL cc_start: 0.8245 (t) cc_final: 0.7982 (m)
REVERT: A  516 GLU cc_start: 0.7011 (pt0) cc_final: 0.6808 (pt0)
REVERT: A  542 ASN cc_start: 0.6767 (t0) cc_final: 0.6537 (t0)
REVERT: A  592 PHE cc_start: 0.1939 (OUTLIER) cc_final: -0.1281 (m-10)
REVERT: A  697 MET cc_start: -0.4450 (ptp) cc_final: -0.5430 (ptt)
  outliers start: 65
  outliers final: 43
  residues processed: 258
  average time/residue: 0.1026
  time to fit residues: 35.7593
Evaluate side-chains
  261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 214
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   33 TYR
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   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   47 LEU
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   67 HIS
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  176 LEU
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  307 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  386 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  450 ASN
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  512 VAL
Chi-restraints excluded: chain A residue  528 LYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 51 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS
L  42 GLN
L 168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.209662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.175912 restraints weight = 18085.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.181116 restraints weight = 9908.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.184505 restraints weight = 6134.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.186764 restraints weight = 4158.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.188236 restraints weight = 3033.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5911
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   8600  Z= 0.151
  Angle     :  0.621   8.685  11713  Z= 0.317
  Chirality :  0.046   0.231   1302
  Planarity :  0.004   0.058   1507
  Dihedral  :  7.233  87.778   1198
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 16.83 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.24), residues: 1065
  helix: -2.52 (0.70), residues: 38
  sheet: -0.99 (0.31), residues: 292
  loop : -2.45 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.016   0.001   TYR A 265 
 PHE   0.027   0.002   PHE H  29 
 TRP   0.018   0.002   TRP L 150 
 HIS   0.003   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8588)
  covalent geometry    : angle       0.61810 (11689)
  SS BOND              : bond        0.00399 (   12)
  SS BOND              : angle       1.50986 (   24)
  hydrogen bonds       : bond        0.03210 (  180)
  hydrogen bonds       : angle       6.62495 (  471)

*********************** 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
  283 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 222
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7826 (mp) cc_final: 0.7241 (tt)
REVERT: H    6 GLN cc_start: 0.6905 (tt0) cc_final: 0.6672 (tt0)
REVERT: H   85 SER cc_start: 0.7644 (t) cc_final: 0.7156 (p)
REVERT: H  103 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.8014 (mt)
REVERT: H  116 THR cc_start: 0.7552 (m) cc_final: 0.6953 (p)
REVERT: H  172 THR cc_start: 0.8461 (m) cc_final: 0.7959 (p)
REVERT: H  176 VAL cc_start: 0.7888 (t) cc_final: 0.7475 (p)
REVERT: H  187 SER cc_start: 0.8262 (t) cc_final: 0.7948 (p)
REVERT: H  189 VAL cc_start: 0.8824 (t) cc_final: 0.8348 (p)
REVERT: H  200 THR cc_start: 0.8664 (m) cc_final: 0.8378 (t)
REVERT: L   62 PHE cc_start: 0.8776 (m-80) cc_final: 0.8274 (m-80)
REVERT: L   82 ASP cc_start: 0.8381 (m-30) cc_final: 0.8112 (m-30)
REVERT: L  107 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6581 (mm-30)
REVERT: L  120 PHE cc_start: 0.7787 (m-80) cc_final: 0.7359 (m-80)
REVERT: L  164 SER cc_start: 0.8467 (t) cc_final: 0.8113 (p)
REVERT: L  178 SER cc_start: 0.8314 (t) cc_final: 0.7518 (m)
REVERT: A   59 PHE cc_start: 0.6853 (m-10) cc_final: 0.6581 (m-10)
REVERT: A  298 GLU cc_start: 0.7617 (tt0) cc_final: 0.7161 (tt0)
REVERT: A  345 THR cc_start: 0.7180 (p) cc_final: 0.6939 (t)
REVERT: A  353 TRP cc_start: 0.8170 (p-90) cc_final: 0.7678 (p-90)
REVERT: A  357 ARG cc_start: 0.7640 (ptm-80) cc_final: 0.7162 (ptm-80)
REVERT: A  369 TYR cc_start: 0.7281 (m-80) cc_final: 0.7056 (m-10)
REVERT: A  378 LYS cc_start: 0.8154 (ptpp) cc_final: 0.7698 (pttm)
REVERT: A  380 TYR cc_start: 0.6201 (m-80) cc_final: 0.5834 (m-80)
REVERT: A  394 ASN cc_start: 0.6646 (t0) cc_final: 0.5991 (t0)
REVERT: A  406 GLU cc_start: 0.7387 (pt0) cc_final: 0.7089 (pt0)
REVERT: A  424 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7626 (ttmm)
REVERT: A  436 TRP cc_start: 0.7477 (p90) cc_final: 0.6890 (p90)
REVERT: A  460 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7736 (mptm)
REVERT: A  465 GLU cc_start: 0.6946 (tt0) cc_final: 0.6312 (tt0)
REVERT: A  531 THR cc_start: 0.6168 (OUTLIER) cc_final: 0.5426 (p)
REVERT: A  542 ASN cc_start: 0.6881 (t0) cc_final: 0.6676 (t0)
REVERT: A  592 PHE cc_start: 0.2222 (OUTLIER) cc_final: -0.0856 (m-10)
REVERT: A  697 MET cc_start: -0.4347 (ptp) cc_final: -0.5474 (ptt)
  outliers start: 61
  outliers final: 43
  residues processed: 253
  average time/residue: 0.1015
  time to fit residues: 34.6766
Evaluate side-chains
  266 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 218
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  158 THR
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   47 LEU
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
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  176 LEU
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  307 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  360 ASN
Chi-restraints excluded: chain A residue  362 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  407 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  512 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0970
   chunk 1 optimal weight:    0.0870
   chunk 98 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0040
   chunk 43 optimal weight:    9.9990
   overall best weight:    0.3368

-------------------------------------------------------------------------------
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
A  70 HIS
A 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.212100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178283 restraints weight = 18073.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.183706 restraints weight = 9616.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.187169 restraints weight = 5831.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.189456 restraints weight = 3875.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.190861 restraints weight = 2781.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8600  Z= 0.107
  Angle     :  0.602  10.626  11713  Z= 0.302
  Chirality :  0.045   0.153   1302
  Planarity :  0.004   0.060   1507
  Dihedral  :  7.106  87.624   1198
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 17.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.24), residues: 1065
  helix: -1.84 (0.79), residues: 32
  sheet: -0.84 (0.31), residues: 292
  loop : -2.33 (0.21), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 110 
 TYR   0.011   0.001   TYR A 265 
 PHE   0.017   0.001   PHE A 375 
 TRP   0.021   0.001   TRP L 150 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8588)
  covalent geometry    : angle       0.60047 (11689)
  SS BOND              : bond        0.00358 (   12)
  SS BOND              : angle       1.10214 (   24)
  hydrogen bonds       : bond        0.02814 (  180)
  hydrogen bonds       : angle       6.29957 (  471)

*********************** 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
  274 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 219
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7807 (mp) cc_final: 0.7231 (tt)
REVERT: H    6 GLN cc_start: 0.6919 (tt0) cc_final: 0.6593 (tt0)
REVERT: H   28 THR cc_start: 0.8220 (m) cc_final: 0.7959 (p)
REVERT: H   54 ASP cc_start: 0.7645 (m-30) cc_final: 0.7321 (m-30)
REVERT: H   85 SER cc_start: 0.7563 (t) cc_final: 0.7098 (p)
REVERT: H  103 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7867 (mt)
REVERT: H  116 THR cc_start: 0.7533 (m) cc_final: 0.7239 (m)
REVERT: H  172 THR cc_start: 0.8407 (m) cc_final: 0.7917 (p)
REVERT: H  176 VAL cc_start: 0.7816 (t) cc_final: 0.7437 (p)
REVERT: H  189 VAL cc_start: 0.8738 (t) cc_final: 0.8273 (p)
REVERT: H  200 THR cc_start: 0.8636 (m) cc_final: 0.8349 (t)
REVERT: L   14 SER cc_start: 0.8491 (m) cc_final: 0.8268 (t)
REVERT: L   62 PHE cc_start: 0.8706 (m-80) cc_final: 0.8439 (m-80)
REVERT: L   82 ASP cc_start: 0.8344 (m-30) cc_final: 0.8089 (m-30)
REVERT: L   97 MET cc_start: 0.6303 (mtm) cc_final: 0.6079 (mtm)
REVERT: L  120 PHE cc_start: 0.7822 (m-80) cc_final: 0.7390 (m-80)
REVERT: L  164 SER cc_start: 0.8494 (t) cc_final: 0.8105 (p)
REVERT: L  178 SER cc_start: 0.8306 (t) cc_final: 0.7510 (m)
REVERT: A   59 PHE cc_start: 0.6749 (m-10) cc_final: 0.6538 (m-10)
REVERT: A  298 GLU cc_start: 0.7525 (tt0) cc_final: 0.7085 (tt0)
REVERT: A  320 VAL cc_start: 0.5208 (m) cc_final: 0.4909 (t)
REVERT: A  353 TRP cc_start: 0.8125 (p-90) cc_final: 0.7653 (p-90)
REVERT: A  357 ARG cc_start: 0.7617 (ptm-80) cc_final: 0.7150 (ptm-80)
REVERT: A  380 TYR cc_start: 0.6208 (m-80) cc_final: 0.5894 (m-80)
REVERT: A  394 ASN cc_start: 0.6748 (t0) cc_final: 0.6105 (t0)
REVERT: A  406 GLU cc_start: 0.7374 (pt0) cc_final: 0.7114 (pt0)
REVERT: A  424 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7492 (ttmm)
REVERT: A  436 TRP cc_start: 0.7455 (p90) cc_final: 0.6852 (p90)
REVERT: A  460 LYS cc_start: 0.8208 (mptm) cc_final: 0.7737 (mptm)
REVERT: A  465 GLU cc_start: 0.6936 (tt0) cc_final: 0.6308 (tt0)
REVERT: A  492 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7009 (pp)
REVERT: A  592 PHE cc_start: 0.1952 (OUTLIER) cc_final: -0.1586 (m-10)
  outliers start: 55
  outliers final: 44
  residues processed: 246
  average time/residue: 0.1055
  time to fit residues: 35.0840
Evaluate side-chains
  264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 216
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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  103 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  158 THR
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   47 LEU
Chi-restraints excluded: chain L residue   73 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  177 LEU
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  176 LEU
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  395 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  468 ILE
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  512 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  556 ASN
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 60 optimal weight:    0.0010
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 86 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 97 optimal weight:    0.3980
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
H 171 HIS
A 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.212031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.178043 restraints weight = 18250.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.183526 restraints weight = 9701.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.187015 restraints weight = 5879.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.189330 restraints weight = 3909.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.190622 restraints weight = 2810.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.4346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.4522

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= 0.111
  Angle     :  0.597   9.343  11713  Z= 0.300
  Chirality :  0.045   0.181   1302
  Planarity :  0.004   0.063   1507
  Dihedral  :  7.038  87.487   1198
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 18.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.25), residues: 1065
  helix: -1.69 (0.82), residues: 32
  sheet: -0.81 (0.31), residues: 297
  loop : -2.25 (0.22), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.035   0.002   PHE H  29 
 TRP   0.017   0.001   TRP L 150 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8588)
  covalent geometry    : angle       0.59619 (11689)
  SS BOND              : bond        0.00373 (   12)
  SS BOND              : angle       0.95522 (   24)
  hydrogen bonds       : bond        0.02727 (  180)
  hydrogen bonds       : angle       6.11941 (  471)

*********************** 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
  264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 212
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7810 (mp) cc_final: 0.7327 (tt)
REVERT: H    6 GLN cc_start: 0.6911 (tt0) cc_final: 0.6542 (tt0)
REVERT: H   28 THR cc_start: 0.8213 (m) cc_final: 0.7963 (p)
REVERT: H   83 LEU cc_start: 0.8568 (tp) cc_final: 0.8353 (tp)
REVERT: H   85 SER cc_start: 0.7440 (t) cc_final: 0.6984 (p)
REVERT: H  103 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7873 (mt)
REVERT: H  116 THR cc_start: 0.7550 (m) cc_final: 0.7254 (m)
REVERT: H  172 THR cc_start: 0.8409 (m) cc_final: 0.7922 (p)
REVERT: H  176 VAL cc_start: 0.7811 (t) cc_final: 0.7432 (p)
REVERT: H  189 VAL cc_start: 0.8685 (t) cc_final: 0.8238 (p)
REVERT: H  200 THR cc_start: 0.8656 (m) cc_final: 0.8352 (t)
REVERT: H  201 TYR cc_start: 0.6129 (m-80) cc_final: 0.5917 (m-80)
REVERT: L   62 PHE cc_start: 0.8732 (m-80) cc_final: 0.8437 (m-80)
REVERT: L   82 ASP cc_start: 0.8351 (m-30) cc_final: 0.8107 (m-30)
REVERT: L   97 MET cc_start: 0.6352 (mtm) cc_final: 0.6070 (mtm)
REVERT: L  107 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6504 (mm-30)
REVERT: L  120 PHE cc_start: 0.7818 (m-80) cc_final: 0.7421 (m-80)
REVERT: L  164 SER cc_start: 0.8502 (t) cc_final: 0.8122 (p)
REVERT: L  178 SER cc_start: 0.8313 (t) cc_final: 0.7489 (m)
REVERT: A  298 GLU cc_start: 0.7506 (tt0) cc_final: 0.7072 (tt0)
REVERT: A  320 VAL cc_start: 0.5152 (m) cc_final: 0.4882 (t)
REVERT: A  353 TRP cc_start: 0.8086 (p-90) cc_final: 0.7594 (p-90)
REVERT: A  357 ARG cc_start: 0.7615 (ptm-80) cc_final: 0.7142 (ptm-80)
REVERT: A  378 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7741 (ptpp)
REVERT: A  380 TYR cc_start: 0.6215 (m-80) cc_final: 0.5733 (m-80)
REVERT: A  394 ASN cc_start: 0.6644 (t0) cc_final: 0.6111 (t0)
REVERT: A  406 GLU cc_start: 0.7317 (pt0) cc_final: 0.7008 (pt0)
REVERT: A  424 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7402 (ttmm)
REVERT: A  433 VAL cc_start: 0.7778 (p) cc_final: 0.7384 (p)
REVERT: A  436 TRP cc_start: 0.7453 (p90) cc_final: 0.6786 (p90)
REVERT: A  458 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8556 (ttmm)
REVERT: A  460 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7646 (mptm)
REVERT: A  465 GLU cc_start: 0.6959 (tt0) cc_final: 0.6347 (tt0)
REVERT: A  492 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6916 (pp)
REVERT: A  592 PHE cc_start: 0.2096 (OUTLIER) cc_final: -0.0950 (m-10)
  outliers start: 52
  outliers final: 43
  residues processed: 240
  average time/residue: 0.0978
  time to fit residues: 31.8958
Evaluate side-chains
  256 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 208
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  103 ILE
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  158 THR
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   47 LEU
Chi-restraints excluded: chain L residue   73 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  177 LEU
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  176 LEU
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  395 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  468 ILE
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  538 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  556 ASN
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 79 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0070
   chunk 104 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0030
   chunk 93 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.3206

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

Flipped N/Q/H residues before XYZ refinement:
H 107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.213477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.180486 restraints weight = 18302.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.185609 restraints weight = 9945.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.188936 restraints weight = 6138.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.191098 restraints weight = 4118.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.192389 restraints weight = 3004.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5836
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057   8600  Z= 0.104
  Angle     :  0.600   9.224  11713  Z= 0.298
  Chirality :  0.045   0.239   1302
  Planarity :  0.005   0.067   1507
  Dihedral  :  6.946  87.355   1198
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 19.06 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.25), residues: 1065
  helix: -1.52 (0.86), residues: 32
  sheet: -0.88 (0.30), residues: 311
  loop : -2.17 (0.22), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 457 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.042   0.002   PHE A 429 
 TRP   0.018   0.001   TRP L 150 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8588)
  covalent geometry    : angle       0.59853 (11689)
  SS BOND              : bond        0.00334 (   12)
  SS BOND              : angle       1.07829 (   24)
  hydrogen bonds       : bond        0.02683 (  180)
  hydrogen bonds       : angle       5.85674 (  471)

*********************** 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: 48
    poor density    : 201
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7849 (mp) cc_final: 0.7331 (tt)
REVERT: H    6 GLN cc_start: 0.6874 (tt0) cc_final: 0.6587 (tt0)
REVERT: H   39 GLN cc_start: 0.7954 (tp40) cc_final: 0.7260 (tt0)
REVERT: H   85 SER cc_start: 0.7342 (t) cc_final: 0.6898 (p)
REVERT: H  103 ILE cc_start: 0.8065 (mt) cc_final: 0.7858 (mt)
REVERT: H  116 THR cc_start: 0.7540 (m) cc_final: 0.6911 (p)
REVERT: H  172 THR cc_start: 0.8360 (m) cc_final: 0.7815 (p)
REVERT: H  176 VAL cc_start: 0.7830 (t) cc_final: 0.7452 (p)
REVERT: H  200 THR cc_start: 0.8635 (m) cc_final: 0.8324 (t)
REVERT: H  201 TYR cc_start: 0.6094 (m-80) cc_final: 0.5892 (m-80)
REVERT: L   14 SER cc_start: 0.8505 (m) cc_final: 0.8255 (t)
REVERT: L   38 GLN cc_start: 0.8227 (tt0) cc_final: 0.7476 (tt0)
REVERT: L   62 PHE cc_start: 0.8704 (m-80) cc_final: 0.8419 (m-80)
REVERT: L   82 ASP cc_start: 0.8315 (m-30) cc_final: 0.8100 (m-30)
REVERT: L   97 MET cc_start: 0.6312 (mtm) cc_final: 0.5928 (mtm)
REVERT: L  107 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6523 (mm-30)
REVERT: L  120 PHE cc_start: 0.7808 (m-80) cc_final: 0.7446 (m-80)
REVERT: L  164 SER cc_start: 0.8524 (t) cc_final: 0.8145 (p)
REVERT: L  178 SER cc_start: 0.8322 (t) cc_final: 0.7503 (m)
REVERT: A  298 GLU cc_start: 0.7490 (tt0) cc_final: 0.7073 (tt0)
REVERT: A  319 ARG cc_start: 0.4243 (OUTLIER) cc_final: 0.3430 (mtm180)
REVERT: A  335 LEU cc_start: 0.7829 (mm) cc_final: 0.7620 (mp)
REVERT: A  353 TRP cc_start: 0.8073 (p-90) cc_final: 0.7583 (p-90)
REVERT: A  357 ARG cc_start: 0.7614 (ptm-80) cc_final: 0.7169 (ptm-80)
REVERT: A  378 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7599 (ptpp)
REVERT: A  380 TYR cc_start: 0.6190 (m-80) cc_final: 0.5529 (m-80)
REVERT: A  394 ASN cc_start: 0.6665 (t0) cc_final: 0.6140 (t0)
REVERT: A  406 GLU cc_start: 0.7321 (pt0) cc_final: 0.6998 (pt0)
REVERT: A  424 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7280 (ttmm)
REVERT: A  433 VAL cc_start: 0.7772 (p) cc_final: 0.7440 (p)
REVERT: A  436 TRP cc_start: 0.7435 (p90) cc_final: 0.6811 (p90)
REVERT: A  458 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8566 (ttmm)
REVERT: A  460 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7619 (mptm)
REVERT: A  465 GLU cc_start: 0.6878 (tt0) cc_final: 0.6300 (tt0)
REVERT: A  592 PHE cc_start: 0.2099 (OUTLIER) cc_final: -0.0969 (m-10)
REVERT: A  697 MET cc_start: -0.3956 (mtt) cc_final: -0.6550 (ptt)
  outliers start: 48
  outliers final: 40
  residues processed: 228
  average time/residue: 0.1005
  time to fit residues: 30.9728
Evaluate side-chains
  246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 202
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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  124 LYS
Chi-restraints excluded: chain H residue  158 THR
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   47 LEU
Chi-restraints excluded: chain L residue   73 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  177 LEU
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  176 LEU
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  307 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  395 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  424 LYS
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  538 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  556 ASN
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 74 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0570
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0770
   overall best weight:    0.9258

-------------------------------------------------------------------------------
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 = 0.4590 r_free = 0.4590 target = 0.209636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.176719 restraints weight = 17670.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.181982 restraints weight = 9446.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.185349 restraints weight = 5746.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.187604 restraints weight = 3834.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.188915 restraints weight = 2757.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5912
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   8600  Z= 0.148
  Angle     :  0.641  11.633  11713  Z= 0.321
  Chirality :  0.046   0.194   1302
  Planarity :  0.005   0.067   1507
  Dihedral  :  7.096  87.108   1198
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 19.60 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.59 (0.25), residues: 1065
  helix: -2.09 (0.75), residues: 38
  sheet: -0.97 (0.30), residues: 314
  loop : -2.18 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  67 
 TYR   0.016   0.001   TYR A 265 
 PHE   0.045   0.002   PHE A 429 
 TRP   0.019   0.002   TRP L 150 
 HIS   0.004   0.001   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8588)
  covalent geometry    : angle       0.63915 (11689)
  SS BOND              : bond        0.00432 (   12)
  SS BOND              : angle       1.26554 (   24)
  hydrogen bonds       : bond        0.03065 (  180)
  hydrogen bonds       : angle       6.04711 (  471)

*********************** 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
  259 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 213
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7815 (mp) cc_final: 0.7241 (tt)
REVERT: H    6 GLN cc_start: 0.6917 (tt0) cc_final: 0.6672 (tt0)
REVERT: H   85 SER cc_start: 0.7427 (t) cc_final: 0.6983 (p)
REVERT: H  103 ILE cc_start: 0.8229 (mt) cc_final: 0.7990 (mt)
REVERT: H  116 THR cc_start: 0.7516 (m) cc_final: 0.6933 (p)
REVERT: H  172 THR cc_start: 0.8383 (m) cc_final: 0.7876 (p)
REVERT: H  176 VAL cc_start: 0.7929 (t) cc_final: 0.7541 (p)
REVERT: H  187 SER cc_start: 0.8164 (t) cc_final: 0.7851 (p)
REVERT: H  200 THR cc_start: 0.8678 (m) cc_final: 0.8427 (t)
REVERT: L    4 LEU cc_start: 0.7619 (mt) cc_final: 0.7221 (tp)
REVERT: L   62 PHE cc_start: 0.8860 (m-80) cc_final: 0.8519 (m-80)
REVERT: L   82 ASP cc_start: 0.8340 (m-30) cc_final: 0.8090 (m-30)
REVERT: L   97 MET cc_start: 0.6282 (mtm) cc_final: 0.5923 (mtm)
REVERT: L  107 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6541 (mm-30)
REVERT: L  120 PHE cc_start: 0.7756 (m-80) cc_final: 0.7378 (m-80)
REVERT: L  147 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7316 (mppt)
REVERT: L  164 SER cc_start: 0.8460 (t) cc_final: 0.8097 (p)
REVERT: L  178 SER cc_start: 0.8351 (t) cc_final: 0.7573 (m)
REVERT: A  298 GLU cc_start: 0.7564 (tt0) cc_final: 0.7169 (tt0)
REVERT: A  353 TRP cc_start: 0.8179 (p-90) cc_final: 0.7616 (p-90)
REVERT: A  357 ARG cc_start: 0.7614 (ptm-80) cc_final: 0.7372 (ptm-80)
REVERT: A  380 TYR cc_start: 0.6291 (m-80) cc_final: 0.5880 (m-80)
REVERT: A  406 GLU cc_start: 0.7328 (pt0) cc_final: 0.7104 (pt0)
REVERT: A  424 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7588 (ttmm)
REVERT: A  436 TRP cc_start: 0.7528 (p90) cc_final: 0.6802 (p90)
REVERT: A  458 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8500 (ttmm)
REVERT: A  460 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7603 (mptm)
REVERT: A  515 PHE cc_start: 0.7796 (m-10) cc_final: 0.7459 (m-10)
REVERT: A  531 THR cc_start: 0.6164 (OUTLIER) cc_final: 0.5205 (m)
REVERT: A  592 PHE cc_start: 0.2659 (OUTLIER) cc_final: -0.0544 (m-80)
REVERT: A  697 MET cc_start: -0.3711 (mtt) cc_final: -0.6243 (ptt)
  outliers start: 46
  outliers final: 38
  residues processed: 237
  average time/residue: 0.0951
  time to fit residues: 31.0044
Evaluate side-chains
  252 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 210
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  158 THR
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   23 CYS
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
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  176 LEU
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  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  460 LYS
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  556 ASN
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 98 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0030
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0770
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 105 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.3750

-------------------------------------------------------------------------------
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 = 0.4615 r_free = 0.4615 target = 0.212142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.179341 restraints weight = 18153.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184642 restraints weight = 9616.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.188002 restraints weight = 5825.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.190234 restraints weight = 3892.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.191531 restraints weight = 2801.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   8600  Z= 0.109
  Angle     :  0.628   9.399  11713  Z= 0.312
  Chirality :  0.046   0.209   1302
  Planarity :  0.005   0.067   1507
  Dihedral  :  6.816  86.996   1194
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.98 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.25), residues: 1065
  helix: -2.03 (0.77), residues: 38
  sheet: -0.94 (0.30), residues: 314
  loop : -2.09 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  38 
 TYR   0.011   0.001   TYR A 265 
 PHE   0.041   0.002   PHE A 429 
 TRP   0.019   0.001   TRP L 150 
 HIS   0.003   0.000   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8588)
  covalent geometry    : angle       0.62753 (11689)
  SS BOND              : bond        0.00268 (   12)
  SS BOND              : angle       0.95246 (   24)
  hydrogen bonds       : bond        0.02717 (  180)
  hydrogen bonds       : angle       5.75079 (  471)

********************** 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
  243 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 203
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.7803 (mp) cc_final: 0.7368 (tt)
REVERT: H   39 GLN cc_start: 0.8027 (tp40) cc_final: 0.7326 (tt0)
REVERT: H   85 SER cc_start: 0.7385 (t) cc_final: 0.6944 (p)
REVERT: H  103 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7849 (mt)
REVERT: H  172 THR cc_start: 0.8357 (m) cc_final: 0.7835 (p)
REVERT: H  176 VAL cc_start: 0.7873 (t) cc_final: 0.7499 (p)
REVERT: H  200 THR cc_start: 0.8678 (m) cc_final: 0.8443 (t)
REVERT: L   62 PHE cc_start: 0.8757 (m-80) cc_final: 0.8467 (m-80)
REVERT: L   82 ASP cc_start: 0.8320 (m-30) cc_final: 0.8105 (m-30)
REVERT: L   97 MET cc_start: 0.6274 (mtm) cc_final: 0.5906 (mtm)
REVERT: L  107 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6482 (mm-30)
REVERT: L  120 PHE cc_start: 0.7802 (m-80) cc_final: 0.7420 (m-80)
REVERT: L  147 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7316 (mppt)
REVERT: L  164 SER cc_start: 0.8493 (t) cc_final: 0.8121 (p)
REVERT: L  178 SER cc_start: 0.8327 (t) cc_final: 0.7521 (m)
REVERT: A  177 MET cc_start: 0.1192 (ttp) cc_final: 0.0934 (ttp)
REVERT: A  269 TYR cc_start: 0.7755 (m-80) cc_final: 0.7535 (m-80)
REVERT: A  298 GLU cc_start: 0.7540 (tt0) cc_final: 0.7118 (tt0)
REVERT: A  319 ARG cc_start: 0.4379 (OUTLIER) cc_final: 0.3709 (mtm180)
REVERT: A  353 TRP cc_start: 0.8079 (p-90) cc_final: 0.7572 (p-90)
REVERT: A  357 ARG cc_start: 0.7667 (ptm-80) cc_final: 0.7314 (ptm-80)
REVERT: A  406 GLU cc_start: 0.7308 (pt0) cc_final: 0.7005 (pt0)
REVERT: A  424 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7249 (ttmm)
REVERT: A  436 TRP cc_start: 0.7458 (p90) cc_final: 0.6761 (p90)
REVERT: A  458 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8549 (ttmm)
REVERT: A  460 LYS cc_start: 0.8083 (mptm) cc_final: 0.7605 (mptm)
REVERT: A  592 PHE cc_start: 0.2730 (OUTLIER) cc_final: -0.0487 (m-10)
REVERT: A  697 MET cc_start: -0.3600 (mtt) cc_final: -0.6209 (ptt)
  outliers start: 40
  outliers final: 34
  residues processed: 224
  average time/residue: 0.0982
  time to fit residues: 29.7547
Evaluate side-chains
  240 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 202
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain H residue  158 THR
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   23 CYS
Chi-restraints excluded: chain L residue   24 ARG
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue  111 THR
Chi-restraints excluded: chain L residue  147 LYS
Chi-restraints excluded: chain L residue  177 LEU
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  176 LEU
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  395 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  556 ASN
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 50 optimal weight:    0.0010
   chunk 95 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 96 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8388

-------------------------------------------------------------------------------
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 = 0.4595 r_free = 0.4595 target = 0.210160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.176488 restraints weight = 17869.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.181983 restraints weight = 9586.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.185427 restraints weight = 5862.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.187704 restraints weight = 3946.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.189238 restraints weight = 2862.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5913
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095   8600  Z= 0.139
  Angle     :  0.638   9.638  11713  Z= 0.319
  Chirality :  0.046   0.184   1302
  Planarity :  0.005   0.068   1507
  Dihedral  :  6.871  86.863   1194
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 20.45 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.51 (0.25), residues: 1065
  helix: -1.96 (0.78), residues: 38
  sheet: -0.93 (0.30), residues: 316
  loop : -2.12 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.015   0.001   TYR A 365 
 PHE   0.040   0.002   PHE A 429 
 TRP   0.018   0.001   TRP L 150 
 HIS   0.003   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8588)
  covalent geometry    : angle       0.63643 (11689)
  SS BOND              : bond        0.00393 (   12)
  SS BOND              : angle       1.12144 (   24)
  hydrogen bonds       : bond        0.02905 (  180)
  hydrogen bonds       : angle       5.83120 (  471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1941.23 seconds
wall clock time: 34 minutes 11.96 seconds (2051.96 seconds total)