Starting phenix.real_space_refine
on Tue Mar  3 20:26:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vwh_21416/03_2026/6vwh_21416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vwh_21416/03_2026/6vwh_21416.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2026/6vwh_21416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2026/6vwh_21416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2026/6vwh_21416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2026/6vwh_21416.cif"
  }
  resolution = 4.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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: 5
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    2726      2.51       5
     N     750      2.21       5
     O     808      1.98       5
     H    4139      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8461
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 2196
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 10, 'TRANS': 125}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 6265
          Classifications: {'peptide': 403}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 377}
          Chain breaks: 4
  Time building chain proxies: 1.57, per 1000 atoms: 0.19
  Number of scatterers: 8461
  At special positions: 0
  Unit cell: (97.52, 119.78, 79.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     O     808      8.00
     N     750      7.00
     C    2726      6.00
     H    4139      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 776 " - pdb=" SG  CYS A 785 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B   3 " - pdb=" SG  CYS B  22 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 152 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 189 " - pdb=" SG  CYS B 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 209 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 205 " - pdb=" SG  CYS B 218 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 221 " - pdb=" SG  CYS B 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 234 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 252 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 277 " - pdb=" SG  CYS B 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 294 " - pdb=" SG  CYS B 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 776 " - pdb=" SG  CYS B 785 " distance=2.04

  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: 0.79
  Conformation dependent library (CDL) restraints added in 176.9 milliseconds
  

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1026

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 13 sheets defined
      11.3% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 684 through 697
      removed outlier: 3.717A  pdb=" N   TYR A 688 " --> pdb=" O   GLU A 684 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE A 692 " --> pdb=" O   TYR A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 784
    Processing helix  chain 'B' and resid 12 through 17
      removed outlier: 3.529A  pdb=" N   LEU B  16 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 12 through 17'
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 4.334A  pdb=" N   ASN B  21 " --> pdb=" O   ARG B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.965A  pdb=" N   ILE B 130 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 137
    Processing helix  chain 'B' and resid 144 through 149
    Processing helix  chain 'B' and resid 249 through 255
    Processing helix  chain 'B' and resid 779 through 784
    Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593
      removed outlier: 4.919A  pdb=" N   ASP A 586 " --> pdb=" O   ASN A 602 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN A 602 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ASN A 592 " --> pdb=" O   GLN A 596 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   GLN A 596 " --> pdb=" O   ASN A 592 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752
      removed outlier: 3.536A  pdb=" N   TYR A 614 " --> pdb=" O   VAL A 752 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR A 769 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA A 793 " --> pdb=" O   TYR A 769 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3
      removed outlier: 3.609A  pdb=" N   ILE B  25 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 10
      removed outlier: 6.735A  pdb=" N   ILE B   7 " --> pdb=" O   HIS B  30 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   LEU B  32 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B  29 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ILE B  31 " --> pdb=" O   PHE B  58 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LEU B  55 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   PHE B  90 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU B  57 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ARG B 112 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL B  88 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   GLU B 114 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   PHE B  90 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 165
    Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177
    Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195
    Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 209
      removed outlier: 8.147A  pdb=" N   SER B 208 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   CYS B 218 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 226
    Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 248
      removed outlier: 3.664A  pdb=" N   ARG B 245 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   CYS B 273 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ARG B 240 " --> pdb=" O   CYS B 273 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 281 through 283
    Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 590
      removed outlier: 4.801A  pdb=" N   ASP B 586 " --> pdb=" O   ASN B 602 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 602 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 747 through 751
      removed outlier: 4.145A  pdb=" N   TYR B 613 " --> pdb=" O   CYS B 776 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   CYS B 776 " --> pdb=" O   TYR B 613 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL B 791 " --> pdb=" O   ILE B 771 " (cutoff:3.500A)

    94 hydrogen bonds defined for protein.
    249 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: 1.87

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        0.83 -     1.04: 4137
        1.04 -     1.24: 526
        1.24 -     1.44: 1429
        1.44 -     1.64: 2432
        1.64 -     1.84: 44
  Bond restraints: 8568
  Sorted by residual:
  bond pdb=" CB  CYS B 205 "
       pdb=" SG  CYS B 205 "
    ideal  model  delta    sigma   weight residual
    1.808  1.737  0.071 3.30e-02 9.18e+02 4.57e+00
  bond pdb=" CB  CYS B 218 "
       pdb=" SG  CYS B 218 "
    ideal  model  delta    sigma   weight residual
    1.808  1.752  0.056 3.30e-02 9.18e+02 2.89e+00
  bond pdb=" N   ASN A 577 "
       pdb=" H   ASN A 577 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.31e+00
  bond pdb=" N   GLU A 682 "
       pdb=" CA  GLU A 682 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.09e+00
  bond pdb=" C   ARG B 620 "
       pdb=" N   GLN B 621 "
    ideal  model  delta    sigma   weight residual
    1.340  1.260  0.080 5.87e-02 2.90e+02 1.87e+00
  ... (remaining 8563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 14251
        1.55 -     3.09: 1015
        3.09 -     4.64: 125
        4.64 -     6.18: 17
        6.18 -     7.73: 5
  Bond angle restraints: 15413
  Sorted by residual:
  angle pdb=" N   ASN B  94 "
        pdb=" CA  ASN B  94 "
        pdb=" C   ASN B  94 "
      ideal   model   delta    sigma   weight residual
     113.28  120.89   -7.61 1.57e+00 4.06e-01 2.35e+01
  angle pdb=" N   ASN B  94 "
        pdb=" CA  ASN B  94 "
        pdb=" CB  ASN B  94 "
      ideal   model   delta    sigma   weight residual
     114.17  108.88    5.29 1.14e+00 7.69e-01 2.16e+01
  angle pdb=" N   LEU B 256 "
        pdb=" CA  LEU B 256 "
        pdb=" C   LEU B 256 "
      ideal   model   delta    sigma   weight residual
     110.20  103.33    6.87 1.58e+00 4.01e-01 1.89e+01
  angle pdb=" N   ASN B 602 "
        pdb=" CA  ASN B 602 "
        pdb=" C   ASN B 602 "
      ideal   model   delta    sigma   weight residual
     110.10  115.17   -5.07 1.53e+00 4.27e-01 1.10e+01
  angle pdb=" CA  TYR B 628 "
        pdb=" CB  TYR B 628 "
        pdb=" CG  TYR B 628 "
      ideal   model   delta    sigma   weight residual
     113.90  119.31   -5.41 1.80e+00 3.09e-01 9.04e+00
  ... (remaining 15408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 3757
       17.84 -    35.68: 258
       35.68 -    53.52: 80
       53.52 -    71.36: 38
       71.36 -    89.20: 5
  Dihedral angle restraints: 4138
    sinusoidal: 2235
      harmonic: 1903
  Sorted by residual:
  dihedral pdb=" CB  CYS B 205 "
           pdb=" SG  CYS B 205 "
           pdb=" SG  CYS B 218 "
           pdb=" CB  CYS B 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.70   55.70     1      1.00e+01 1.00e-02 4.19e+01
  dihedral pdb=" CA  SER A 788 "
           pdb=" C   SER A 788 "
           pdb=" N   ASN A 789 "
           pdb=" CA  ASN A 789 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.77   29.23     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  SER B 788 "
           pdb=" C   SER B 788 "
           pdb=" N   ASN B 789 "
           pdb=" CA  ASN B 789 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.22   28.78     0      5.00e+00 4.00e-02 3.31e+01
  ... (remaining 4135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 362
       0.045 -    0.089: 194
       0.089 -    0.134: 68
       0.134 -    0.179: 13
       0.179 -    0.223: 3
  Chirality restraints: 640
  Sorted by residual:
  chirality pdb=" CA  PHE B 766 "
            pdb=" N   PHE B 766 "
            pdb=" C   PHE B 766 "
            pdb=" CB  PHE B 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ASN B  94 "
            pdb=" N   ASN B  94 "
            pdb=" C   ASN B  94 "
            pdb=" CB  ASN B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" CB  ILE B 615 "
            pdb=" CA  ILE B 615 "
            pdb=" CG1 ILE B 615 "
            pdb=" CG2 ILE B 615 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.36e-01
  ... (remaining 637 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 770 "   -0.095 9.50e-02 1.11e+02   4.64e-02 2.69e+01
        pdb=" NE  ARG A 770 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 770 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 770 "    0.058 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 770 "    0.039 2.00e-02 2.50e+03
        pdb="HH11 ARG A 770 "   -0.014 2.00e-02 2.50e+03
        pdb="HH12 ARG A 770 "   -0.011 2.00e-02 2.50e+03
        pdb="HH21 ARG A 770 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 770 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 283 "    0.060 9.50e-02 1.11e+02   3.92e-02 2.60e+01
        pdb=" NE  ARG B 283 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 283 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 283 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 283 "   -0.049 2.00e-02 2.50e+03
        pdb="HH11 ARG B 283 "    0.009 2.00e-02 2.50e+03
        pdb="HH12 ARG B 283 "    0.038 2.00e-02 2.50e+03
        pdb="HH21 ARG B 283 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG B 283 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 689 "    0.034 9.50e-02 1.11e+02   3.42e-02 2.36e+01
        pdb=" NE  ARG A 689 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 689 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 689 "   -0.074 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 689 "    0.011 2.00e-02 2.50e+03
        pdb="HH11 ARG A 689 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG A 689 "    0.057 2.00e-02 2.50e+03
        pdb="HH21 ARG A 689 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 689 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 273
        2.10 -     2.72: 14639
        2.72 -     3.35: 23897
        3.35 -     3.97: 29803
        3.97 -     4.60: 46113
  Nonbonded interactions: 114725
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 614 "
            pdb=" H   VAL B 752 "
     model   vdw
     1.470 2.450
  nonbonded pdb=" O   TYR A 626 "
            pdb=" H   TYR A 628 "
     model   vdw
     1.485 2.450
  nonbonded pdb=" HG  SER B 257 "
            pdb=" O   GLU B 264 "
     model   vdw
     1.490 2.450
  nonbonded pdb=" O   ARG A 764 "
            pdb=" HG1 THR A 767 "
     model   vdw
     1.517 2.450
  nonbonded pdb=" O   TYR B 626 "
            pdb=" H   TYR B 628 "
     model   vdw
     1.517 2.450
  ... (remaining 114720 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:             5.830
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.040
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5785
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      :  0.006   0.080   4444  Z= 0.245
  Angle     :  1.073   7.731   6040  Z= 0.615
  Chirality :  0.058   0.223    640
  Planarity :  0.005   0.053    787
  Dihedral  : 13.745  89.202   1642
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  6.69 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  5.97 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.34), residues: 523
  helix: -3.57 (0.58), residues: 40
  sheet: -0.34 (0.46), residues: 131
  loop : -1.21 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.079   0.007   ARG A 770 
 TYR   0.042   0.006   TYR B 769 
 PHE   0.018   0.003   PHE B  90 
 TRP   0.021   0.006   TRP B 618 
 HIS   0.012   0.003   HIS B 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 4429)
  covalent geometry    : angle       1.06292 ( 6010)
  SS BOND              : bond        0.00535 (   15)
  SS BOND              : angle       2.38139 (   30)
  hydrogen bonds       : bond        0.28841 (   94)
  hydrogen bonds       : angle      12.07725 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 ILE cc_start: 0.8430 (mt) cc_final: 0.8204 (mm)
REVERT: B  184 MET cc_start: 0.7692 (mtp) cc_final: 0.7432 (mtt)
REVERT: B  242 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7453 (mm-30)
REVERT: B  270 ASP cc_start: 0.6463 (t0) cc_final: 0.6110 (t0)
REVERT: B  601 TRP cc_start: 0.6939 (p90) cc_final: 0.6050 (p90)
REVERT: B  613 TYR cc_start: 0.4841 (p90) cc_final: 0.4202 (p90)
  outliers start: 4
  outliers final: 1
  residues processed: 89
  average time/residue: 0.1898
  time to fit residues: 20.5028
Evaluate side-chains
  56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 619 GLN
A 697 HIS
B  14 GLN
B  72 ASN
B  94 ASN
B 102 ASN
B 136 ASN
B 198 ASN
B 592 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.124523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.109168 restraints weight = 59469.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.113026 restraints weight = 30731.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.115616 restraints weight = 19029.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.117322 restraints weight = 13389.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.118507 restraints weight = 10189.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4444  Z= 0.186
  Angle     :  0.726   5.854   6040  Z= 0.398
  Chirality :  0.048   0.167    640
  Planarity :  0.005   0.039    787
  Dihedral  :  7.018  29.389    597
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.69 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.35), residues: 523
  helix: -2.45 (0.74), residues: 33
  sheet: -0.84 (0.43), residues: 130
  loop : -0.72 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 620 
 TYR   0.018   0.002   TYR B 628 
 PHE   0.010   0.001   PHE B  90 
 TRP   0.016   0.002   TRP B 618 
 HIS   0.010   0.002   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4429)
  covalent geometry    : angle       0.71837 ( 6010)
  SS BOND              : bond        0.00241 (   15)
  SS BOND              : angle       1.67042 (   30)
  hydrogen bonds       : bond        0.05354 (   94)
  hydrogen bonds       : angle       9.53825 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  582 SER cc_start: 0.8223 (t) cc_final: 0.7999 (m)
REVERT: A  598 ILE cc_start: 0.7708 (pt) cc_final: 0.7453 (mp)
REVERT: B  601 TRP cc_start: 0.7104 (p90) cc_final: 0.6162 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1410
  time to fit residues: 11.5494
Evaluate side-chains
  47 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0870
   chunk 51 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0970
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
A 619 GLN
B  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.125634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.109785 restraints weight = 58523.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.113752 restraints weight = 30113.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.116391 restraints weight = 18516.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.118182 restraints weight = 12889.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.119383 restraints weight = 9733.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.4424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5822
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4444  Z= 0.112
  Angle     :  0.593   4.389   6040  Z= 0.322
  Chirality :  0.046   0.140    640
  Planarity :  0.004   0.040    787
  Dihedral  :  6.197  26.394    597
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.69 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.36), residues: 523
  helix: -1.83 (0.75), residues: 28
  sheet: -1.14 (0.42), residues: 134
  loop : -0.63 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  59 
 TYR   0.016   0.001   TYR B 628 
 PHE   0.010   0.001   PHE A 747 
 TRP   0.015   0.002   TRP B 618 
 HIS   0.008   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4429)
  covalent geometry    : angle       0.59033 ( 6010)
  SS BOND              : bond        0.00229 (   15)
  SS BOND              : angle       1.00890 (   30)
  hydrogen bonds       : bond        0.03633 (   94)
  hydrogen bonds       : angle       8.21815 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  582 SER cc_start: 0.8309 (t) cc_final: 0.8082 (m)
REVERT: A  598 ILE cc_start: 0.7728 (pt) cc_final: 0.7501 (mp)
REVERT: B  136 ASN cc_start: 0.8490 (t0) cc_final: 0.8138 (t0)
REVERT: B  242 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8222 (mm-30)
REVERT: B  601 TRP cc_start: 0.6930 (p90) cc_final: 0.5940 (p90)
REVERT: B  773 ILE cc_start: 0.7966 (mt) cc_final: 0.7567 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1462
  time to fit residues: 12.3937
Evaluate side-chains
  52 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0370
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0870
   chunk 13 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
B  11 ASN
B  72 ASN
B 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.126422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.111041 restraints weight = 59135.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.114783 restraints weight = 30265.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.117227 restraints weight = 18620.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.118931 restraints weight = 13126.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.120053 restraints weight = 10016.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5810
moved from start:          0.4877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4444  Z= 0.100
  Angle     :  0.563   4.929   6040  Z= 0.303
  Chirality :  0.045   0.141    640
  Planarity :  0.004   0.035    787
  Dihedral  :  5.695  24.960    597
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.07 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.36), residues: 523
  helix: -1.31 (0.83), residues: 28
  sheet: -1.04 (0.43), residues: 128
  loop : -0.61 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 174 
 TYR   0.015   0.001   TYR B 628 
 PHE   0.005   0.001   PHE B 748 
 TRP   0.015   0.002   TRP B 618 
 HIS   0.007   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4429)
  covalent geometry    : angle       0.55997 ( 6010)
  SS BOND              : bond        0.00206 (   15)
  SS BOND              : angle       1.04819 (   30)
  hydrogen bonds       : bond        0.03144 (   94)
  hydrogen bonds       : angle       7.39726 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7741 (pt) cc_final: 0.7526 (mp)
REVERT: B  136 ASN cc_start: 0.8437 (t0) cc_final: 0.8063 (t0)
REVERT: B  244 TRP cc_start: 0.6807 (p-90) cc_final: 0.6427 (p-90)
REVERT: B  601 TRP cc_start: 0.6801 (p90) cc_final: 0.5792 (p90)
REVERT: B  773 ILE cc_start: 0.7941 (mt) cc_final: 0.7511 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1307
  time to fit residues: 10.5047
Evaluate side-chains
  49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 ASN
B 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.123526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.107902 restraints weight = 59485.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.111685 restraints weight = 29816.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.114262 restraints weight = 18204.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.115868 restraints weight = 12700.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.117127 restraints weight = 9805.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5964
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   4444  Z= 0.161
  Angle     :  0.612   5.903   6040  Z= 0.332
  Chirality :  0.047   0.171    640
  Planarity :  0.004   0.035    787
  Dihedral  :  5.656  25.320    597
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.80 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.36), residues: 523
  helix: -1.24 (0.77), residues: 28
  sheet: -1.42 (0.42), residues: 129
  loop : -0.85 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 112 
 TYR   0.016   0.002   TYR B 628 
 PHE   0.013   0.002   PHE A 747 
 TRP   0.020   0.002   TRP B 618 
 HIS   0.004   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4429)
  covalent geometry    : angle       0.60323 ( 6010)
  SS BOND              : bond        0.00318 (   15)
  SS BOND              : angle       1.56650 (   30)
  hydrogen bonds       : bond        0.03644 (   94)
  hydrogen bonds       : angle       7.68882 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7931 (pt) cc_final: 0.7665 (mp)
REVERT: B   25 ILE cc_start: 0.7168 (mp) cc_final: 0.6498 (mt)
REVERT: B  136 ASN cc_start: 0.8506 (t0) cc_final: 0.8188 (t0)
REVERT: B  242 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7933 (mm-30)
REVERT: B  244 TRP cc_start: 0.7188 (p-90) cc_final: 0.6390 (p-90)
REVERT: B  274 MET cc_start: 0.7660 (mpp) cc_final: 0.7166 (mpp)
REVERT: B  586 ASP cc_start: 0.6570 (t0) cc_final: 0.6298 (t0)
REVERT: B  601 TRP cc_start: 0.7009 (p90) cc_final: 0.5901 (p90)
REVERT: B  773 ILE cc_start: 0.7998 (mt) cc_final: 0.7677 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1339
  time to fit residues: 10.7993
Evaluate side-chains
  48 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 630 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.123799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.109111 restraints weight = 59747.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.112680 restraints weight = 30656.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.115110 restraints weight = 18938.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.116737 restraints weight = 13264.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.117844 restraints weight = 10092.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5929
moved from start:          0.5836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4444  Z= 0.136
  Angle     :  0.577   5.070   6040  Z= 0.311
  Chirality :  0.045   0.136    640
  Planarity :  0.004   0.039    787
  Dihedral  :  5.572  24.048    597
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.41 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.36), residues: 523
  helix: -1.60 (0.78), residues: 28
  sheet: -1.70 (0.40), residues: 135
  loop : -0.97 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 112 
 TYR   0.016   0.002   TYR B 626 
 PHE   0.010   0.001   PHE A 747 
 TRP   0.018   0.003   TRP B 618 
 HIS   0.005   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4429)
  covalent geometry    : angle       0.57135 ( 6010)
  SS BOND              : bond        0.00369 (   15)
  SS BOND              : angle       1.27383 (   30)
  hydrogen bonds       : bond        0.03365 (   94)
  hydrogen bonds       : angle       7.43435 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ILE cc_start: 0.6221 (mp) cc_final: 0.5778 (mt)
REVERT: B  136 ASN cc_start: 0.8473 (t0) cc_final: 0.8259 (t0)
REVERT: B  244 TRP cc_start: 0.7371 (p-90) cc_final: 0.6306 (p-90)
REVERT: B  274 MET cc_start: 0.7738 (mpp) cc_final: 0.7508 (mpp)
REVERT: B  601 TRP cc_start: 0.6905 (p90) cc_final: 0.5919 (p90)
REVERT: B  773 ILE cc_start: 0.7947 (mt) cc_final: 0.7676 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1373
  time to fit residues: 11.1651
Evaluate side-chains
  52 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
B  11 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.127321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.114856 restraints weight = 66740.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.117998 restraints weight = 35681.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.120145 restraints weight = 22483.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.121488 restraints weight = 15789.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.122525 restraints weight = 12161.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.6148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4444  Z= 0.123
  Angle     :  0.564   5.874   6040  Z= 0.303
  Chirality :  0.045   0.142    640
  Planarity :  0.004   0.034    787
  Dihedral  :  5.439  22.759    597
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.99 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.36), residues: 523
  helix: -1.40 (0.80), residues: 28
  sheet: -1.59 (0.41), residues: 135
  loop : -1.09 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 757 
 TYR   0.018   0.002   TYR B 626 
 PHE   0.007   0.001   PHE A 747 
 TRP   0.016   0.002   TRP B 618 
 HIS   0.005   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4429)
  covalent geometry    : angle       0.55999 ( 6010)
  SS BOND              : bond        0.00292 (   15)
  SS BOND              : angle       1.14399 (   30)
  hydrogen bonds       : bond        0.03142 (   94)
  hydrogen bonds       : angle       7.23549 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ILE cc_start: 0.6191 (mp) cc_final: 0.5668 (mt)
REVERT: B  136 ASN cc_start: 0.8618 (t0) cc_final: 0.8399 (t0)
REVERT: B  601 TRP cc_start: 0.6847 (p90) cc_final: 0.5935 (p90)
REVERT: B  602 ASN cc_start: 0.7828 (m110) cc_final: 0.7590 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1380
  time to fit residues: 11.4778
Evaluate side-chains
  52 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.122952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.107529 restraints weight = 59271.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.111204 restraints weight = 30555.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.113743 restraints weight = 19031.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.115379 restraints weight = 13396.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.116533 restraints weight = 10322.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5997
moved from start:          0.6425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4444  Z= 0.133
  Angle     :  0.565   4.270   6040  Z= 0.304
  Chirality :  0.045   0.150    640
  Planarity :  0.005   0.050    787
  Dihedral  :  5.391  22.757    597
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.13 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.36), residues: 523
  helix: -1.39 (0.83), residues: 28
  sheet: -1.71 (0.42), residues: 135
  loop : -1.15 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 180 
 TYR   0.015   0.002   TYR B 745 
 PHE   0.007   0.001   PHE A 747 
 TRP   0.017   0.002   TRP B 618 
 HIS   0.006   0.002   HIS B 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4429)
  covalent geometry    : angle       0.55939 ( 6010)
  SS BOND              : bond        0.00403 (   15)
  SS BOND              : angle       1.22525 (   30)
  hydrogen bonds       : bond        0.03100 (   94)
  hydrogen bonds       : angle       7.27881 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 ASN cc_start: 0.8588 (t0) cc_final: 0.8256 (t0)
REVERT: B  274 MET cc_start: 0.7592 (mpp) cc_final: 0.6995 (mpp)
REVERT: B  601 TRP cc_start: 0.6851 (p90) cc_final: 0.5988 (p90)
REVERT: B  602 ASN cc_start: 0.7758 (m110) cc_final: 0.7544 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1540
  time to fit residues: 12.6473
Evaluate side-chains
  54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0870
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.127258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.114806 restraints weight = 66281.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.118045 restraints weight = 35420.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.120235 restraints weight = 22193.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.121622 restraints weight = 15507.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.122682 restraints weight = 11794.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5936
moved from start:          0.6627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   4444  Z= 0.101
  Angle     :  0.531   4.156   6040  Z= 0.284
  Chirality :  0.045   0.154    640
  Planarity :  0.004   0.034    787
  Dihedral  :  5.154  22.568    597
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.41 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.82 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.36), residues: 523
  helix: -1.27 (0.80), residues: 28
  sheet: -1.55 (0.43), residues: 133
  loop : -1.18 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 112 
 TYR   0.015   0.001   TYR B 626 
 PHE   0.007   0.001   PHE A 747 
 TRP   0.014   0.001   TRP B 618 
 HIS   0.007   0.001   HIS B 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4429)
  covalent geometry    : angle       0.52758 ( 6010)
  SS BOND              : bond        0.00186 (   15)
  SS BOND              : angle       1.02324 (   30)
  hydrogen bonds       : bond        0.02759 (   94)
  hydrogen bonds       : angle       6.95549 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  690 LYS cc_start: 0.9461 (tptt) cc_final: 0.9219 (tptp)
REVERT: B  136 ASN cc_start: 0.8642 (t0) cc_final: 0.8286 (t0)
REVERT: B  274 MET cc_start: 0.7434 (mpp) cc_final: 0.6872 (mpp)
REVERT: B  287 GLN cc_start: 0.6930 (pp30) cc_final: 0.6690 (pp30)
REVERT: B  586 ASP cc_start: 0.7096 (t0) cc_final: 0.6875 (t0)
REVERT: B  602 ASN cc_start: 0.7891 (m110) cc_final: 0.7510 (m110)
REVERT: B  773 ILE cc_start: 0.8056 (mm) cc_final: 0.7786 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1535
  time to fit residues: 12.7901
Evaluate side-chains
  56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 14 optimal weight:    0.1980
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.4982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.123195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.107213 restraints weight = 58057.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.111114 restraints weight = 29442.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.113772 restraints weight = 17955.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.115552 restraints weight = 12408.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.116730 restraints weight = 9409.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5980
moved from start:          0.6748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4444  Z= 0.112
  Angle     :  0.540   3.911   6040  Z= 0.288
  Chirality :  0.045   0.145    640
  Planarity :  0.004   0.034    787
  Dihedral  :  5.116  21.059    597
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  9.18 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.36), residues: 523
  helix: -1.18 (0.81), residues: 28
  sheet: -1.53 (0.43), residues: 133
  loop : -1.20 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 112 
 TYR   0.014   0.001   TYR B 628 
 PHE   0.007   0.001   PHE A 747 
 TRP   0.015   0.001   TRP B 618 
 HIS   0.006   0.001   HIS B 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4429)
  covalent geometry    : angle       0.53584 ( 6010)
  SS BOND              : bond        0.00224 (   15)
  SS BOND              : angle       1.04379 (   30)
  hydrogen bonds       : bond        0.02904 (   94)
  hydrogen bonds       : angle       6.87813 (  249)

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 ASN cc_start: 0.8630 (t0) cc_final: 0.8296 (t0)
REVERT: B  274 MET cc_start: 0.7466 (mpp) cc_final: 0.6929 (mpp)
REVERT: B  287 GLN cc_start: 0.7022 (pp30) cc_final: 0.6812 (pp30)
REVERT: B  602 ASN cc_start: 0.7803 (m110) cc_final: 0.7466 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1704
  time to fit residues: 13.5539
Evaluate side-chains
  54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.121308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.105955 restraints weight = 58829.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.109813 restraints weight = 29933.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.112378 restraints weight = 18242.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.114063 restraints weight = 12627.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.115242 restraints weight = 9576.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6073
moved from start:          0.7092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4444  Z= 0.155
  Angle     :  0.588   4.104   6040  Z= 0.316
  Chirality :  0.046   0.137    640
  Planarity :  0.005   0.046    787
  Dihedral  :  5.408  22.570    597
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.71 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.36), residues: 523
  helix: -1.22 (0.82), residues: 28
  sheet: -1.66 (0.44), residues: 133
  loop : -1.32 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 112 
 TYR   0.019   0.002   TYR B 745 
 PHE   0.011   0.001   PHE A 747 
 TRP   0.018   0.002   TRP B 618 
 HIS   0.007   0.002   HIS B 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4429)
  covalent geometry    : angle       0.58375 ( 6010)
  SS BOND              : bond        0.00290 (   15)
  SS BOND              : angle       1.19017 (   30)
  hydrogen bonds       : bond        0.03247 (   94)
  hydrogen bonds       : angle       7.21841 (  249)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2256.06 seconds
wall clock time: 38 minutes 55.52 seconds (2335.52 seconds total)