Starting phenix.real_space_refine
on Sat Aug 23 06:30:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fas_31505/08_2025/7fas_31505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fas_31505/08_2025/7fas_31505.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fas_31505/08_2025/7fas_31505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fas_31505/08_2025/7fas_31505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fas_31505/08_2025/7fas_31505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fas_31505/08_2025/7fas_31505.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.002
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      75      5.16       5
     C    6414      2.51       5
     N    1753      2.21       5
     O    1931      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 10173
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1229, 10173
          Classifications: {'peptide': 1229}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 31, 'TRANS': 1197}
          Chain breaks: 46
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 2.70, per 1000 atoms: 0.27
  Number of scatterers: 10173
  At special positions: 0
  Unit cell: (109.62, 140.94, 103.356, 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      75     16.00
     O    1931      8.00
     N    1753      7.00
     C    6414      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 588 " - pdb=" SG  CYS A 592 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 643 " - pdb=" SG  CYS A 732 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 769 " - pdb=" SG  CYS A 901 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 783 " - pdb=" SG  CYS A 801 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 797 " - pdb=" SG  CYS A 957 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 966 " - pdb=" SG  CYS A1090 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1088 " - pdb=" SG  CYS A1193 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1140 " - pdb=" SG  CYS A1171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1470 " - pdb=" SG  CYS A1483 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1670 " - pdb=" SG  CYS A1777 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1802 " - pdb=" SG  CYS A1904 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1816 " - pdb=" SG  CYS A1833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1837 " - pdb=" SG  CYS A1955 " distance=2.39
    Simple disulfide: pdb=" SG  CYS A1891 " - pdb=" SG  CYS A1902 " 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: 1.10
  Conformation dependent library (CDL) restraints added in 507.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2350

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 1 sheets defined
      61.4% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 142
      removed outlier: 3.979A  pdb=" N   PHE A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 167
    Processing helix  chain 'A' and resid 178 through 189
    Processing helix  chain 'A' and resid 208 through 226
      removed outlier: 5.605A  pdb=" N   GLN A 219 " --> pdb=" O   ASN A 215 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LYS A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR A 226 " --> pdb=" O   TRP A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 273 through 299
      removed outlier: 3.724A  pdb=" N   ARG A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 305
    Processing helix  chain 'A' and resid 319 through 339
      removed outlier: 3.763A  pdb=" N   GLU A 338 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TRP A 339 " --> pdb=" O   TRP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 608 through 627
      removed outlier: 3.556A  pdb=" N   ASN A 626 " --> pdb=" O   HIS A 622 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 627 " --> pdb=" O   GLU A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 641 through 658
    Processing helix  chain 'A' and resid 667 through 683
    Processing helix  chain 'A' and resid 703 through 713
    Processing helix  chain 'A' and resid 713 through 725
      removed outlier: 3.752A  pdb=" N   ILE A 717 " --> pdb=" O   ASN A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 754
    Processing helix  chain 'A' and resid 755 through 781
      Proline residue:  A 778  - end of helix
    Processing helix  chain 'A' and resid 801 through 813
      removed outlier: 3.540A  pdb=" N   GLU A 806 " --> pdb=" O   LYS A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 847
    Processing helix  chain 'A' and resid 872 through 884
    Processing helix  chain 'A' and resid 887 through 896
    Processing helix  chain 'A' and resid 943 through 945
      No H-bonds generated for 'chain 'A' and resid 943 through 945'
    Processing helix  chain 'A' and resid 961 through 968
    Processing helix  chain 'A' and resid 1016 through 1043
      removed outlier: 3.866A  pdb=" N   VAL A1020 " --> pdb=" O   ASP A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1117
      removed outlier: 3.608A  pdb=" N   ILE A1117 " --> pdb=" O   GLN A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1146
    Processing helix  chain 'A' and resid 1163 through 1171
    Processing helix  chain 'A' and resid 1180 through 1199
    Processing helix  chain 'A' and resid 1291 through 1306
      removed outlier: 4.560A  pdb=" N   GLN A1296 " --> pdb=" O   LYS A1292 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   HIS A1306 " --> pdb=" O   LEU A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1337 through 1355
      removed outlier: 4.299A  pdb=" N   ALA A1341 " --> pdb=" O   GLY A1337 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY A1355 " --> pdb=" O   ASN A1351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1396 through 1405
    Processing helix  chain 'A' and resid 1405 through 1419
    Processing helix  chain 'A' and resid 1444 through 1468
      removed outlier: 3.552A  pdb=" N   LYS A1464 " --> pdb=" O   LEU A1460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1481 through 1512
      removed outlier: 3.945A  pdb=" N   ARG A1485 " --> pdb=" O   GLY A1481 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU A1500 " --> pdb=" O   GLU A1496 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS A1503 " --> pdb=" O   GLN A1499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1607 through 1612
    Processing helix  chain 'A' and resid 1617 through 1624
      removed outlier: 4.104A  pdb=" N   ILE A1621 " --> pdb=" O   GLU A1617 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ILE A1622 " --> pdb=" O   LEU A1618 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS A1624 " --> pdb=" O   PRO A1620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1628 through 1657
    Processing helix  chain 'A' and resid 1662 through 1685
    Processing helix  chain 'A' and resid 1692 through 1706
      removed outlier: 3.540A  pdb=" N   GLU A1704 " --> pdb=" O   SER A1700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1712 through 1726
      removed outlier: 3.610A  pdb=" N   THR A1721 " --> pdb=" O   LYS A1717 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   TRP A1724 " --> pdb=" O   ARG A1720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1744 through 1762
    Processing helix  chain 'A' and resid 1788 through 1816
    Processing helix  chain 'A' and resid 1832 through 1859
      removed outlier: 3.618A  pdb=" N   ALA A1836 " --> pdb=" O   GLU A1832 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TRP A1843 " --> pdb=" O   ASN A1839 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A1844 " --> pdb=" O   TYR A1840 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A1845 " --> pdb=" O   THR A1841 " (cutoff:3.500A)
      Proline residue:  A1846  - end of helix
    Processing helix  chain 'A' and resid 1882 through 1888
    Processing helix  chain 'A' and resid 1952 through 1969
    Processing helix  chain 'A' and resid 1969 through 1974
    Processing sheet with id=AA1, first strand: chain 'A' and resid 911 through 915

    541 hydrogen bonds defined for protein.
    1611 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: 1.63

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3265
        1.35 -     1.47: 2491
        1.47 -     1.59: 4509
        1.59 -     1.71: 0
        1.71 -     1.83: 90
  Bond restraints: 10355
  Sorted by residual:
  bond pdb=" CA  ARG A 848 "
       pdb=" C   ARG A 848 "
    ideal  model  delta    sigma   weight residual
    1.522  1.541 -0.019 1.38e-02 5.25e+03 1.89e+00
  bond pdb=" C   ILE A 900 "
       pdb=" O   ILE A 900 "
    ideal  model  delta    sigma   weight residual
    1.241  1.227  0.014 1.06e-02 8.90e+03 1.77e+00
  bond pdb=" CB  ASN A1898 "
       pdb=" CG  ASN A1898 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.06e+00
  bond pdb=" C   PRO A  98 "
       pdb=" N   PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.326  1.339 -0.013 1.44e-02 4.82e+03 7.98e-01
  bond pdb=" C   ASP A1741 "
       pdb=" N   PRO A1742 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.85e-01
  ... (remaining 10350 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 13664
        1.73 -     3.46: 167
        3.46 -     5.19: 27
        5.19 -     6.92: 12
        6.92 -     8.65: 2
  Bond angle restraints: 13872
  Sorted by residual:
  angle pdb=" N   LYS A1952 "
        pdb=" CA  LYS A1952 "
        pdb=" C   LYS A1952 "
      ideal   model   delta    sigma   weight residual
     112.93  107.70    5.23 1.33e+00 5.65e-01 1.55e+01
  angle pdb=" N   ILE A1831 "
        pdb=" CA  ILE A1831 "
        pdb=" C   ILE A1831 "
      ideal   model   delta    sigma   weight residual
     113.47  109.52    3.95 1.01e+00 9.80e-01 1.53e+01
  angle pdb=" N   ILE A 900 "
        pdb=" CA  ILE A 900 "
        pdb=" C   ILE A 900 "
      ideal   model   delta    sigma   weight residual
     113.42  109.23    4.19 1.17e+00 7.31e-01 1.28e+01
  angle pdb=" C   LYS A1087 "
        pdb=" N   CYS A1088 "
        pdb=" CA  CYS A1088 "
      ideal   model   delta    sigma   weight residual
     122.06  115.79    6.27 1.86e+00 2.89e-01 1.14e+01
  angle pdb=" N   CYS A 901 "
        pdb=" CA  CYS A 901 "
        pdb=" C   CYS A 901 "
      ideal   model   delta    sigma   weight residual
     112.26  116.69   -4.43 1.32e+00 5.74e-01 1.13e+01
  ... (remaining 13867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5490
       17.88 -    35.76: 649
       35.76 -    53.63: 136
       53.63 -    71.51: 20
       71.51 -    89.39: 10
  Dihedral angle restraints: 6305
    sinusoidal: 2710
      harmonic: 3595
  Sorted by residual:
  dihedral pdb=" CB  CYS A 783 "
           pdb=" SG  CYS A 783 "
           pdb=" SG  CYS A 801 "
           pdb=" CB  CYS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.63   57.37     1      1.00e+01 1.00e-02 4.42e+01
  dihedral pdb=" CB  CYS A1088 "
           pdb=" SG  CYS A1088 "
           pdb=" SG  CYS A1193 "
           pdb=" CB  CYS A1193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.45   52.45     1      1.00e+01 1.00e-02 3.75e+01
  dihedral pdb=" CB  CYS A1670 "
           pdb=" SG  CYS A1670 "
           pdb=" SG  CYS A1777 "
           pdb=" CB  CYS A1777 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.25  -35.25     1      1.00e+01 1.00e-02 1.76e+01
  ... (remaining 6302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 973
       0.030 -    0.061: 325
       0.061 -    0.091: 99
       0.091 -    0.122: 39
       0.122 -    0.152: 5
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CA  ILE A 900 "
            pdb=" N   ILE A 900 "
            pdb=" C   ILE A 900 "
            pdb=" CB  ILE A 900 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CA  CYS A1088 "
            pdb=" N   CYS A1088 "
            pdb=" C   CYS A1088 "
            pdb=" CB  CYS A1088 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  CYS A 901 "
            pdb=" N   CYS A 901 "
            pdb=" C   CYS A 901 "
            pdb=" CB  CYS A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 1438 not shown)

  Planarity restraints: 1753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1619 "    0.060 5.00e-02 4.00e+02   8.90e-02 1.27e+01
        pdb=" N   PRO A1620 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A1620 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A1620 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 665 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.45e+00
        pdb=" C   ASN A 665 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ASN A 665 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 666 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1607 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO A1608 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A1608 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A1608 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1750 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 566
        2.73 -     3.28: 10608
        3.28 -     3.82: 16582
        3.82 -     4.36: 18234
        4.36 -     4.90: 31435
  Nonbonded interactions: 77425
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A1609 "
            pdb=" OD2 ASP A1679 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" O   ASP A 169 "
            pdb=" NE2 GLN A 274 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" NH1 ARG A 772 "
            pdb=" O   CYS A 901 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" O   THR A1180 "
            pdb=" OG  SER A1183 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   LYS A 264 "
            pdb=" N   THR A 267 "
     model   vdw
     2.273 3.120
  ... (remaining 77420 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             2.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.470
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
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      :  0.004   0.356  10369  Z= 0.208
  Angle     :  0.536  14.643  13900  Z= 0.297
  Chirality :  0.036   0.152   1441
  Planarity :  0.004   0.089   1753
  Dihedral  : 15.626  89.391   3913
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.80 %
    Favored  : 99.11 %
  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:  0.85 (0.25), residues: 1135
  helix:  2.01 (0.19), residues: 701
  sheet:  0.85 (1.48), residues: 10
  loop : -2.09 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.017   0.001   TYR A 261 
 PHE   0.012   0.001   PHE A1164 
 TRP   0.024   0.001   TRP A 335 
 HIS   0.005   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (10355)
  covalent geometry    : angle       0.51887 (13872)
  SS BOND              : bond        0.09512 (   14)
  SS BOND              : angle       2.99826 (   28)
  hydrogen bonds       : bond        0.11998 (  541)
  hydrogen bonds       : angle       4.52573 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7707 (t0) cc_final: 0.7381 (t0)
REVERT: A 1812 MET cc_start: 0.8979 (ttm) cc_final: 0.8742 (ttm)
  outliers start: 1
  outliers final: 1
  residues processed: 152
  average time/residue: 0.1096
  time to fit residues: 23.3318
Evaluate side-chains
  120 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1956 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.0770
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    0.4980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 601 GLN
A 832 GLN
** A 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.139432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.111981 restraints weight = 20415.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.114328 restraints weight = 10313.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.114431 restraints weight = 7888.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.115195 restraints weight = 7900.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.115250 restraints weight = 6747.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.1034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10369  Z= 0.125
  Angle     :  0.502   8.217  13900  Z= 0.269
  Chirality :  0.037   0.148   1441
  Planarity :  0.004   0.052   1753
  Dihedral  :  3.490  20.223   1296
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  8.56 %
    Favored  : 91.18 %
  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:  0.99 (0.25), residues: 1135
  helix:  2.11 (0.19), residues: 712
  sheet:  0.69 (1.51), residues: 10
  loop : -2.10 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1610 
 TYR   0.020   0.001   TYR A1512 
 PHE   0.032   0.002   PHE A1164 
 TRP   0.024   0.001   TRP A 282 
 HIS   0.004   0.001   HIS A1951 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10355)
  covalent geometry    : angle       0.50038 (13872)
  SS BOND              : bond        0.00279 (   14)
  SS BOND              : angle       1.10504 (   28)
  hydrogen bonds       : bond        0.04150 (  541)
  hydrogen bonds       : angle       3.72566 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 128
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A  160 ASP cc_start: 0.7786 (t0) cc_final: 0.7376 (t0)
REVERT: A  335 TRP cc_start: 0.5336 (t60) cc_final: 0.4676 (t60)
REVERT: A 1143 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: A 1587 TRP cc_start: 0.6877 (p-90) cc_final: 0.6595 (p-90)
REVERT: A 1812 MET cc_start: 0.9025 (ttm) cc_final: 0.8813 (ttm)
REVERT: A 1848 ARG cc_start: 0.3961 (mmt180) cc_final: 0.3754 (mmt-90)
  outliers start: 3
  outliers final: 2
  residues processed: 131
  average time/residue: 0.1153
  time to fit residues: 21.4010
Evaluate side-chains
  117 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1683 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 89 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 114 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 102 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 974 ASN
A1036 GLN
A1099 ASN
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1962 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.138466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.110393 restraints weight = 20333.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.112477 restraints weight = 11090.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.113936 restraints weight = 7522.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.114381 restraints weight = 7236.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.114401 restraints weight = 6114.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10369  Z= 0.129
  Angle     :  0.479   7.173  13900  Z= 0.257
  Chirality :  0.037   0.154   1441
  Planarity :  0.003   0.041   1753
  Dihedral  :  3.423  17.893   1295
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.14 %
    Favored  : 88.06 %
  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:  1.04 (0.26), residues: 1135
  helix:  2.12 (0.19), residues: 712
  sheet:  0.43 (1.52), residues: 10
  loop : -2.03 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1609 
 TYR   0.016   0.001   TYR A1512 
 PHE   0.016   0.001   PHE A1138 
 TRP   0.026   0.001   TRP A 282 
 HIS   0.003   0.001   HIS A1951 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10355)
  covalent geometry    : angle       0.47723 (13872)
  SS BOND              : bond        0.00271 (   14)
  SS BOND              : angle       1.12425 (   28)
  hydrogen bonds       : bond        0.03872 (  541)
  hydrogen bonds       : angle       3.58127 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  160 ASP cc_start: 0.7759 (t0) cc_final: 0.7341 (t0)
REVERT: A  284 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: A  335 TRP cc_start: 0.5241 (t60) cc_final: 0.4798 (t60)
REVERT: A 1587 TRP cc_start: 0.6869 (p-90) cc_final: 0.6646 (p-90)
REVERT: A 1812 MET cc_start: 0.9072 (ttm) cc_final: 0.8671 (ttm)
REVERT: A 1834 LYS cc_start: 0.8225 (tmmt) cc_final: 0.7531 (tmmt)
REVERT: A 1848 ARG cc_start: 0.4163 (mmt180) cc_final: 0.3950 (mmt180)
  outliers start: 9
  outliers final: 4
  residues processed: 131
  average time/residue: 0.1094
  time to fit residues: 20.1226
Evaluate side-chains
  120 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1683 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN
A1343 GLN
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.135835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.107123 restraints weight = 20539.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.109346 restraints weight = 11197.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.109531 restraints weight = 7669.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.110200 restraints weight = 7951.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.110684 restraints weight = 6784.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10369  Z= 0.190
  Angle     :  0.537   8.418  13900  Z= 0.287
  Chirality :  0.039   0.169   1441
  Planarity :  0.004   0.043   1753
  Dihedral  :  3.683  16.987   1295
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.73 %
    Favored  : 84.40 %
  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:  0.85 (0.26), residues: 1135
  helix:  1.93 (0.19), residues: 724
  sheet:  0.50 (1.37), residues: 10
  loop : -2.15 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1609 
 TYR   0.015   0.002   TYR A1512 
 PHE   0.017   0.002   PHE A 650 
 TRP   0.050   0.002   TRP A 282 
 HIS   0.005   0.001   HIS A 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10355)
  covalent geometry    : angle       0.53352 (13872)
  SS BOND              : bond        0.00335 (   14)
  SS BOND              : angle       1.50167 (   28)
  hydrogen bonds       : bond        0.04028 (  541)
  hydrogen bonds       : angle       3.67401 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7806 (t0) cc_final: 0.7376 (t0)
REVERT: A  269 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7494 (pp)
REVERT: A  653 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8041 (m-10)
REVERT: A  840 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8135 (m-10)
REVERT: A  942 SER cc_start: 0.8835 (p) cc_final: 0.8605 (m)
REVERT: A 1812 MET cc_start: 0.9053 (ttm) cc_final: 0.8615 (ttm)
REVERT: A 1834 LYS cc_start: 0.8264 (tmmt) cc_final: 0.7646 (tttt)
REVERT: A 1848 ARG cc_start: 0.4195 (mmt180) cc_final: 0.3173 (mmt90)
  outliers start: 21
  outliers final: 10
  residues processed: 132
  average time/residue: 0.1062
  time to fit residues: 19.6755
Evaluate side-chains
  126 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 TRP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  840 TYR
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1956 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN
A1340 HIS
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.138321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.112122 restraints weight = 20048.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.113725 restraints weight = 11793.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.114337 restraints weight = 10676.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.114788 restraints weight = 8423.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.116573 restraints weight = 8266.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10369  Z= 0.134
  Angle     :  0.493   8.143  13900  Z= 0.263
  Chirality :  0.037   0.159   1441
  Planarity :  0.003   0.043   1753
  Dihedral  :  3.542  16.085   1295
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.33 %
    Favored  : 82.62 %
  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:  0.96 (0.26), residues: 1135
  helix:  2.03 (0.19), residues: 721
  sheet:  0.61 (1.39), residues: 10
  loop : -2.10 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1610 
 TYR   0.015   0.001   TYR A1886 
 PHE   0.019   0.002   PHE A1023 
 TRP   0.065   0.002   TRP A 282 
 HIS   0.003   0.001   HIS A1962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10355)
  covalent geometry    : angle       0.48964 (13872)
  SS BOND              : bond        0.00281 (   14)
  SS BOND              : angle       1.43956 (   28)
  hydrogen bonds       : bond        0.03771 (  541)
  hydrogen bonds       : angle       3.55739 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7734 (t0) cc_final: 0.7348 (t0)
REVERT: A  269 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7353 (pp)
REVERT: A  284 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: A  601 GLN cc_start: 0.4230 (OUTLIER) cc_final: 0.2898 (pm20)
REVERT: A  653 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8003 (m-10)
REVERT: A 1697 TYR cc_start: 0.8437 (t80) cc_final: 0.8191 (t80)
REVERT: A 1812 MET cc_start: 0.9012 (ttm) cc_final: 0.8593 (ttm)
REVERT: A 1848 ARG cc_start: 0.4176 (mmt180) cc_final: 0.3941 (mmt180)
  outliers start: 23
  outliers final: 13
  residues processed: 138
  average time/residue: 0.1082
  time to fit residues: 21.0581
Evaluate side-chains
  129 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 TRP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1955 CYS
Chi-restraints excluded: chain A residue 1956 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN
A1579 HIS
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.137976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.110991 restraints weight = 20106.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.112522 restraints weight = 11216.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.113932 restraints weight = 7987.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.114316 restraints weight = 7754.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.114449 restraints weight = 6753.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10369  Z= 0.145
  Angle     :  0.506   7.248  13900  Z= 0.268
  Chirality :  0.037   0.143   1441
  Planarity :  0.003   0.043   1753
  Dihedral  :  3.526  16.450   1295
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.13 %
    Favored  : 81.37 %
  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:  0.92 (0.26), residues: 1135
  helix:  1.98 (0.19), residues: 727
  sheet:  0.31 (1.41), residues: 10
  loop : -2.14 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.015   0.001   TYR A1886 
 PHE   0.021   0.002   PHE A1138 
 TRP   0.044   0.001   TRP A 282 
 HIS   0.004   0.001   HIS A1579 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10355)
  covalent geometry    : angle       0.50173 (13872)
  SS BOND              : bond        0.00241 (   14)
  SS BOND              : angle       1.47944 (   28)
  hydrogen bonds       : bond        0.03768 (  541)
  hydrogen bonds       : angle       3.55091 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7742 (t0) cc_final: 0.7364 (t0)
REVERT: A  284 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: A  297 MET cc_start: 0.3436 (ppp) cc_final: 0.3219 (ppp)
REVERT: A  601 GLN cc_start: 0.4232 (OUTLIER) cc_final: 0.2886 (pm20)
REVERT: A  653 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8093 (m-10)
REVERT: A  666 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7117 (pp20)
REVERT: A 1697 TYR cc_start: 0.8450 (t80) cc_final: 0.8236 (t80)
REVERT: A 1812 MET cc_start: 0.8998 (ttm) cc_final: 0.8643 (ttm)
REVERT: A 1848 ARG cc_start: 0.4261 (mmt180) cc_final: 0.3193 (mmt90)
  outliers start: 28
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1023
  time to fit residues: 20.2353
Evaluate side-chains
  135 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  171 TRP
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  666 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1619 PHE
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1956 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0870
   chunk 90 optimal weight:    0.0470
   chunk 75 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.8260

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

Flipped N/Q/H residues before XYZ refinement:
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.133758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.108627 restraints weight = 19923.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.109217 restraints weight = 13900.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.110478 restraints weight = 13424.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.110594 restraints weight = 9857.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.110937 restraints weight = 9463.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10369  Z= 0.144
  Angle     :  0.515   8.046  13900  Z= 0.274
  Chirality :  0.037   0.140   1441
  Planarity :  0.003   0.044   1753
  Dihedral  :  3.493  13.635   1295
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.20 %
    Favored  : 80.48 %
  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:  0.93 (0.26), residues: 1135
  helix:  2.01 (0.19), residues: 725
  sheet:  0.19 (1.42), residues: 10
  loop : -2.15 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1610 
 TYR   0.015   0.001   TYR A1886 
 PHE   0.017   0.002   PHE A1138 
 TRP   0.036   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A1962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10355)
  covalent geometry    : angle       0.51163 (13872)
  SS BOND              : bond        0.00292 (   14)
  SS BOND              : angle       1.32636 (   28)
  hydrogen bonds       : bond        0.03750 (  541)
  hydrogen bonds       : angle       3.53546 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.6966 (mmm160) cc_final: 0.6616 (mmt-90)
REVERT: A  160 ASP cc_start: 0.7621 (t0) cc_final: 0.7316 (t0)
REVERT: A  281 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: A  284 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: A  601 GLN cc_start: 0.4268 (OUTLIER) cc_final: 0.2967 (pm20)
REVERT: A  653 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (m-10)
REVERT: A 1812 MET cc_start: 0.8895 (ttm) cc_final: 0.8563 (ttm)
REVERT: A 1848 ARG cc_start: 0.4457 (mmt180) cc_final: 0.3345 (mmt90)
  outliers start: 26
  outliers final: 22
  residues processed: 134
  average time/residue: 0.1002
  time to fit residues: 19.3109
Evaluate side-chains
  138 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  171 TRP
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1619 PHE
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1802 CYS
Chi-restraints excluded: chain A residue 1895 ILE
Chi-restraints excluded: chain A residue 1955 CYS
Chi-restraints excluded: chain A residue 1956 THR
Chi-restraints excluded: chain A residue 1967 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.133711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.108355 restraints weight = 20154.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108905 restraints weight = 14012.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.110073 restraints weight = 14049.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.110225 restraints weight = 9857.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.110471 restraints weight = 10429.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10369  Z= 0.146
  Angle     :  0.514   7.185  13900  Z= 0.271
  Chirality :  0.037   0.147   1441
  Planarity :  0.003   0.047   1753
  Dihedral  :  3.489  13.760   1295
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.20 %
    Favored  : 80.04 %
  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:  0.94 (0.26), residues: 1135
  helix:  2.02 (0.19), residues: 722
  sheet:  0.05 (1.43), residues: 10
  loop : -2.10 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1610 
 TYR   0.015   0.001   TYR A1886 
 PHE   0.016   0.002   PHE A1138 
 TRP   0.030   0.001   TRP A1451 
 HIS   0.003   0.001   HIS A1962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10355)
  covalent geometry    : angle       0.51087 (13872)
  SS BOND              : bond        0.00264 (   14)
  SS BOND              : angle       1.34645 (   28)
  hydrogen bonds       : bond        0.03747 (  541)
  hydrogen bonds       : angle       3.50441 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7659 (t0) cc_final: 0.7312 (t0)
REVERT: A  281 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8260 (tm-30)
REVERT: A  284 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8313 (tm-30)
REVERT: A  601 GLN cc_start: 0.4236 (OUTLIER) cc_final: 0.2894 (pm20)
REVERT: A  653 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8104 (m-10)
REVERT: A  666 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6941 (pp20)
REVERT: A 1812 MET cc_start: 0.8926 (ttm) cc_final: 0.8588 (ttm)
REVERT: A 1834 LYS cc_start: 0.8294 (tmmt) cc_final: 0.7667 (tttt)
REVERT: A 1848 ARG cc_start: 0.4352 (mmt180) cc_final: 0.3237 (mmt90)
  outliers start: 31
  outliers final: 20
  residues processed: 139
  average time/residue: 0.1099
  time to fit residues: 21.8853
Evaluate side-chains
  137 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  171 TRP
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  666 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1619 PHE
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1680 LEU
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1802 CYS
Chi-restraints excluded: chain A residue 1895 ILE
Chi-restraints excluded: chain A residue 1955 CYS
Chi-restraints excluded: chain A residue 1956 THR
Chi-restraints excluded: chain A residue 1967 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   chunk 83 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
A 723 HIS
A1099 ASN
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.131573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.106554 restraints weight = 19977.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.106063 restraints weight = 14522.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.107172 restraints weight = 15382.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.107480 restraints weight = 11250.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.107772 restraints weight = 11262.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10369  Z= 0.218
  Angle     :  0.582   9.919  13900  Z= 0.307
  Chirality :  0.040   0.144   1441
  Planarity :  0.004   0.048   1753
  Dihedral  :  3.804  14.786   1295
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.74 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1135
  helix:  1.81 (0.19), residues: 722
  sheet:  0.19 (1.28), residues: 10
  loop : -2.24 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1674 
 TYR   0.028   0.002   TYR A1862 
 PHE   0.019   0.002   PHE A 650 
 TRP   0.037   0.002   TRP A 335 
 HIS   0.004   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (10355)
  covalent geometry    : angle       0.57911 (13872)
  SS BOND              : bond        0.00370 (   14)
  SS BOND              : angle       1.42017 (   28)
  hydrogen bonds       : bond        0.04101 (  541)
  hydrogen bonds       : angle       3.69006 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7625 (t0) cc_final: 0.7322 (t0)
REVERT: A  601 GLN cc_start: 0.4322 (OUTLIER) cc_final: 0.2919 (pm20)
REVERT: A  653 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8226 (m-10)
REVERT: A  867 LYS cc_start: 0.6219 (pttt) cc_final: 0.5794 (mmtt)
REVERT: A  942 SER cc_start: 0.8911 (p) cc_final: 0.8607 (m)
REVERT: A 1812 MET cc_start: 0.8901 (ttm) cc_final: 0.8602 (ttm)
REVERT: A 1834 LYS cc_start: 0.8322 (tmmt) cc_final: 0.7661 (tttt)
REVERT: A 1848 ARG cc_start: 0.4380 (mmt180) cc_final: 0.3745 (mmt-90)
  outliers start: 28
  outliers final: 21
  residues processed: 137
  average time/residue: 0.1061
  time to fit residues: 21.0280
Evaluate side-chains
  134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  171 TRP
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1619 PHE
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1680 LEU
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1802 CYS
Chi-restraints excluded: chain A residue 1895 ILE
Chi-restraints excluded: chain A residue 1956 THR
Chi-restraints excluded: chain A residue 1967 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   chunk 70 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.138091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.110901 restraints weight = 19865.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.112380 restraints weight = 10995.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.113139 restraints weight = 8267.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.113928 restraints weight = 7843.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.113861 restraints weight = 6816.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10369  Z= 0.137
  Angle     :  0.538  10.292  13900  Z= 0.281
  Chirality :  0.037   0.138   1441
  Planarity :  0.003   0.047   1753
  Dihedral  :  3.629  14.570   1295
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.45 %
    Favored  : 79.59 %
  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:  0.81 (0.26), residues: 1135
  helix:  1.92 (0.19), residues: 722
  sheet:  0.57 (1.39), residues: 10
  loop : -2.19 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1610 
 TYR   0.030   0.001   TYR A1862 
 PHE   0.018   0.002   PHE A 877 
 TRP   0.042   0.002   TRP A 335 
 HIS   0.003   0.001   HIS A1962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10355)
  covalent geometry    : angle       0.53560 (13872)
  SS BOND              : bond        0.00248 (   14)
  SS BOND              : angle       1.29545 (   28)
  hydrogen bonds       : bond        0.03772 (  541)
  hydrogen bonds       : angle       3.55276 ( 1611)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7617 (t0) cc_final: 0.7271 (t0)
REVERT: A  284 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: A  601 GLN cc_start: 0.3944 (OUTLIER) cc_final: 0.2743 (pm20)
REVERT: A  653 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8132 (m-80)
REVERT: A  867 LYS cc_start: 0.6276 (pttt) cc_final: 0.5790 (mmtt)
REVERT: A  942 SER cc_start: 0.8983 (p) cc_final: 0.8701 (m)
REVERT: A 1812 MET cc_start: 0.8974 (ttm) cc_final: 0.8627 (ttm)
REVERT: A 1834 LYS cc_start: 0.8295 (tmmt) cc_final: 0.7700 (tttt)
REVERT: A 1848 ARG cc_start: 0.4166 (mmt180) cc_final: 0.2932 (mmt90)
  outliers start: 22
  outliers final: 18
  residues processed: 135
  average time/residue: 0.1077
  time to fit residues: 21.0150
Evaluate side-chains
  134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  592 CYS
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  656 LEU
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1619 PHE
Chi-restraints excluded: chain A residue 1622 ILE
Chi-restraints excluded: chain A residue 1673 ILE
Chi-restraints excluded: chain A residue 1680 LEU
Chi-restraints excluded: chain A residue 1683 ILE
Chi-restraints excluded: chain A residue 1802 CYS
Chi-restraints excluded: chain A residue 1955 CYS
Chi-restraints excluded: chain A residue 1967 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 76 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN
** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.140113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.115863 restraints weight = 19919.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.115649 restraints weight = 15499.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.116753 restraints weight = 16535.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.116941 restraints weight = 11495.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.117165 restraints weight = 12211.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10369  Z= 0.151
  Angle     :  0.538   7.775  13900  Z= 0.283
  Chirality :  0.038   0.140   1441
  Planarity :  0.003   0.044   1753
  Dihedral  :  3.648  16.818   1295
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.45 %
    Favored  : 79.59 %
  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:  0.80 (0.26), residues: 1135
  helix:  1.91 (0.19), residues: 724
  sheet:  0.51 (1.36), residues: 10
  loop : -2.19 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1674 
 TYR   0.024   0.001   TYR A1862 
 PHE   0.016   0.002   PHE A 877 
 TRP   0.049   0.002   TRP A 335 
 HIS   0.003   0.001   HIS A1962 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10355)
  covalent geometry    : angle       0.53503 (13872)
  SS BOND              : bond        0.00254 (   14)
  SS BOND              : angle       1.30693 (   28)
  hydrogen bonds       : bond        0.03773 (  541)
  hydrogen bonds       : angle       3.55858 ( 1611)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.13 seconds
wall clock time: 29 minutes 32.04 seconds (1772.04 seconds total)