Starting phenix.real_space_refine
on Sat Aug 23 13:53:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e2f_27834/08_2025/8e2f_27834.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e2f_27834/08_2025/8e2f_27834.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e2f_27834/08_2025/8e2f_27834.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e2f_27834/08_2025/8e2f_27834.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e2f_27834/08_2025/8e2f_27834.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e2f_27834/08_2025/8e2f_27834.map"
  }
  resolution = 2.47
  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=  -0.004 sd=   0.080
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    3905      2.51       5
     N    1046      2.21       5
     O    1107      1.98       5
     H    6207      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 12305
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 771, 12305
          Classifications: {'peptide': 771}
          Link IDs: {'PTRANS': 35, 'TRANS': 735}
          Chain breaks: 13
  Time building chain proxies: 2.44, per 1000 atoms: 0.20
  Number of scatterers: 12305
  At special positions: 0
  Unit cell: (82.72, 84.48, 115.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     O    1107      8.00
     N    1046      7.00
     C    3905      6.00
     H    6207      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 405.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      52.9% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1018 through 1028
    Processing helix  chain 'A' and resid 1050 through 1055
    Processing helix  chain 'A' and resid 1060 through 1067
      removed outlier: 4.424A  pdb=" N   GLN A1065 " --> pdb=" O   LEU A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1171 through 1177
    Processing helix  chain 'A' and resid 1189 through 1192
    Processing helix  chain 'A' and resid 1205 through 1210
    Processing helix  chain 'A' and resid 1291 through 1294
    Processing helix  chain 'A' and resid 1313 through 1324
    Processing helix  chain 'A' and resid 1324 through 1336
      removed outlier: 3.614A  pdb=" N   HIS A1328 " --> pdb=" O   PHE A1324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1343
    Processing helix  chain 'A' and resid 1345 through 1364
    Processing helix  chain 'A' and resid 1377 through 1384
    Processing helix  chain 'A' and resid 1384 through 1395
      removed outlier: 3.559A  pdb=" N   GLU A1395 " --> pdb=" O   VAL A1391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1397 through 1414
    Processing helix  chain 'A' and resid 1423 through 1436
      removed outlier: 4.211A  pdb=" N   VAL A1427 " --> pdb=" O   ALA A1423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1437 through 1442
      Proline residue:  A1440  - end of helix
      No H-bonds generated for 'chain 'A' and resid 1437 through 1442'
    Processing helix  chain 'A' and resid 1444 through 1459
      removed outlier: 3.614A  pdb=" N   TRP A1450 " --> pdb=" O   GLY A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1462 through 1484
      removed outlier: 3.624A  pdb=" N   ARG A1479 " --> pdb=" O   THR A1475 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLN A1480 " --> pdb=" O   ALA A1476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1496
    Processing helix  chain 'A' and resid 1823 through 1828
    Processing helix  chain 'A' and resid 2012 through 2018
    Processing helix  chain 'A' and resid 2019 through 2041
    Processing helix  chain 'A' and resid 2055 through 2067
    Processing helix  chain 'A' and resid 2071 through 2087
    Processing helix  chain 'A' and resid 2091 through 2105
    Processing helix  chain 'A' and resid 2113 through 2128
    Processing helix  chain 'A' and resid 2132 through 2147
      removed outlier: 3.546A  pdb=" N   GLU A2136 " --> pdb=" O   SER A2132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2148 through 2150
      No H-bonds generated for 'chain 'A' and resid 2148 through 2150'
    Processing helix  chain 'A' and resid 2164 through 2182
    Processing helix  chain 'A' and resid 2326 through 2341
    Processing helix  chain 'A' and resid 2348 through 2365
      removed outlier: 3.570A  pdb=" N   LEU A2352 " --> pdb=" O   ALA A2348 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   PHE A2353 " --> pdb=" O   ASP A2349 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A2365 " --> pdb=" O   ILE A2361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2568 through 2574
      removed outlier: 3.565A  pdb=" N   GLU A2572 " --> pdb=" O   ALA A2569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2576 through 2599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1031 through 1033
      removed outlier: 6.504A  pdb=" N   GLN A1297 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1031 through 1033
      removed outlier: 5.450A  pdb=" N   PHE A1306 " --> pdb=" O   VAL A1101 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL A1101 " --> pdb=" O   PHE A1306 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1039 through 1041
      removed outlier: 6.621A  pdb=" N   ILE A1120 " --> pdb=" O   VAL A1186 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   VAL A1186 " --> pdb=" O   ILE A1120 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   VAL A1122 " --> pdb=" O   GLY A1184 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   GLY A1184 " --> pdb=" O   VAL A1122 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   LEU A1124 " --> pdb=" O   LEU A1182 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1564 through 1565
      removed outlier: 6.679A  pdb=" N   HIS A1881 " --> pdb=" O   LEU A1801 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   LEU A1801 " --> pdb=" O   HIS A1881 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   ARG A1854 " --> pdb=" O   PHE A1795 " (cutoff:3.500A)
      removed outlier: 10.462A  pdb=" N   ARG A1797 " --> pdb=" O   VAL A1852 " (cutoff:3.500A)
      removed outlier: 9.210A  pdb=" N   VAL A1852 " --> pdb=" O   ARG A1797 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   PHE A1855 " --> pdb=" O   ILE A1819 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE A1819 " --> pdb=" O   PHE A1855 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LYS A1857 " --> pdb=" O   ILE A1817 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE A1817 " --> pdb=" O   LYS A1857 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   THR A1859 " --> pdb=" O   LEU A1815 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LEU A1815 " --> pdb=" O   THR A1859 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ILE A1861 " --> pdb=" O   ALA A1813 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU A1815 " --> pdb=" O   VAL A1833 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   VAL A1833 " --> pdb=" O   LEU A1815 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE A1817 " --> pdb=" O   LEU A1831 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1569 through 1573
      removed outlier: 6.795A  pdb=" N   THR A1792 " --> pdb=" O   VAL A1571 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   THR A1573 " --> pdb=" O   PHE A1790 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   PHE A1790 " --> pdb=" O   THR A1573 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1578 through 1580

    339 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6184
        1.03 -     1.23: 29
        1.23 -     1.42: 2497
        1.42 -     1.62: 3654
        1.62 -     1.81: 57
  Bond restraints: 12421
  Sorted by residual:
  bond pdb=" CB  GLN A2057 "
       pdb=" CG  GLN A2057 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.37e+00
  bond pdb=" N   VAL A1506 "
       pdb=" CA  VAL A1506 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.15e-02 7.56e+03 1.21e+00
  bond pdb=" N   GLY A1880 "
       pdb=" CA  GLY A1880 "
    ideal  model  delta    sigma   weight residual
    1.455  1.443  0.011 1.05e-02 9.07e+03 1.18e+00
  bond pdb=" CB  GLU A2326 "
       pdb=" CG  GLU A2326 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.04e+00
  bond pdb=" CB  PRO A1036 "
       pdb=" CG  PRO A1036 "
    ideal  model  delta    sigma   weight residual
    1.492  1.543 -0.051 5.00e-02 4.00e+02 1.02e+00
  ... (remaining 12416 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 22190
        1.66 -     3.33: 281
        3.33 -     4.99: 38
        4.99 -     6.65: 6
        6.65 -     8.32: 1
  Bond angle restraints: 22516
  Sorted by residual:
  angle pdb=" N   GLN A2051 "
        pdb=" CA  GLN A2051 "
        pdb=" C   GLN A2051 "
      ideal   model   delta    sigma   weight residual
     113.55  108.58    4.97 1.26e+00 6.30e-01 1.55e+01
  angle pdb=" CB  MET A1783 "
        pdb=" CG  MET A1783 "
        pdb=" SD  MET A1783 "
      ideal   model   delta    sigma   weight residual
     112.70  121.02   -8.32 3.00e+00 1.11e-01 7.69e+00
  angle pdb=" CA  GLN A2057 "
        pdb=" CB  GLN A2057 "
        pdb=" CG  GLN A2057 "
      ideal   model   delta    sigma   weight residual
     114.10  119.63   -5.53 2.00e+00 2.50e-01 7.65e+00
  angle pdb=" C   ALA A1198 "
        pdb=" N   GLY A1199 "
        pdb=" CA  GLY A1199 "
      ideal   model   delta    sigma   weight residual
     121.83  118.42    3.41 1.30e+00 5.92e-01 6.88e+00
  angle pdb=" N   ALA A1198 "
        pdb=" CA  ALA A1198 "
        pdb=" C   ALA A1198 "
      ideal   model   delta    sigma   weight residual
     110.80  106.04    4.76 2.13e+00 2.20e-01 5.00e+00
  ... (remaining 22511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 5188
       17.46 -    34.91: 409
       34.91 -    52.37: 148
       52.37 -    69.83: 49
       69.83 -    87.29: 8
  Dihedral angle restraints: 5802
    sinusoidal: 3198
      harmonic: 2604
  Sorted by residual:
  dihedral pdb=" CA  GLN A1323 "
           pdb=" C   GLN A1323 "
           pdb=" N   PHE A1324 "
           pdb=" CA  PHE A1324 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  ILE A1848 "
           pdb=" C   ILE A1848 "
           pdb=" N   PRO A1849 "
           pdb=" CA  PRO A1849 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.20   16.80     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ALA A2048 "
           pdb=" C   ALA A2048 "
           pdb=" N   VAL A2049 "
           pdb=" CA  VAL A2049 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.44   16.56     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 5799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 699
       0.032 -    0.065: 215
       0.065 -    0.097: 63
       0.097 -    0.129: 27
       0.129 -    0.161: 5
  Chirality restraints: 1009
  Sorted by residual:
  chirality pdb=" CA  ILE A1858 "
            pdb=" N   ILE A1858 "
            pdb=" C   ILE A1858 "
            pdb=" CB  ILE A1858 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.49e-01
  chirality pdb=" CA  ILE A1873 "
            pdb=" N   ILE A1873 "
            pdb=" C   ILE A1873 "
            pdb=" CB  ILE A1873 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  ILE A1780 "
            pdb=" N   ILE A1780 "
            pdb=" C   ILE A1780 "
            pdb=" CB  ILE A1780 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 1006 not shown)

  Planarity restraints: 1775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A1113 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   ASN A1113 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASN A1113 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A1114 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1385 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.92e+00
        pdb=" C   LEU A1385 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LEU A1385 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER A1386 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1425 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO A1426 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A1426 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1426 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1772 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 159
        2.05 -     2.69: 19554
        2.69 -     3.32: 38110
        3.32 -     3.96: 49726
        3.96 -     4.60: 77291
  Nonbonded interactions: 184840
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A2326 "
            pdb=" H   GLU A2326 "
     model   vdw
     1.409 2.450
  nonbonded pdb=" OD2 ASP A1105 "
            pdb="HH11 ARG A1304 "
     model   vdw
     1.561 2.450
  nonbonded pdb=" OE1 GLU A1825 "
            pdb=" H   GLU A1825 "
     model   vdw
     1.577 2.450
  nonbonded pdb=" OD1 ASP A1193 "
            pdb=" H   LEU A1194 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" O   SER A1085 "
            pdb=" HE2 HIS A1089 "
     model   vdw
     1.626 2.450
  ... (remaining 184835 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 individual isotropic
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:             7.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.210
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6214  Z= 0.139
  Angle     :  0.619   8.319   8425  Z= 0.337
  Chirality :  0.038   0.161   1009
  Planarity :  0.004   0.031   1052
  Dihedral  : 16.352  87.285   2279
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.84 %
    Favored  : 80.58 %
  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:  1.05 (0.32), residues: 743
  helix:  1.61 (0.27), residues: 368
  sheet:  0.10 (0.49), residues: 108
  loop : -0.23 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1406 
 TYR   0.008   0.001   TYR A1878 
 PHE   0.009   0.001   PHE A1452 
 TRP   0.011   0.001   TRP A1077 
 HIS   0.005   0.001   HIS A1784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6214)
  covalent geometry    : angle       0.61942 ( 8425)
  hydrogen bonds       : bond        0.10884 (  337)
  hydrogen bonds       : angle       5.67519 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 9
  residues processed: 100
  average time/residue: 1.0961
  time to fit residues: 116.1242
Evaluate side-chains
  94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1112 SER
Chi-restraints excluded: chain A residue 1127 ASN
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1481 LEU
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1811 ASP
Chi-restraints excluded: chain A residue 2128 SER
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2330 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A1051 GLN
A1127 ASN
A1414 ASN
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.156736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135814 restraints weight = 21326.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.70
r_work: 0.3678 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.0513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6214  Z= 0.169
  Angle     :  0.575   5.873   8425  Z= 0.296
  Chirality :  0.039   0.141   1009
  Planarity :  0.004   0.036   1052
  Dihedral  :  5.710  46.267    822
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.69 %
    Favored  : 81.15 %
  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:  1.02 (0.31), residues: 743
  helix:  1.58 (0.27), residues: 369
  sheet:  0.13 (0.50), residues: 108
  loop : -0.27 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1406 
 TYR   0.012   0.001   TYR A1878 
 PHE   0.010   0.001   PHE A1452 
 TRP   0.007   0.001   TRP A1450 
 HIS   0.005   0.001   HIS A1784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6214)
  covalent geometry    : angle       0.57488 ( 8425)
  hydrogen bonds       : bond        0.03970 (  337)
  hydrogen bonds       : angle       4.88069 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1298 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6236 (tt0)
REVERT: A 1896 ASP cc_start: 0.7251 (t0) cc_final: 0.7037 (m-30)
REVERT: A 2013 ASP cc_start: 0.7217 (m-30) cc_final: 0.6917 (p0)
REVERT: A 2084 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7819 (mt0)
  outliers start: 15
  outliers final: 6
  residues processed: 107
  average time/residue: 1.0300
  time to fit residues: 117.0405
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1298 GLU
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1839 THR
Chi-restraints excluded: chain A residue 2084 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A1127 ASN
A1840 HIS
A2057 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.156145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.135455 restraints weight = 21657.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 1.71
r_work: 0.3676 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.0813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6214  Z= 0.156
  Angle     :  0.554   5.853   8425  Z= 0.284
  Chirality :  0.039   0.142   1009
  Planarity :  0.004   0.037   1052
  Dihedral  :  4.812  30.010    811
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.68 %
    Favored  : 81.29 %
  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 (0.31), residues: 743
  helix:  1.63 (0.27), residues: 371
  sheet:  0.10 (0.51), residues: 102
  loop : -0.32 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1406 
 TYR   0.012   0.001   TYR A1878 
 PHE   0.016   0.001   PHE A1790 
 TRP   0.007   0.001   TRP A1450 
 HIS   0.004   0.001   HIS A1089 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6214)
  covalent geometry    : angle       0.55360 ( 8425)
  hydrogen bonds       : bond        0.03683 (  337)
  hydrogen bonds       : angle       4.67777 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1298 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6513 (tm-30)
REVERT: A 1346 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7148 (pt0)
REVERT: A 1511 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7848 (mt-10)
REVERT: A 2013 ASP cc_start: 0.7249 (m-30) cc_final: 0.6992 (p0)
REVERT: A 2084 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7766 (mt0)
  outliers start: 21
  outliers final: 6
  residues processed: 109
  average time/residue: 0.9873
  time to fit residues: 114.4978
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1298 GLU
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1511 GLU
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 1839 THR
Chi-restraints excluded: chain A residue 2084 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A1127 ASN
A1414 ASN
** A2057 GLN ** 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 = 0.3978 r_free = 0.3978 target = 0.155255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.134537 restraints weight = 21200.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 1.67
r_work: 0.3668 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6214  Z= 0.184
  Angle     :  0.566   5.869   8425  Z= 0.290
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.040   1052
  Dihedral  :  4.848  30.260    811
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.96 %
    Favored  : 81.29 %
  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:  1.07 (0.31), residues: 743
  helix:  1.71 (0.27), residues: 365
  sheet:  0.02 (0.50), residues: 104
  loop : -0.30 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1797 
 TYR   0.013   0.001   TYR A1878 
 PHE   0.011   0.002   PHE A1452 
 TRP   0.008   0.001   TRP A1077 
 HIS   0.005   0.001   HIS A1089 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6214)
  covalent geometry    : angle       0.56595 ( 8425)
  hydrogen bonds       : bond        0.03684 (  337)
  hydrogen bonds       : angle       4.57667 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8146 (mt)
REVERT: A 1346 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7191 (pt0)
REVERT: A 1511 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7841 (mt-10)
REVERT: A 2013 ASP cc_start: 0.7206 (m-30) cc_final: 0.6967 (p0)
REVERT: A 2084 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7712 (mt0)
REVERT: A 2577 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8129 (tt0)
  outliers start: 26
  outliers final: 12
  residues processed: 110
  average time/residue: 1.1986
  time to fit residues: 139.3310
Evaluate side-chains
  108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1481 LEU
Chi-restraints excluded: chain A residue 1511 GLU
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 1859 THR
Chi-restraints excluded: chain A residue 2084 GLN
Chi-restraints excluded: chain A residue 2330 SER
Chi-restraints excluded: chain A residue 2577 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1113 ASN
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.156357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135618 restraints weight = 21471.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.69
r_work: 0.3677 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6214  Z= 0.144
  Angle     :  0.541   5.786   8425  Z= 0.277
  Chirality :  0.038   0.139   1009
  Planarity :  0.004   0.034   1052
  Dihedral  :  4.717  30.042    811
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.83 %
    Favored  : 80.86 %
  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:  1.17 (0.32), residues: 743
  helix:  1.81 (0.27), residues: 365
  sheet: -0.01 (0.51), residues: 104
  loop : -0.23 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1788 
 TYR   0.010   0.001   TYR A1878 
 PHE   0.010   0.001   PHE A1452 
 TRP   0.009   0.001   TRP A1077 
 HIS   0.005   0.001   HIS A1089 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6214)
  covalent geometry    : angle       0.54108 ( 8425)
  hydrogen bonds       : bond        0.03417 (  337)
  hydrogen bonds       : angle       4.48028 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8150 (mt)
REVERT: A 1346 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7193 (pt0)
REVERT: A 1511 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7821 (mt-10)
REVERT: A 2084 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7644 (mt0)
REVERT: A 2577 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8071 (tt0)
  outliers start: 23
  outliers final: 9
  residues processed: 109
  average time/residue: 1.0168
  time to fit residues: 117.5134
Evaluate side-chains
  104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1035 THR
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1481 LEU
Chi-restraints excluded: chain A residue 1511 GLU
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 2084 GLN
Chi-restraints excluded: chain A residue 2577 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 70 optimal weight:    0.1980
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A1113 ASN
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.155296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.134493 restraints weight = 21401.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.68
r_work: 0.3664 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6214  Z= 0.181
  Angle     :  0.562   5.861   8425  Z= 0.288
  Chirality :  0.039   0.137   1009
  Planarity :  0.004   0.039   1052
  Dihedral  :  4.776  30.263    811
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.26 %
    Favored  : 80.00 %
  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:  1.10 (0.31), residues: 743
  helix:  1.73 (0.27), residues: 363
  sheet:  0.04 (0.51), residues: 104
  loop : -0.28 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1398 
 TYR   0.013   0.002   TYR A1878 
 PHE   0.012   0.001   PHE A1452 
 TRP   0.009   0.001   TRP A1077 
 HIS   0.004   0.001   HIS A1895 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6214)
  covalent geometry    : angle       0.56219 ( 8425)
  hydrogen bonds       : bond        0.03558 (  337)
  hydrogen bonds       : angle       4.47383 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8210 (mt)
REVERT: A 1346 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7186 (pt0)
REVERT: A 1511 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7867 (mt-10)
REVERT: A 2084 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7660 (mt0)
REVERT: A 2577 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8081 (tt0)
  outliers start: 26
  outliers final: 14
  residues processed: 109
  average time/residue: 1.0437
  time to fit residues: 120.6846
Evaluate side-chains
  109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1035 THR
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1298 GLU
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1481 LEU
Chi-restraints excluded: chain A residue 1511 GLU
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 1859 THR
Chi-restraints excluded: chain A residue 2084 GLN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2330 SER
Chi-restraints excluded: chain A residue 2577 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A1113 ASN
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.156593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135761 restraints weight = 21468.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 1.70
r_work: 0.3675 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6214  Z= 0.129
  Angle     :  0.533   5.761   8425  Z= 0.272
  Chirality :  0.038   0.157   1009
  Planarity :  0.004   0.056   1052
  Dihedral  :  4.627  30.000    811
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.98 %
    Favored  : 79.86 %
  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:  1.25 (0.32), residues: 743
  helix:  1.89 (0.27), residues: 363
  sheet:  0.05 (0.51), residues: 104
  loop : -0.21 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A2360 
 TYR   0.010   0.001   TYR A1878 
 PHE   0.010   0.001   PHE A1452 
 TRP   0.008   0.001   TRP A1077 
 HIS   0.003   0.001   HIS A1089 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6214)
  covalent geometry    : angle       0.53265 ( 8425)
  hydrogen bonds       : bond        0.03242 (  337)
  hydrogen bonds       : angle       4.38266 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8227 (mt)
REVERT: A 1346 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7195 (pt0)
REVERT: A 1779 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7938 (mt)
REVERT: A 2084 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7575 (mt0)
REVERT: A 2326 GLU cc_start: 0.6525 (pm20) cc_final: 0.5984 (pm20)
REVERT: A 2577 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8079 (tt0)
  outliers start: 22
  outliers final: 11
  residues processed: 106
  average time/residue: 0.9383
  time to fit residues: 105.7636
Evaluate side-chains
  102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1112 SER
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 2084 GLN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2330 SER
Chi-restraints excluded: chain A residue 2577 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 42 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A1113 ASN
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.156153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.135491 restraints weight = 21385.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 1.68
r_work: 0.3676 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6214  Z= 0.141
  Angle     :  0.537   6.506   8425  Z= 0.273
  Chirality :  0.038   0.147   1009
  Planarity :  0.004   0.034   1052
  Dihedral  :  4.607  30.156    811
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.55 %
    Favored  : 79.86 %
  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:  1.31 (0.32), residues: 743
  helix:  1.92 (0.27), residues: 363
  sheet:  0.17 (0.51), residues: 103
  loop : -0.19 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2360 
 TYR   0.010   0.001   TYR A1878 
 PHE   0.010   0.001   PHE A1452 
 TRP   0.008   0.001   TRP A1077 
 HIS   0.003   0.001   HIS A1089 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6214)
  covalent geometry    : angle       0.53688 ( 8425)
  hydrogen bonds       : bond        0.03270 (  337)
  hydrogen bonds       : angle       4.35581 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8232 (mt)
REVERT: A 1346 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7171 (pt0)
REVERT: A 2084 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7585 (mt0)
  outliers start: 25
  outliers final: 14
  residues processed: 104
  average time/residue: 1.1959
  time to fit residues: 131.3512
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1035 THR
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1112 SER
Chi-restraints excluded: chain A residue 1113 ASN
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 2084 GLN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2330 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A1113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.155875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.135099 restraints weight = 21490.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 1.69
r_work: 0.3669 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6214  Z= 0.163
  Angle     :  0.558   7.144   8425  Z= 0.285
  Chirality :  0.039   0.149   1009
  Planarity :  0.004   0.036   1052
  Dihedral  :  4.637  30.338    811
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.70 %
    Favored  : 79.86 %
  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:  1.42 (0.32), residues: 743
  helix:  1.99 (0.27), residues: 357
  sheet:  0.18 (0.51), residues: 103
  loop : -0.06 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2360 
 TYR   0.011   0.001   TYR A1878 
 PHE   0.011   0.001   PHE A1452 
 TRP   0.007   0.001   TRP A1450 
 HIS   0.003   0.001   HIS A1895 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6214)
  covalent geometry    : angle       0.55757 ( 8425)
  hydrogen bonds       : bond        0.03367 (  337)
  hydrogen bonds       : angle       4.36722 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8215 (mt)
REVERT: A 1346 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7196 (pt0)
REVERT: A 2084 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7582 (mt0)
REVERT: A 2326 GLU cc_start: 0.6639 (pm20) cc_final: 0.6008 (pm20)
  outliers start: 17
  outliers final: 10
  residues processed: 95
  average time/residue: 1.1223
  time to fit residues: 112.7101
Evaluate side-chains
  97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1057 ARG
Chi-restraints excluded: chain A residue 1112 SER
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1346 GLU
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 2084 GLN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2330 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0870
   chunk 57 optimal weight:    0.2980
   chunk 71 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0000
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.3962

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

Flipped N/Q/H residues before XYZ refinement:
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.157492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136916 restraints weight = 21502.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 1.69
r_work: 0.3694 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6214  Z= 0.113
  Angle     :  0.526   6.308   8425  Z= 0.267
  Chirality :  0.037   0.150   1009
  Planarity :  0.004   0.034   1052
  Dihedral  :  4.468  30.228    811
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.42 %
    Favored  : 79.71 %
  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:  1.57 (0.32), residues: 743
  helix:  2.15 (0.28), residues: 357
  sheet:  0.17 (0.51), residues: 103
  loop :  0.03 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1797 
 TYR   0.007   0.001   TYR A1878 
 PHE   0.009   0.001   PHE A1106 
 TRP   0.008   0.001   TRP A1077 
 HIS   0.003   0.001   HIS A1223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6214)
  covalent geometry    : angle       0.52570 ( 8425)
  hydrogen bonds       : bond        0.03050 (  337)
  hydrogen bonds       : angle       4.28427 (  948)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1194 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8213 (mt)
REVERT: A 1511 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7819 (mt-10)
REVERT: A 2326 GLU cc_start: 0.6687 (pm20) cc_final: 0.6055 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 98
  average time/residue: 1.0189
  time to fit residues: 105.8990
Evaluate side-chains
  93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1205 SER
Chi-restraints excluded: chain A residue 1364 SER
Chi-restraints excluded: chain A residue 1430 LYS
Chi-restraints excluded: chain A residue 1511 GLU
Chi-restraints excluded: chain A residue 1573 THR
Chi-restraints excluded: chain A residue 1816 SER
Chi-restraints excluded: chain A residue 1833 VAL
Chi-restraints excluded: chain A residue 2137 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A1113 ASN
** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.155673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.135073 restraints weight = 21331.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 1.67
r_work: 0.3667 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6214  Z= 0.172
  Angle     :  0.560   7.171   8425  Z= 0.284
  Chirality :  0.039   0.146   1009
  Planarity :  0.004   0.041   1052
  Dihedral  :  4.614  30.693    811
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.71 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.32), residues: 743
  helix:  2.04 (0.27), residues: 357
  sheet:  0.20 (0.51), residues: 103
  loop : -0.05 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2360 
 TYR   0.013   0.001   TYR A1878 
 PHE   0.012   0.001   PHE A1452 
 TRP   0.016   0.001   TRP A1077 
 HIS   0.004   0.001   HIS A1895 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6214)
  covalent geometry    : angle       0.55990 ( 8425)
  hydrogen bonds       : bond        0.03414 (  337)
  hydrogen bonds       : angle       4.35456 (  948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5039.30 seconds
wall clock time: 86 minutes 8.03 seconds (5168.03 seconds total)