Starting phenix.real_space_refine
on Tue Jul 29 16:19:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o3d_12704/07_2025/7o3d_12704.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o3d_12704/07_2025/7o3d_12704.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o3d_12704/07_2025/7o3d_12704.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o3d_12704/07_2025/7o3d_12704.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o3d_12704/07_2025/7o3d_12704.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o3d_12704/07_2025/7o3d_12704.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.020
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      16      5.16       5
     C    3650      2.51       5
     N     983      2.21       5
     O    1115      1.98       5
     H    5694      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11458
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 11458
          Classifications: {'peptide': 709}
          Link IDs: {'PTRANS': 29, 'TRANS': 679}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 6.17, per 1000 atoms: 0.54
  Number of scatterers: 11458
  At special positions: 0
  Unit cell: (65.412, 120.06, 101.844, 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      16     16.00
     O    1115      8.00
     N     983      7.00
     C    3650      6.00
     H    5694      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1152 " - pdb=" SG  CYS A1160 " distance=2.06

  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: 3.43
  Conformation dependent library (CDL) restraints added in 913.3 milliseconds
  

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1370

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 3 sheets defined
      59.4% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 323 through 330
    Processing helix  chain 'A' and resid 340 through 360
      removed outlier: 3.875A  pdb=" N   ASP A 358 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.244A  pdb=" N   PHE A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 396 through 400
      removed outlier: 3.562A  pdb=" N   SER A 400 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 434
    Processing helix  chain 'A' and resid 618 through 622
      removed outlier: 4.044A  pdb=" N   ASP A 622 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 635
    Processing helix  chain 'A' and resid 637 through 650
      removed outlier: 4.248A  pdb=" N   PHE A 641 " --> pdb=" O   ASP A 637 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A 642 " --> pdb=" O   PRO A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 734
      removed outlier: 4.668A  pdb=" N   GLU A 708 " --> pdb=" O   ASP A 704 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   VAL A 709 " --> pdb=" O   ILE A 705 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A 724 " --> pdb=" O   LEU A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 807
    Processing helix  chain 'A' and resid 818 through 835
      removed outlier: 3.878A  pdb=" N   LYS A 822 " --> pdb=" O   PRO A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 860
      removed outlier: 4.033A  pdb=" N   ASN A 859 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 867
    Processing helix  chain 'A' and resid 871 through 886
    Processing helix  chain 'A' and resid 886 through 894
      removed outlier: 3.545A  pdb=" N   LEU A 894 " --> pdb=" O   GLU A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 902
    Processing helix  chain 'A' and resid 907 through 911
    Processing helix  chain 'A' and resid 912 through 931
    Processing helix  chain 'A' and resid 934 through 939
    Processing helix  chain 'A' and resid 941 through 946
    Processing helix  chain 'A' and resid 947 through 951
    Processing helix  chain 'A' and resid 955 through 970
      removed outlier: 3.630A  pdb=" N   ILE A 960 " --> pdb=" O   LYS A 956 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP A 961 " --> pdb=" O   ARG A 957 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN A 970 " --> pdb=" O   LEU A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 982
    Processing helix  chain 'A' and resid 986 through 994
    Processing helix  chain 'A' and resid 1014 through 1019
    Processing helix  chain 'A' and resid 1022 through 1024
      No H-bonds generated for 'chain 'A' and resid 1022 through 1024'
    Processing helix  chain 'A' and resid 1025 through 1038
    Processing helix  chain 'A' and resid 1040 through 1051
      removed outlier: 3.765A  pdb=" N   ALA A1045 " --> pdb=" O   PRO A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1063
      removed outlier: 4.007A  pdb=" N   ILE A1057 " --> pdb=" O   MET A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1071
    Processing helix  chain 'A' and resid 1074 through 1087
      removed outlier: 3.573A  pdb=" N   TYR A1078 " --> pdb=" O   ASN A1074 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1103
      removed outlier: 3.904A  pdb=" N   LEU A1102 " --> pdb=" O   VAL A1098 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ASP A1103 " --> pdb=" O   LEU A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1126
    Processing helix  chain 'A' and resid 1169 through 1173
      removed outlier: 3.943A  pdb=" N   LEU A1172 " --> pdb=" O   GLY A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1210
    Processing helix  chain 'A' and resid 1226 through 1241
      removed outlier: 3.579A  pdb=" N   ALA A1234 " --> pdb=" O   GLU A1230 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   GLU A1235 " --> pdb=" O   LEU A1231 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLU A1236 " --> pdb=" O   GLU A1232 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   MET A1241 " --> pdb=" O   GLU A1237 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 606
    Processing sheet with id=AA2, first strand: chain 'A' and resid 776 through 782
      removed outlier: 3.659A  pdb=" N   ARG A 778 " --> pdb=" O   TYR A 769 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE A 766 " --> pdb=" O   THR A 754 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY A 812 " --> pdb=" O   LEU A 751 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE A 811 " --> pdb=" O   ILE A 847 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1137 through 1141
      removed outlier: 6.283A  pdb=" N   GLU A1201 " --> pdb=" O   ILE A1191 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ILE A1193 " --> pdb=" O   THR A1199 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   THR A1199 " --> pdb=" O   ILE A1193 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A1202 " --> pdb=" O   VAL A1161 " (cutoff:3.500A)

    279 hydrogen bonds defined for protein.
    798 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: 4.52

  Time building geometry restraints manager: 4.10 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 5690
        1.03 -     1.23: 103
        1.23 -     1.43: 2362
        1.43 -     1.63: 3388
        1.63 -     1.83: 26
  Bond restraints: 11569
  Sorted by residual:
  bond pdb=" CB  THR A 895 "
       pdb=" CG2 THR A 895 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  bond pdb=" CD  GLN A 707 "
       pdb=" OE1 GLN A 707 "
    ideal  model  delta    sigma   weight residual
    1.231  1.206  0.025 1.90e-02 2.77e+03 1.69e+00
  bond pdb=" NH1 ARG A 325 "
       pdb="HH12 ARG A 325 "
    ideal  model  delta    sigma   weight residual
    0.860  0.835  0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" CA  ILE A 705 "
       pdb=" C   ILE A 705 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 1.59e-02 3.96e+03 1.34e+00
  bond pdb=" NH1 ARG A1066 "
       pdb="HH12 ARG A1066 "
    ideal  model  delta    sigma   weight residual
    0.860  0.837  0.023 2.00e-02 2.50e+03 1.28e+00
  ... (remaining 11564 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 20810
        2.79 -     5.57: 106
        5.57 -     8.36: 11
        8.36 -    11.15: 0
       11.15 -    13.93: 1
  Bond angle restraints: 20928
  Sorted by residual:
  angle pdb=" CA  CYS A1152 "
        pdb=" CB  CYS A1152 "
        pdb=" SG  CYS A1152 "
      ideal   model   delta    sigma   weight residual
     114.40  128.33  -13.93 2.30e+00 1.89e-01 3.67e+01
  angle pdb=" CA  ARG A1141 "
        pdb=" CB  ARG A1141 "
        pdb=" CG  ARG A1141 "
      ideal   model   delta    sigma   weight residual
     114.10  122.25   -8.15 2.00e+00 2.50e-01 1.66e+01
  angle pdb=" N   CYS A1152 "
        pdb=" CA  CYS A1152 "
        pdb=" CB  CYS A1152 "
      ideal   model   delta    sigma   weight residual
     111.20  106.07    5.13 1.62e+00 3.81e-01 1.00e+01
  angle pdb=" N   SER A 706 "
        pdb=" CA  SER A 706 "
        pdb=" C   SER A 706 "
      ideal   model   delta    sigma   weight residual
     112.90  116.99   -4.09 1.31e+00 5.83e-01 9.75e+00
  angle pdb=" N   ILE A1179 "
        pdb=" CA  ILE A1179 "
        pdb=" C   ILE A1179 "
      ideal   model   delta    sigma   weight residual
     109.34  115.82   -6.48 2.08e+00 2.31e-01 9.72e+00
  ... (remaining 20923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.42: 4951
       16.42 -    32.85: 367
       32.85 -    49.27: 83
       49.27 -    65.70: 28
       65.70 -    82.12: 10
  Dihedral angle restraints: 5439
    sinusoidal: 2968
      harmonic: 2471
  Sorted by residual:
  dihedral pdb=" CB  CYS A1152 "
           pdb=" SG  CYS A1152 "
           pdb=" SG  CYS A1160 "
           pdb=" CB  CYS A1160 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -12.83  -73.17     1      1.00e+01 1.00e-02 6.82e+01
  dihedral pdb=" CD  ARG A1089 "
           pdb=" NE  ARG A1089 "
           pdb=" CZ  ARG A1089 "
           pdb=" NH1 ARG A1089 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   33.56  -33.56     1      1.00e+01 1.00e-02 1.60e+01
  dihedral pdb=" C   CYS A1160 "
           pdb=" N   CYS A1160 "
           pdb=" CA  CYS A1160 "
           pdb=" CB  CYS A1160 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.84   -9.76     0      2.50e+00 1.60e-01 1.52e+01
  ... (remaining 5436 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 705
       0.051 -    0.102: 132
       0.102 -    0.153: 34
       0.153 -    0.205: 4
       0.205 -    0.256: 3
  Chirality restraints: 878
  Sorted by residual:
  chirality pdb=" CA  GLN A 707 "
            pdb=" N   GLN A 707 "
            pdb=" C   GLN A 707 "
            pdb=" CB  GLN A 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  CYS A1160 "
            pdb=" N   CYS A1160 "
            pdb=" C   CYS A1160 "
            pdb=" CB  CYS A1160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  LYS A1239 "
            pdb=" N   LYS A1239 "
            pdb=" C   LYS A1239 "
            pdb=" CB  LYS A1239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 875 not shown)

  Planarity restraints: 1712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1109 "   -0.432 9.50e-02 1.11e+02   1.55e-01 9.26e+01
        pdb=" NE  ARG A1109 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1109 "   -0.053 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1109 "   -0.076 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1109 "    0.062 2.00e-02 2.50e+03
        pdb="HH11 ARG A1109 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A1109 "    0.094 2.00e-02 2.50e+03
        pdb="HH21 ARG A1109 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A1109 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 325 "   -0.028 9.50e-02 1.11e+02   5.50e-02 6.61e+01
        pdb=" NE  ARG A 325 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 325 "    0.034 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 325 "    0.100 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 325 "   -0.042 2.00e-02 2.50e+03
        pdb="HH11 ARG A 325 "    0.006 2.00e-02 2.50e+03
        pdb="HH12 ARG A 325 "   -0.103 2.00e-02 2.50e+03
        pdb="HH21 ARG A 325 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 325 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1066 "    0.138 9.50e-02 1.11e+02   6.85e-02 6.01e+01
        pdb=" NE  ARG A1066 "    0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1066 "   -0.047 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1066 "   -0.097 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1066 "   -0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A1066 "   -0.005 2.00e-02 2.50e+03
        pdb="HH12 ARG A1066 "    0.096 2.00e-02 2.50e+03
        pdb="HH21 ARG A1066 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A1066 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1709 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 325
        2.12 -     2.74: 20927
        2.74 -     3.36: 32125
        3.36 -     3.98: 38275
        3.98 -     4.60: 60392
  Nonbonded interactions: 152044
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 866 "
            pdb="HH22 ARG A 882 "
     model   vdw
     1.503 2.450
  nonbonded pdb=" HZ1 LYS A 728 "
            pdb=" O   ILE A 904 "
     model   vdw
     1.589 2.450
  nonbonded pdb="HH11 ARG A 826 "
            pdb=" OE2 GLU A 829 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" OE1 GLU A 914 "
            pdb=" H   GLU A 914 "
     model   vdw
     1.612 2.450
  nonbonded pdb=" OE1 GLU A 934 "
            pdb=" HH  TYR A 998 "
     model   vdw
     1.636 2.450
  ... (remaining 152039 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:             1.140
  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:             0.210
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     29.520
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
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   0.043   5876  Z= 0.147
  Angle     :  0.769  13.934   7945  Z= 0.452
  Chirality :  0.046   0.256    878
  Planarity :  0.014   0.221   1038
  Dihedral  : 13.165  82.121   2230
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.31), residues: 697
  helix:  0.11 (0.26), residues: 336
  sheet: -1.32 (0.62), residues: 62
  loop : -0.65 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.007   TRP A1225 
 HIS   0.021   0.004   HIS A1027 
 PHE   0.023   0.003   PHE A 424 
 TYR   0.036   0.006   TYR A 392 
 ARG   0.050   0.006   ARG A1109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16754 (  279)
  hydrogen bonds       : angle       7.28781 (  798)
  SS BOND              : bond        0.02944 (    1)
  SS BOND              : angle       2.81215 (    2)
  covalent geometry    : bond        0.00301 ( 5875)
  covalent geometry    : angle       0.76776 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7584 (mpt180) cc_final: 0.6980 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.3391
  time to fit residues: 39.7065
Evaluate side-chains
  68 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    9.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.117287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.102694 restraints weight = 55743.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.106103 restraints weight = 23552.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.108237 restraints weight = 12867.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5876  Z= 0.210
  Angle     :  0.616   6.451   7945  Z= 0.344
  Chirality :  0.042   0.164    878
  Planarity :  0.005   0.046   1038
  Dihedral  :  4.209  16.125    768
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.26 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.32), residues: 697
  helix:  0.42 (0.26), residues: 349
  sheet: -1.56 (0.59), residues: 64
  loop : -0.71 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1146 
 HIS   0.006   0.002   HIS A1167 
 PHE   0.014   0.002   PHE A1133 
 TYR   0.019   0.002   TYR A1039 
 ARG   0.004   0.001   ARG A 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05420 (  279)
  hydrogen bonds       : angle       6.37357 (  798)
  SS BOND              : bond        0.00916 (    1)
  SS BOND              : angle       1.75142 (    2)
  covalent geometry    : bond        0.00446 ( 5875)
  covalent geometry    : angle       0.61575 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7782 (mpt180) cc_final: 0.6742 (mmp80)
REVERT: A  634 PHE cc_start: 0.6808 (m-80) cc_final: 0.6475 (m-80)
REVERT: A  898 GLU cc_start: 0.8583 (mp0) cc_final: 0.8383 (mp0)
REVERT: A 1106 GLU cc_start: 0.8187 (tp30) cc_final: 0.7762 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 76
  average time/residue: 0.3217
  time to fit residues: 33.7701
Evaluate side-chains
  71 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1152 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 28 optimal weight:    0.2980
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.118798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.104236 restraints weight = 55292.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.107727 restraints weight = 23232.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.109924 restraints weight = 12593.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5876  Z= 0.115
  Angle     :  0.510   6.378   7945  Z= 0.276
  Chirality :  0.039   0.145    878
  Planarity :  0.004   0.031   1038
  Dihedral  :  4.110  15.002    768
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.95 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.33), residues: 697
  helix:  0.98 (0.27), residues: 343
  sheet: -1.66 (0.57), residues: 64
  loop : -0.48 (0.41), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 
 PHE   0.013   0.001   PHE A1133 
 TYR   0.012   0.001   TYR A 876 
 ARG   0.002   0.000   ARG A 636 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04761 (  279)
  hydrogen bonds       : angle       5.69697 (  798)
  SS BOND              : bond        0.00989 (    1)
  SS BOND              : angle       2.13379 (    2)
  covalent geometry    : bond        0.00243 ( 5875)
  covalent geometry    : angle       0.50902 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  74 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7762 (mpt180) cc_final: 0.6784 (mmp80)
  outliers start: 5
  outliers final: 4
  residues processed: 73
  average time/residue: 0.3629
  time to fit residues: 35.9790
Evaluate side-chains
  71 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.118676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.104231 restraints weight = 56407.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.107699 restraints weight = 24020.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.109870 restraints weight = 13082.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5876  Z= 0.111
  Angle     :  0.498   6.285   7945  Z= 0.268
  Chirality :  0.039   0.144    878
  Planarity :  0.004   0.030   1038
  Dihedral  :  4.117  22.397    768
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 10.05 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.32), residues: 697
  helix:  1.00 (0.27), residues: 352
  sheet: -1.74 (0.57), residues: 64
  loop : -0.59 (0.41), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 
 PHE   0.011   0.001   PHE A1133 
 TYR   0.012   0.001   TYR A 876 
 ARG   0.001   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04337 (  279)
  hydrogen bonds       : angle       5.47927 (  798)
  SS BOND              : bond        0.00947 (    1)
  SS BOND              : angle       2.29873 (    2)
  covalent geometry    : bond        0.00236 ( 5875)
  covalent geometry    : angle       0.49661 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7727 (mpt180) cc_final: 0.6732 (mmp80)
REVERT: A  898 GLU cc_start: 0.8616 (mp0) cc_final: 0.8325 (mp0)
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.3134
  time to fit residues: 33.3061
Evaluate side-chains
  71 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.118171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.103748 restraints weight = 55555.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.107173 restraints weight = 23616.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.109336 restraints weight = 12850.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5876  Z= 0.120
  Angle     :  0.494   6.376   7945  Z= 0.266
  Chirality :  0.039   0.142    878
  Planarity :  0.004   0.031   1038
  Dihedral  :  4.098  16.567    768
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.68 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.32), residues: 697
  helix:  1.09 (0.27), residues: 350
  sheet: -1.81 (0.57), residues: 64
  loop : -0.69 (0.41), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1146 
 HIS   0.005   0.001   HIS A1167 
 PHE   0.014   0.001   PHE A1056 
 TYR   0.014   0.001   TYR A1039 
 ARG   0.001   0.000   ARG A 636 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  279)
  hydrogen bonds       : angle       5.36940 (  798)
  SS BOND              : bond        0.00927 (    1)
  SS BOND              : angle       2.27568 (    2)
  covalent geometry    : bond        0.00258 ( 5875)
  covalent geometry    : angle       0.49299 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7721 (mpt180) cc_final: 0.6747 (mmp80)
REVERT: A  898 GLU cc_start: 0.8434 (mp0) cc_final: 0.8168 (mp0)
  outliers start: 6
  outliers final: 6
  residues processed: 73
  average time/residue: 0.4076
  time to fit residues: 41.6479
Evaluate side-chains
  74 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1039 TYR
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.118460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.104007 restraints weight = 56344.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.107469 restraints weight = 23983.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.109646 restraints weight = 13091.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5876  Z= 0.106
  Angle     :  0.479   6.293   7945  Z= 0.256
  Chirality :  0.038   0.143    878
  Planarity :  0.003   0.030   1038
  Dihedral  :  4.015  14.732    768
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.83 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.33), residues: 697
  helix:  1.21 (0.27), residues: 351
  sheet: -1.75 (0.58), residues: 63
  loop : -0.64 (0.41), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1146 
 HIS   0.005   0.001   HIS A1167 
 PHE   0.012   0.001   PHE A 641 
 TYR   0.011   0.001   TYR A 876 
 ARG   0.001   0.000   ARG A 856 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  279)
  hydrogen bonds       : angle       5.17835 (  798)
  SS BOND              : bond        0.00942 (    1)
  SS BOND              : angle       2.21452 (    2)
  covalent geometry    : bond        0.00230 ( 5875)
  covalent geometry    : angle       0.47757 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7696 (mpt180) cc_final: 0.6716 (mmp80)
REVERT: A  801 ASN cc_start: 0.8311 (m110) cc_final: 0.8002 (m110)
REVERT: A  898 GLU cc_start: 0.8453 (mp0) cc_final: 0.8241 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 77
  average time/residue: 0.3176
  time to fit residues: 34.0401
Evaluate side-chains
  76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  707 GLN
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1039 TYR
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.116899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.102315 restraints weight = 56749.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.105799 restraints weight = 24061.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.107959 restraints weight = 13100.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5876  Z= 0.158
  Angle     :  0.515   6.383   7945  Z= 0.281
  Chirality :  0.039   0.144    878
  Planarity :  0.004   0.033   1038
  Dihedral  :  4.118  14.959    768
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.46 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.32), residues: 697
  helix:  1.06 (0.27), residues: 351
  sheet: -1.86 (0.58), residues: 63
  loop : -0.85 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1146 
 HIS   0.005   0.001   HIS A1167 
 PHE   0.014   0.002   PHE A1056 
 TYR   0.014   0.001   TYR A 876 
 ARG   0.003   0.000   ARG A 882 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  279)
  hydrogen bonds       : angle       5.36378 (  798)
  SS BOND              : bond        0.00892 (    1)
  SS BOND              : angle       2.31407 (    2)
  covalent geometry    : bond        0.00338 ( 5875)
  covalent geometry    : angle       0.51411 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7752 (mpt180) cc_final: 0.6750 (mmp80)
REVERT: A  898 GLU cc_start: 0.8445 (mp0) cc_final: 0.8212 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 79
  average time/residue: 0.3151
  time to fit residues: 34.9475
Evaluate side-chains
  75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  707 GLN
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1039 TYR
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    3.4188

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

Flipped N/Q/H residues before XYZ refinement:
A1116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.116141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.101734 restraints weight = 55737.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.105199 restraints weight = 23591.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.107363 restraints weight = 12856.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5876  Z= 0.230
  Angle     :  0.590   6.409   7945  Z= 0.329
  Chirality :  0.041   0.151    878
  Planarity :  0.005   0.034   1038
  Dihedral  :  4.484  15.259    768
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.56 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.32), residues: 697
  helix:  0.58 (0.26), residues: 352
  sheet: -1.99 (0.60), residues: 63
  loop : -1.22 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 918 
 HIS   0.007   0.002   HIS A 727 
 PHE   0.020   0.002   PHE A 641 
 TYR   0.020   0.002   TYR A 876 
 ARG   0.005   0.001   ARG A 882 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  279)
  hydrogen bonds       : angle       5.82479 (  798)
  SS BOND              : bond        0.00820 (    1)
  SS BOND              : angle       2.42928 (    2)
  covalent geometry    : bond        0.00491 ( 5875)
  covalent geometry    : angle       0.58853 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7880 (mpt180) cc_final: 0.6802 (mmp80)
REVERT: A  898 GLU cc_start: 0.8436 (mp0) cc_final: 0.8173 (mp0)
  outliers start: 10
  outliers final: 9
  residues processed: 75
  average time/residue: 0.3238
  time to fit residues: 34.0858
Evaluate side-chains
  76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  707 GLN
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1039 TYR
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.0980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.118361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.103736 restraints weight = 54439.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.107276 restraints weight = 22597.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.109474 restraints weight = 12215.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5876  Z= 0.111
  Angle     :  0.502   6.337   7945  Z= 0.270
  Chirality :  0.039   0.148    878
  Planarity :  0.004   0.034   1038
  Dihedral  :  4.268  17.571    768
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.03 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.32), residues: 697
  helix:  0.95 (0.27), residues: 352
  sheet: -1.86 (0.61), residues: 63
  loop : -0.90 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 
 PHE   0.008   0.001   PHE A1133 
 TYR   0.018   0.001   TYR A1039 
 ARG   0.004   0.000   ARG A1144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  279)
  hydrogen bonds       : angle       5.26792 (  798)
  SS BOND              : bond        0.01006 (    1)
  SS BOND              : angle       2.31655 (    2)
  covalent geometry    : bond        0.00244 ( 5875)
  covalent geometry    : angle       0.50045 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7789 (mpt180) cc_final: 0.6702 (mmp80)
REVERT: A  642 LEU cc_start: 0.8733 (mm) cc_final: 0.8511 (mm)
REVERT: A  898 GLU cc_start: 0.8438 (mp0) cc_final: 0.8168 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 75
  average time/residue: 0.3401
  time to fit residues: 35.7078
Evaluate side-chains
  75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  707 GLN
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1039 TYR
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.117770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.103199 restraints weight = 54668.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.106743 restraints weight = 22866.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.108952 restraints weight = 12361.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5876  Z= 0.137
  Angle     :  0.504   6.371   7945  Z= 0.275
  Chirality :  0.039   0.146    878
  Planarity :  0.004   0.035   1038
  Dihedral  :  4.241  17.090    768
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.50 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.32), residues: 697
  helix:  1.02 (0.27), residues: 352
  sheet: -1.89 (0.61), residues: 64
  loop : -0.97 (0.40), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 
 PHE   0.008   0.001   PHE A 641 
 TYR   0.016   0.001   TYR A1039 
 ARG   0.002   0.000   ARG A 882 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  279)
  hydrogen bonds       : angle       5.30569 (  798)
  SS BOND              : bond        0.00938 (    1)
  SS BOND              : angle       2.26224 (    2)
  covalent geometry    : bond        0.00297 ( 5875)
  covalent geometry    : angle       0.50310 ( 7943)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  427 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  629 ARG cc_start: 0.7786 (mpt180) cc_final: 0.6819 (mmp80)
REVERT: A  898 GLU cc_start: 0.8410 (mp0) cc_final: 0.8152 (mp0)
  outliers start: 7
  outliers final: 7
  residues processed: 76
  average time/residue: 0.3256
  time to fit residues: 34.8677
Evaluate side-chains
  75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  707 GLN
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1039 TYR
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1152 CYS
Chi-restraints excluded: chain A residue 1160 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.119222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.104596 restraints weight = 54096.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.108193 restraints weight = 22610.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.110420 restraints weight = 12197.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5876  Z= 0.102
  Angle     :  0.485   6.358   7945  Z= 0.259
  Chirality :  0.038   0.144    878
  Planarity :  0.004   0.034   1038
  Dihedral  :  4.124  17.168    768
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.34 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.33), residues: 697
  helix:  1.23 (0.27), residues: 352
  sheet: -1.90 (0.61), residues: 64
  loop : -0.79 (0.41), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 
 PHE   0.012   0.001   PHE A 641 
 TYR   0.015   0.001   TYR A1039 
 ARG   0.003   0.000   ARG A1109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  279)
  hydrogen bonds       : angle       5.05534 (  798)
  SS BOND              : bond        0.00994 (    1)
  SS BOND              : angle       2.14512 (    2)
  covalent geometry    : bond        0.00224 ( 5875)
  covalent geometry    : angle       0.48362 ( 7943)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3894.18 seconds
wall clock time: 68 minutes 14.85 seconds (4094.85 seconds total)