Starting phenix.real_space_refine
on Wed Mar  4 06:21:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o3d_12704/03_2026/7o3d_12704.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o3d_12704/03_2026/7o3d_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_12704/03_2026/7o3d_12704.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o3d_12704/03_2026/7o3d_12704.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o3d_12704/03_2026/7o3d_12704.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o3d_12704/03_2026/7o3d_12704.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.020
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.05, per 1000 atoms: 0.18
  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: 0.96
  Conformation dependent library (CDL) restraints added in 269.2 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: 0.23
  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: 1.80

  Time building geometry restraints manager: 1.29 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:             1.050
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.350
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.070
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.050   0.006   ARG A1109 
 TYR   0.036   0.006   TYR A 392 
 PHE   0.023   0.003   PHE A 424 
 TRP   0.029   0.007   TRP A1225 
 HIS   0.021   0.004   HIS A1027 

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

*********************** 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  : 0.315 
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: 0.1449
  time to fit residues: 17.0367
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  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.119355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.104417 restraints weight = 55274.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.107981 restraints weight = 23229.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.110122 restraints weight = 12556.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.111516 restraints weight = 8073.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.112313 restraints weight = 5797.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5876  Z= 0.139
  Angle     :  0.564   6.346   7945  Z= 0.309
  Chirality :  0.040   0.154    878
  Planarity :  0.005   0.039   1038
  Dihedral  :  4.017  16.580    768
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  8.01 %
    Favored  : 91.05 %
  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 are not related in a simple way.
  whole: -0.02 (0.32), residues: 697
  helix:  0.74 (0.26), residues: 349
  sheet: -1.34 (0.59), residues: 64
  loop : -0.52 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 636 
 TYR   0.012   0.001   TYR A 876 
 PHE   0.016   0.002   PHE A1133 
 TRP   0.011   0.002   TRP A1146 
 HIS   0.005   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5875)
  covalent geometry    : angle       0.56296 ( 7943)
  SS BOND              : bond        0.01474 (    1)
  SS BOND              : angle       1.96288 (    2)
  hydrogen bonds       : bond        0.05182 (  279)
  hydrogen bonds       : angle       6.10308 (  798)

*********************** 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
  79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.328 
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: 0.7650 (mpt180) cc_final: 0.6727 (mmp80)
REVERT: A  632 MET cc_start: 0.6097 (tmm) cc_final: 0.5626 (tpt)
REVERT: A  634 PHE cc_start: 0.6678 (m-80) cc_final: 0.6159 (m-80)
REVERT: A  898 GLU cc_start: 0.8543 (mp0) cc_final: 0.8316 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 77
  average time/residue: 0.1448
  time to fit residues: 15.4226
Evaluate side-chains
  72 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 GLU
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 12 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 11 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.118658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.104118 restraints weight = 55866.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.107592 restraints weight = 23452.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.109782 restraints weight = 12717.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.111103 restraints weight = 8048.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.111972 restraints weight = 5825.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5876  Z= 0.138
  Angle     :  0.517   6.280   7945  Z= 0.281
  Chirality :  0.039   0.143    878
  Planarity :  0.004   0.038   1038
  Dihedral  :  4.068  15.336    768
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.32), residues: 697
  helix:  0.95 (0.27), residues: 349
  sheet: -1.59 (0.58), residues: 64
  loop : -0.59 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 636 
 TYR   0.013   0.001   TYR A 876 
 PHE   0.014   0.001   PHE A1133 
 TRP   0.007   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5875)
  covalent geometry    : angle       0.51569 ( 7943)
  SS BOND              : bond        0.00879 (    1)
  SS BOND              : angle       2.20410 (    2)
  hydrogen bonds       : bond        0.04718 (  279)
  hydrogen bonds       : angle       5.69478 (  798)

*********************** 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
  75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.313 
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: 0.7700 (mpt180) cc_final: 0.6743 (mmp80)
  outliers start: 6
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1459
  time to fit residues: 14.6045
Evaluate side-chains
  70 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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 41 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.118031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.103360 restraints weight = 57735.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.106846 restraints weight = 24865.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.109011 restraints weight = 13761.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.110300 restraints weight = 8881.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.111186 restraints weight = 6550.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5876  Z= 0.178
  Angle     :  0.539   6.427   7945  Z= 0.298
  Chirality :  0.040   0.147    878
  Planarity :  0.004   0.037   1038
  Dihedral  :  4.287  21.387    768
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.32), residues: 697
  helix:  0.76 (0.26), residues: 351
  sheet: -1.78 (0.57), residues: 64
  loop : -0.80 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 882 
 TYR   0.017   0.001   TYR A 876 
 PHE   0.015   0.002   PHE A 641 
 TRP   0.008   0.001   TRP A 918 
 HIS   0.006   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5875)
  covalent geometry    : angle       0.53810 ( 7943)
  SS BOND              : bond        0.00841 (    1)
  SS BOND              : angle       2.43087 (    2)
  hydrogen bonds       : bond        0.04504 (  279)
  hydrogen bonds       : angle       5.74799 (  798)

*********************** 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
  76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.268 
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: 0.7747 (mpt180) cc_final: 0.6756 (mmp80)
  outliers start: 6
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1303
  time to fit residues: 14.2418
Evaluate side-chains
  72 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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 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 66 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.118446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.103802 restraints weight = 57088.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.107272 restraints weight = 24543.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.109419 restraints weight = 13575.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.110762 restraints weight = 8783.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.111630 restraints weight = 6423.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5876  Z= 0.134
  Angle     :  0.507   6.368   7945  Z= 0.276
  Chirality :  0.039   0.146    878
  Planarity :  0.004   0.037   1038
  Dihedral  :  4.230  20.296    768
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 10.99 %
    Favored  : 88.23 %
  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 are not related in a simple way.
  whole: -0.14 (0.32), residues: 697
  helix:  0.88 (0.27), residues: 351
  sheet: -1.89 (0.56), residues: 64
  loop : -0.80 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 882 
 TYR   0.014   0.001   TYR A 876 
 PHE   0.012   0.001   PHE A1056 
 TRP   0.007   0.001   TRP A1146 
 HIS   0.005   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5875)
  covalent geometry    : angle       0.50610 ( 7943)
  SS BOND              : bond        0.00875 (    1)
  SS BOND              : angle       2.27584 (    2)
  hydrogen bonds       : bond        0.04279 (  279)
  hydrogen bonds       : angle       5.55430 (  798)

*********************** 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: 5
    poor density    : 68
  time to evaluate  : 0.333 
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: 0.7702 (mpt180) cc_final: 0.6698 (mmp80)
  outliers start: 5
  outliers final: 5
  residues processed: 73
  average time/residue: 0.1369
  time to fit residues: 14.0650
Evaluate side-chains
  71 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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 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 35 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0870
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.118883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.104400 restraints weight = 55412.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.107901 restraints weight = 23405.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.110077 restraints weight = 12667.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.111423 restraints weight = 8036.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.112160 restraints weight = 5773.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5876  Z= 0.097
  Angle     :  0.484   6.384   7945  Z= 0.257
  Chirality :  0.039   0.144    878
  Planarity :  0.003   0.032   1038
  Dihedral  :  4.097  23.326    768
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.15 %
    Favored  : 87.60 %
  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 are not related in a simple way.
  whole:  0.22 (0.33), residues: 697
  helix:  1.17 (0.27), residues: 351
  sheet: -1.85 (0.56), residues: 64
  loop : -0.58 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 396 
 TYR   0.012   0.001   TYR A1039 
 PHE   0.017   0.001   PHE A1056 
 TRP   0.007   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 5875)
  covalent geometry    : angle       0.48241 ( 7943)
  SS BOND              : bond        0.00992 (    1)
  SS BOND              : angle       2.23738 (    2)
  hydrogen bonds       : bond        0.03941 (  279)
  hydrogen bonds       : angle       5.17528 (  798)

*********************** 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
  80 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.276 
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: 0.7615 (mpt180) cc_final: 0.6643 (mmp80)
REVERT: A  898 GLU cc_start: 0.8471 (mp0) cc_final: 0.8115 (pm20)
  outliers start: 8
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1448
  time to fit residues: 15.7654
Evaluate side-chains
  77 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  902 LEU
Chi-restraints excluded: chain A residue  993 SER
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 65 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.117655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.103233 restraints weight = 56677.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.106671 restraints weight = 24310.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.108784 restraints weight = 13335.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.110072 restraints weight = 8581.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.110937 restraints weight = 6278.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5876  Z= 0.132
  Angle     :  0.494   6.354   7945  Z= 0.267
  Chirality :  0.039   0.144    878
  Planarity :  0.004   0.036   1038
  Dihedral  :  4.119  20.118    768
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.87 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.32), residues: 697
  helix:  1.08 (0.27), residues: 352
  sheet: -1.84 (0.57), residues: 63
  loop : -0.67 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 882 
 TYR   0.013   0.001   TYR A 876 
 PHE   0.011   0.001   PHE A 641 
 TRP   0.006   0.001   TRP A1146 
 HIS   0.005   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5875)
  covalent geometry    : angle       0.49257 ( 7943)
  SS BOND              : bond        0.00940 (    1)
  SS BOND              : angle       2.25857 (    2)
  hydrogen bonds       : bond        0.03920 (  279)
  hydrogen bonds       : angle       5.28006 (  798)

*********************** 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
  76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.280 
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: 0.7660 (mpt180) cc_final: 0.6676 (mmp80)
REVERT: A  898 GLU cc_start: 0.8506 (mp0) cc_final: 0.8151 (pm20)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1351
  time to fit residues: 14.3556
Evaluate side-chains
  75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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 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 20 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3921 r_free = 0.3921 target = 0.117961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.103464 restraints weight = 56319.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.106925 restraints weight = 24133.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.109048 restraints weight = 13214.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.110380 restraints weight = 8544.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.111220 restraints weight = 6190.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5876  Z= 0.113
  Angle     :  0.486   6.344   7945  Z= 0.261
  Chirality :  0.039   0.143    878
  Planarity :  0.004   0.034   1038
  Dihedral  :  4.068  17.482    768
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.32), residues: 697
  helix:  1.13 (0.27), residues: 352
  sheet: -1.82 (0.58), residues: 63
  loop : -0.69 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 396 
 TYR   0.012   0.001   TYR A 876 
 PHE   0.006   0.001   PHE A1133 
 TRP   0.006   0.001   TRP A 918 
 HIS   0.007   0.001   HIS A 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5875)
  covalent geometry    : angle       0.48422 ( 7943)
  SS BOND              : bond        0.00964 (    1)
  SS BOND              : angle       2.32057 (    2)
  hydrogen bonds       : bond        0.03835 (  279)
  hydrogen bonds       : angle       5.14934 (  798)

*********************** 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: 7
    poor density    : 70
  time to evaluate  : 0.310 
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: 0.7660 (mpt180) cc_final: 0.6634 (mmp80)
REVERT: A  898 GLU cc_start: 0.8524 (mp0) cc_final: 0.8176 (mp0)
  outliers start: 7
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1436
  time to fit residues: 15.2104
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  : 0.374 
-------------------------------------------------------------------------------
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 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 24 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.117307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.102815 restraints weight = 57505.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.106246 restraints weight = 24992.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.108365 restraints weight = 13934.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.109675 restraints weight = 9143.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.110551 restraints weight = 6695.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5876  Z= 0.186
  Angle     :  0.535   6.368   7945  Z= 0.296
  Chirality :  0.040   0.146    878
  Planarity :  0.004   0.036   1038
  Dihedral  :  4.268  15.830    768
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 14.13 %
    Favored  : 84.93 %
  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 are not related in a simple way.
  whole: -0.19 (0.32), residues: 697
  helix:  0.88 (0.26), residues: 352
  sheet: -1.91 (0.59), residues: 63
  loop : -0.91 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 882 
 TYR   0.017   0.001   TYR A 876 
 PHE   0.010   0.001   PHE A 380 
 TRP   0.008   0.001   TRP A 918 
 HIS   0.005   0.002   HIS A 727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5875)
  covalent geometry    : angle       0.53403 ( 7943)
  SS BOND              : bond        0.00894 (    1)
  SS BOND              : angle       2.35865 (    2)
  hydrogen bonds       : bond        0.04118 (  279)
  hydrogen bonds       : angle       5.47804 (  798)

*********************** 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
  73 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.319 
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: 0.7746 (mpt180) cc_final: 0.6839 (mmp80)
  outliers start: 6
  outliers final: 6
  residues processed: 73
  average time/residue: 0.1404
  time to fit residues: 14.0713
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  : 0.307 
-------------------------------------------------------------------------------
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 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 8 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0010
   chunk 68 optimal weight:    0.0000
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.118127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.103674 restraints weight = 56323.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.107158 restraints weight = 23866.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.109328 restraints weight = 13022.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.110653 restraints weight = 8300.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.111392 restraints weight = 5990.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5876  Z= 0.102
  Angle     :  0.497   6.373   7945  Z= 0.265
  Chirality :  0.039   0.145    878
  Planarity :  0.004   0.034   1038
  Dihedral  :  4.127  18.053    768
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.13 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.33), residues: 697
  helix:  1.13 (0.27), residues: 352
  sheet: -1.81 (0.61), residues: 63
  loop : -0.59 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 396 
 TYR   0.014   0.001   TYR A 392 
 PHE   0.012   0.001   PHE A 641 
 TRP   0.007   0.001   TRP A1146 
 HIS   0.004   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 5875)
  covalent geometry    : angle       0.49634 ( 7943)
  SS BOND              : bond        0.00954 (    1)
  SS BOND              : angle       2.12846 (    2)
  hydrogen bonds       : bond        0.03833 (  279)
  hydrogen bonds       : angle       5.04170 (  798)

********************** 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  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 GLU cc_start: 0.8033 (mp0) cc_final: 0.7785 (mp0)
REVERT: A  629 ARG cc_start: 0.7660 (mpt180) cc_final: 0.6680 (mmp80)
REVERT: A  898 GLU cc_start: 0.8477 (mp0) cc_final: 0.8191 (pm20)
  outliers start: 7
  outliers final: 6
  residues processed: 75
  average time/residue: 0.1355
  time to fit residues: 14.2897
Evaluate side-chains
  75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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 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 10 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.118193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.103704 restraints weight = 55373.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.107199 restraints weight = 23298.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.109345 restraints weight = 12624.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.110685 restraints weight = 8089.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.111567 restraints weight = 5798.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5876  Z= 0.104
  Angle     :  0.491   6.324   7945  Z= 0.262
  Chirality :  0.038   0.141    878
  Planarity :  0.003   0.032   1038
  Dihedral  :  4.022  18.171    768
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.13 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.33), residues: 697
  helix:  1.22 (0.27), residues: 353
  sheet: -1.82 (0.62), residues: 63
  loop : -0.52 (0.41), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 726 
 TYR   0.011   0.001   TYR A 392 
 PHE   0.031   0.002   PHE A 634 
 TRP   0.006   0.001   TRP A 918 
 HIS   0.004   0.001   HIS A1167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 5875)
  covalent geometry    : angle       0.48959 ( 7943)
  SS BOND              : bond        0.00966 (    1)
  SS BOND              : angle       2.09694 (    2)
  hydrogen bonds       : bond        0.03725 (  279)
  hydrogen bonds       : angle       4.98458 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1906.66 seconds
wall clock time: 33 minutes 9.32 seconds (1989.32 seconds total)