Starting phenix.real_space_refine
on Wed Mar  4 06:10:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7si7_25139/03_2026/7si7_25139.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7si7_25139/03_2026/7si7_25139.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7si7_25139/03_2026/7si7_25139.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7si7_25139/03_2026/7si7_25139.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7si7_25139/03_2026/7si7_25139.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7si7_25139/03_2026/7si7_25139.cif"
  }
  resolution = 3.49
  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
-------------------------------------------------------------------------------
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=  -0.000 sd=   1.000
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     Mg      1      5.21       5
     S      38      5.16       5
     C    3545      2.51       5
     N     923      2.21       5
     O     998      1.98       5
     F       4      1.80       5
     H    5777      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 11287
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 728, 11281
          Classifications: {'peptide': 728}
          Link IDs: {'PTRANS': 28, 'TRANS': 699}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.18, per 1000 atoms: 0.19
  Number of scatterers: 11287
  At special positions: 0
  Unit cell: (71.4, 80.75, 141.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      38     16.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O     998      8.00
     N     923      7.00
     C    3545      6.00
     H    5777      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 397.5 milliseconds
  

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      59.9% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 640 through 671
      Proline residue:  A 660  - end of helix
    Processing helix  chain 'A' and resid 679 through 683
    Processing helix  chain 'A' and resid 690 through 707
    Processing helix  chain 'A' and resid 707 through 721
      removed outlier: 4.355A  pdb=" N   PHE A 711 " --> pdb=" O   GLY A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 752
    Processing helix  chain 'A' and resid 762 through 783
    Processing helix  chain 'A' and resid 787 through 796
      removed outlier: 3.652A  pdb=" N   GLN A 796 " --> pdb=" O   LEU A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 890
    Processing helix  chain 'A' and resid 891 through 907
      removed outlier: 3.523A  pdb=" N   LYS A 907 " --> pdb=" O   ALA A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 943
      removed outlier: 3.619A  pdb=" N   TYR A 920 " --> pdb=" O   LYS A 916 " (cutoff:3.500A)
      Proline residue:  A 923  - end of helix
    Processing helix  chain 'A' and resid 944 through 951
    Processing helix  chain 'A' and resid 952 through 956
    Processing helix  chain 'A' and resid 959 through 980
      removed outlier: 3.625A  pdb=" N   CYS A 980 " --> pdb=" O   LEU A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 986
      removed outlier: 3.561A  pdb=" N   GLY A 985 " --> pdb=" O   CYS A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 1002
      removed outlier: 4.263A  pdb=" N   ALA A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1016
      removed outlier: 4.756A  pdb=" N   HIS A1016 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1061
    Processing helix  chain 'A' and resid 1066 through 1080
    Processing helix  chain 'A' and resid 1105 through 1112
      removed outlier: 3.602A  pdb=" N   VAL A1109 " --> pdb=" O   ASN A1105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1164
    Processing helix  chain 'A' and resid 1168 through 1181
    Processing helix  chain 'A' and resid 1205 through 1218
      removed outlier: 4.385A  pdb=" N   ALA A1209 " --> pdb=" O   LYS A1205 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LEU A1210 " --> pdb=" O   GLN A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1250 through 1264
    Processing helix  chain 'A' and resid 1277 through 1284
    Processing helix  chain 'A' and resid 1294 through 1301
    Processing helix  chain 'A' and resid 1310 through 1346
      removed outlier: 4.218A  pdb=" N   VAL A1314 " --> pdb=" O   LEU A1310 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   TYR A1337 " --> pdb=" O   PHE A1333 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   ASN A1338 " --> pdb=" O   ALA A1334 " (cutoff:3.500A)
      Proline residue:  A1343  - end of helix
    Processing helix  chain 'A' and resid 1357 through 1379
      removed outlier: 4.089A  pdb=" N   GLY A1361 " --> pdb=" O   GLN A1357 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   SER A1362 " --> pdb=" O   PRO A1358 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   MET A1365 " --> pdb=" O   GLY A1361 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A1375 " --> pdb=" O   SER A1371 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A1379 " --> pdb=" O   SER A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1380 through 1382
      No H-bonds generated for 'chain 'A' and resid 1380 through 1382'
    Processing helix  chain 'A' and resid 1386 through 1394
    Processing sheet with id=AA1, first strand: chain 'A' and resid 814 through 818
      removed outlier: 4.091A  pdb=" N   ALA A 801 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   ILE A 827 " --> pdb=" O   VAL A 803 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU A 881 " --> pdb=" O   ILE A 843 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   ASP A 839 " --> pdb=" O   THR A 885 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 861 through 863
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1004 through 1006
      removed outlier: 6.020A  pdb=" N   GLY A1287 " --> pdb=" O   ILE A1303 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LEU A1305 " --> pdb=" O   GLY A1287 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ALA A1289 " --> pdb=" O   LEU A1305 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL A1268 " --> pdb=" O   VAL A1286 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ILE A1288 " --> pdb=" O   VAL A1268 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   MET A1270 " --> pdb=" O   ILE A1288 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ILE A1290 " --> pdb=" O   MET A1270 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ALA A1020 " --> pdb=" O   ALA A1269 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   VAL A1271 " --> pdb=" O   ALA A1020 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   MET A1022 " --> pdb=" O   VAL A1271 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   VAL A1222 " --> pdb=" O   LYS A1244 " (cutoff:3.500A)
      removed outlier: 8.463A  pdb=" N   PHE A1246 " --> pdb=" O   VAL A1222 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU A1224 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1035 through 1041
      removed outlier: 6.793A  pdb=" N   ALA A1199 " --> pdb=" O   MET A1037 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   VAL A1039 " --> pdb=" O   MET A1197 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET A1197 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   LEU A1041 " --> pdb=" O   CYS A1195 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   CYS A1195 " --> pdb=" O   LEU A1041 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   LEU A1194 " --> pdb=" O   ILE A1190 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   ILE A1190 " --> pdb=" O   LEU A1194 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1008 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5768
        1.03 -     1.23: 11
        1.23 -     1.42: 2144
        1.42 -     1.62: 3379
        1.62 -     1.81: 71
  Bond restraints: 11373
  Sorted by residual:
  bond pdb=" F1  ALF A1502 "
       pdb="AL   ALF A1502 "
    ideal  model  delta    sigma   weight residual
    1.684  1.784 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" F3  ALF A1502 "
       pdb="AL   ALF A1502 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" F2  ALF A1502 "
       pdb="AL   ALF A1502 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.45e+01
  bond pdb=" F4  ALF A1502 "
       pdb="AL   ALF A1502 "
    ideal  model  delta    sigma   weight residual
    1.686  1.784 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" CA  VAL A 922 "
       pdb=" CB  VAL A 922 "
    ideal  model  delta    sigma   weight residual
    1.539  1.532  0.007 5.40e-03 3.43e+04 1.49e+00
  ... (remaining 11368 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.25: 20724
       14.25 -    28.50: 4
       28.50 -    42.75: 0
       42.75 -    57.00: 0
       57.00 -    71.25: 2
  Bond angle restraints: 20730
  Sorted by residual:
  angle pdb=" F1  ALF A1502 "
        pdb="AL   ALF A1502 "
        pdb=" F2  ALF A1502 "
      ideal   model   delta    sigma   weight residual
     108.68  179.93  -71.25 3.00e+00 1.11e-01 5.64e+02
  angle pdb=" F3  ALF A1502 "
        pdb="AL   ALF A1502 "
        pdb=" F4  ALF A1502 "
      ideal   model   delta    sigma   weight residual
     109.63  179.97  -70.34 3.00e+00 1.11e-01 5.50e+02
  angle pdb=" F2  ALF A1502 "
        pdb="AL   ALF A1502 "
        pdb=" F4  ALF A1502 "
      ideal   model   delta    sigma   weight residual
     110.21   90.05   20.16 3.00e+00 1.11e-01 4.52e+01
  angle pdb=" F2  ALF A1502 "
        pdb="AL   ALF A1502 "
        pdb=" F3  ALF A1502 "
      ideal   model   delta    sigma   weight residual
     109.59   89.92   19.67 3.00e+00 1.11e-01 4.30e+01
  angle pdb=" F1  ALF A1502 "
        pdb="AL   ALF A1502 "
        pdb=" F3  ALF A1502 "
      ideal   model   delta    sigma   weight residual
     109.69   90.05   19.64 3.00e+00 1.11e-01 4.28e+01
  ... (remaining 20725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4829
       17.96 -    35.93: 345
       35.93 -    53.89: 85
       53.89 -    71.85: 18
       71.85 -    89.82: 5
  Dihedral angle restraints: 5282
    sinusoidal: 2934
      harmonic: 2348
  Sorted by residual:
  dihedral pdb=" CB  GLU A1013 "
           pdb=" CG  GLU A1013 "
           pdb=" CD  GLU A1013 "
           pdb=" OE1 GLU A1013 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.52   80.52     1      3.00e+01 1.11e-03 8.91e+00
  dihedral pdb=" CA  ARG A 824 "
           pdb=" CB  ARG A 824 "
           pdb=" CG  ARG A 824 "
           pdb=" CD  ARG A 824 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.04   49.96     3      1.50e+01 4.44e-03 8.84e+00
  dihedral pdb=" CA  LYS A 907 "
           pdb=" CB  LYS A 907 "
           pdb=" CG  LYS A 907 "
           pdb=" CD  LYS A 907 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.26   48.26     3      1.50e+01 4.44e-03 8.61e+00
  ... (remaining 5279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 607
       0.027 -    0.055: 167
       0.055 -    0.082: 89
       0.082 -    0.109: 46
       0.109 -    0.136: 28
  Chirality restraints: 937
  Sorted by residual:
  chirality pdb=" CA  ILE A1154 "
            pdb=" N   ILE A1154 "
            pdb=" C   ILE A1154 "
            pdb=" CB  ILE A1154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  VAL A1152 "
            pdb=" N   VAL A1152 "
            pdb=" C   VAL A1152 "
            pdb=" CB  VAL A1152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  VAL A 686 "
            pdb=" N   VAL A 686 "
            pdb=" C   VAL A 686 "
            pdb=" CB  VAL A 686 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 934 not shown)

  Planarity restraints: 1636
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1322 "   -0.007 2.00e-02 2.50e+03   1.45e-02 2.11e+00
        pdb=" C   ARG A1322 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ARG A1322 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR A1323 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1325 "   -0.007 2.00e-02 2.50e+03   1.39e-02 1.93e+00
        pdb=" C   ARG A1325 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ARG A1325 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG A1326 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1323 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   THR A1323 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   THR A1323 "    0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A1324 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1633 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 2648
        2.31 -     2.88: 26841
        2.88 -     3.46: 29180
        3.46 -     4.03: 39314
        4.03 -     4.60: 59511
  Nonbonded interactions: 157494
  Sorted by model distance:
  nonbonded pdb=" O   ALA A1367 "
            pdb=" HG  SER A1371 "
     model   vdw
     1.740 2.450
  nonbonded pdb=" OE1 GLU A 643 "
            pdb=" H   GLU A 643 "
     model   vdw
     1.788 2.450
  nonbonded pdb=" OD1 ASN A 943 "
            pdb=" H   ASP A 945 "
     model   vdw
     1.796 2.450
  nonbonded pdb="HH11 ARG A1267 "
            pdb=" OD2 ASP A1285 "
     model   vdw
     1.796 2.450
  nonbonded pdb=" H   GLY A 833 "
            pdb=" O   ASN A 875 "
     model   vdw
     1.810 2.450
  ... (remaining 157489 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:             0.040
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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   0.100   5596  Z= 0.169
  Angle     :  1.323  71.250   7587  Z= 0.489
  Chirality :  0.041   0.136    937
  Planarity :  0.003   0.029    940
  Dihedral  : 13.128  89.815   2042
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.32), residues: 720
  helix:  2.18 (0.26), residues: 405
  sheet:  1.20 (0.48), residues: 107
  loop :  0.71 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 862 
 TYR   0.015   0.001   TYR A 716 
 PHE   0.006   0.001   PHE A1023 
 TRP   0.005   0.001   TRP A1159 
 HIS   0.002   0.000   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5596)
  covalent geometry    : angle       1.32250 ( 7587)
  hydrogen bonds       : bond        0.13830 (  348)
  hydrogen bonds       : angle       6.12888 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1188
  time to fit residues: 17.7021
Evaluate side-chains
  89 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
A 704 GLN
A1318 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.185161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.131475 restraints weight = 18359.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.54
r_work: 0.3199 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   5596  Z= 0.112
  Angle     :  0.904  30.906   7587  Z= 0.361
  Chirality :  0.043   0.147    937
  Planarity :  0.003   0.031    940
  Dihedral  :  3.501  16.624    762
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.14 %
    Favored  : 93.20 %
  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:  2.65 (0.31), residues: 720
  helix:  2.57 (0.25), residues: 414
  sheet:  1.17 (0.48), residues: 107
  loop :  0.38 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1157 
 TYR   0.007   0.001   TYR A 667 
 PHE   0.007   0.001   PHE A 951 
 TRP   0.005   0.001   TRP A1159 
 HIS   0.002   0.001   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5596)
  covalent geometry    : angle       0.90421 ( 7587)
  hydrogen bonds       : bond        0.04256 (  348)
  hydrogen bonds       : angle       4.57211 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  641 LYS cc_start: 0.7563 (pttm) cc_final: 0.7132 (mmmt)
REVERT: A  642 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: A  646 GLN cc_start: 0.6519 (mt0) cc_final: 0.6310 (mm-40)
  outliers start: 4
  outliers final: 3
  residues processed: 99
  average time/residue: 0.1327
  time to fit residues: 18.3781
Evaluate side-chains
  94 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:   30.0000
   chunk 25 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.178566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.125932 restraints weight = 18516.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.34
r_work: 0.3123 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5596  Z= 0.167
  Angle     :  0.917  31.271   7587  Z= 0.372
  Chirality :  0.043   0.140    937
  Planarity :  0.003   0.031    940
  Dihedral  :  3.680  17.907    762
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.63 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.31), residues: 720
  helix:  2.49 (0.25), residues: 417
  sheet:  0.90 (0.47), residues: 111
  loop :  0.33 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 775 
 TYR   0.005   0.001   TYR A 738 
 PHE   0.010   0.002   PHE A 657 
 TRP   0.007   0.001   TRP A 936 
 HIS   0.004   0.001   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 5596)
  covalent geometry    : angle       0.91677 ( 7587)
  hydrogen bonds       : bond        0.04329 (  348)
  hydrogen bonds       : angle       4.39962 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  641 LYS cc_start: 0.7578 (pttm) cc_final: 0.7150 (mmmt)
REVERT: A  642 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7380 (tp30)
REVERT: A 1202 ASP cc_start: 0.8241 (m-30) cc_final: 0.7995 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 102
  average time/residue: 0.1519
  time to fit residues: 20.7532
Evaluate side-chains
  100 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue 1228 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 693 ASN
** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.173407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.120386 restraints weight = 18577.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.31
r_work: 0.3038 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   5596  Z= 0.268
  Angle     :  0.959  33.428   7587  Z= 0.406
  Chirality :  0.045   0.145    937
  Planarity :  0.004   0.032    940
  Dihedral  :  4.044  18.999    762
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.12 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.31), residues: 720
  helix:  1.91 (0.25), residues: 418
  sheet:  0.83 (0.49), residues: 105
  loop :  0.01 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 775 
 TYR   0.008   0.001   TYR A1075 
 PHE   0.018   0.002   PHE A 657 
 TRP   0.009   0.001   TRP A 936 
 HIS   0.005   0.001   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 ( 5596)
  covalent geometry    : angle       0.95862 ( 7587)
  hydrogen bonds       : bond        0.04862 (  348)
  hydrogen bonds       : angle       4.57772 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  784 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7563 (ptpt)
REVERT: A 1202 ASP cc_start: 0.8280 (m-30) cc_final: 0.7995 (m-30)
REVERT: A 1228 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8621 (t70)
REVERT: A 1264 ASP cc_start: 0.7727 (m-30) cc_final: 0.6829 (t0)
REVERT: A 1270 MET cc_start: 0.8635 (tpt) cc_final: 0.8373 (tpt)
REVERT: A 1302 ASP cc_start: 0.8490 (m-30) cc_final: 0.8171 (m-30)
REVERT: A 1365 MET cc_start: 0.6274 (mmt) cc_final: 0.6024 (mmt)
  outliers start: 8
  outliers final: 3
  residues processed: 107
  average time/residue: 0.1480
  time to fit residues: 21.3313
Evaluate side-chains
  103 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  784 LYS
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue 1228 ASP
Chi-restraints excluded: chain A residue 1355 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:   40.0000
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 796 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.177770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.125065 restraints weight = 18308.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.33
r_work: 0.3100 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5596  Z= 0.106
  Angle     :  0.905  30.440   7587  Z= 0.360
  Chirality :  0.043   0.138    937
  Planarity :  0.003   0.033    940
  Dihedral  :  3.773  17.799    762
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 11.61 %
    Favored  : 87.73 %
  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:  2.20 (0.31), residues: 720
  helix:  2.32 (0.25), residues: 420
  sheet:  0.66 (0.47), residues: 111
  loop :  0.04 (0.42), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1283 
 TYR   0.007   0.001   TYR A1075 
 PHE   0.008   0.001   PHE A 951 
 TRP   0.007   0.001   TRP A1359 
 HIS   0.002   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5596)
  covalent geometry    : angle       0.90455 ( 7587)
  hydrogen bonds       : bond        0.03838 (  348)
  hydrogen bonds       : angle       4.22088 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7567 (tp30)
REVERT: A 1202 ASP cc_start: 0.8241 (m-30) cc_final: 0.8011 (m-30)
REVERT: A 1228 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8644 (t70)
REVERT: A 1264 ASP cc_start: 0.7608 (m-30) cc_final: 0.6839 (t0)
REVERT: A 1270 MET cc_start: 0.8584 (tpt) cc_final: 0.8336 (tpt)
REVERT: A 1273 ASP cc_start: 0.9231 (p0) cc_final: 0.8903 (p0)
REVERT: A 1365 MET cc_start: 0.6162 (mmt) cc_final: 0.5945 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 105
  average time/residue: 0.1394
  time to fit residues: 20.2162
Evaluate side-chains
  106 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1228 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 66 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 54 optimal weight:    0.0370
   chunk 3 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    2.7464

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.176004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.123473 restraints weight = 18467.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.31
r_work: 0.3081 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5596  Z= 0.143
  Angle     :  0.905  31.554   7587  Z= 0.362
  Chirality :  0.043   0.140    937
  Planarity :  0.003   0.034    940
  Dihedral  :  3.754  18.037    762
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.44 %
    Favored  : 87.23 %
  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:  2.19 (0.31), residues: 720
  helix:  2.32 (0.25), residues: 420
  sheet:  0.60 (0.47), residues: 111
  loop :  0.06 (0.43), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 775 
 TYR   0.005   0.001   TYR A 712 
 PHE   0.009   0.001   PHE A 657 
 TRP   0.006   0.001   TRP A 936 
 HIS   0.003   0.001   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5596)
  covalent geometry    : angle       0.90467 ( 7587)
  hydrogen bonds       : bond        0.03923 (  348)
  hydrogen bonds       : angle       4.19560 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1181 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7847 (mmtm)
REVERT: A 1202 ASP cc_start: 0.8275 (m-30) cc_final: 0.8002 (m-30)
REVERT: A 1228 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8643 (t70)
REVERT: A 1264 ASP cc_start: 0.7659 (m-30) cc_final: 0.6872 (t0)
REVERT: A 1270 MET cc_start: 0.8640 (tpt) cc_final: 0.8392 (tpt)
REVERT: A 1273 ASP cc_start: 0.9247 (p0) cc_final: 0.8884 (p0)
REVERT: A 1365 MET cc_start: 0.6313 (mmt) cc_final: 0.6060 (mmt)
  outliers start: 8
  outliers final: 4
  residues processed: 106
  average time/residue: 0.1402
  time to fit residues: 20.1980
Evaluate side-chains
  109 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1228 ASP
Chi-restraints excluded: chain A residue 1355 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0270
   chunk 68 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 71 optimal weight:    0.5980
   overall best weight:    1.2842

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.177959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.125727 restraints weight = 18414.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.31
r_work: 0.3112 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5596  Z= 0.098
  Angle     :  0.899  30.157   7587  Z= 0.354
  Chirality :  0.042   0.155    937
  Planarity :  0.003   0.034    940
  Dihedral  :  3.625  17.509    762
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 12.44 %
    Favored  : 87.06 %
  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:  2.43 (0.31), residues: 720
  helix:  2.55 (0.25), residues: 421
  sheet:  0.59 (0.46), residues: 113
  loop :  0.10 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 966 
 TYR   0.004   0.001   TYR A1075 
 PHE   0.007   0.001   PHE A 951 
 TRP   0.005   0.001   TRP A1359 
 HIS   0.002   0.001   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 5596)
  covalent geometry    : angle       0.89876 ( 7587)
  hydrogen bonds       : bond        0.03506 (  348)
  hydrogen bonds       : angle       4.04443 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7396 (tp30)
REVERT: A 1181 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7824 (mmtm)
REVERT: A 1228 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8619 (t70)
REVERT: A 1264 ASP cc_start: 0.7664 (m-30) cc_final: 0.6885 (t0)
REVERT: A 1270 MET cc_start: 0.8602 (tpt) cc_final: 0.8352 (tpt)
REVERT: A 1273 ASP cc_start: 0.9206 (p0) cc_final: 0.8855 (p0)
REVERT: A 1365 MET cc_start: 0.6203 (mmt) cc_final: 0.5965 (mmt)
  outliers start: 3
  outliers final: 2
  residues processed: 108
  average time/residue: 0.1353
  time to fit residues: 20.2927
Evaluate side-chains
  106 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1228 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.176634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.124160 restraints weight = 18412.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.31
r_work: 0.3086 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5596  Z= 0.131
  Angle     :  0.903  31.238   7587  Z= 0.359
  Chirality :  0.043   0.167    937
  Planarity :  0.003   0.034    940
  Dihedral  :  3.647  17.704    762
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.27 %
    Favored  : 86.07 %
  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:  2.36 (0.31), residues: 720
  helix:  2.49 (0.25), residues: 421
  sheet:  0.57 (0.46), residues: 113
  loop :  0.08 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 775 
 TYR   0.008   0.001   TYR A 716 
 PHE   0.008   0.001   PHE A 657 
 TRP   0.006   0.001   TRP A 936 
 HIS   0.002   0.001   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5596)
  covalent geometry    : angle       0.90339 ( 7587)
  hydrogen bonds       : bond        0.03681 (  348)
  hydrogen bonds       : angle       4.06212 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1181 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7860 (mmtm)
REVERT: A 1228 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8616 (t70)
REVERT: A 1264 ASP cc_start: 0.7707 (m-30) cc_final: 0.6862 (t0)
REVERT: A 1270 MET cc_start: 0.8660 (tpt) cc_final: 0.8393 (tpt)
REVERT: A 1273 ASP cc_start: 0.9243 (p0) cc_final: 0.8876 (p0)
REVERT: A 1365 MET cc_start: 0.6293 (mmt) cc_final: 0.6026 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 107
  average time/residue: 0.1410
  time to fit residues: 20.6760
Evaluate side-chains
  107 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1228 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.176480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.123535 restraints weight = 18539.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.34
r_work: 0.3083 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5596  Z= 0.136
  Angle     :  0.910  31.152   7587  Z= 0.364
  Chirality :  0.043   0.180    937
  Planarity :  0.003   0.034    940
  Dihedral  :  3.676  17.842    762
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.10 %
    Favored  : 86.07 %
  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:  2.35 (0.31), residues: 720
  helix:  2.50 (0.25), residues: 421
  sheet:  0.55 (0.46), residues: 113
  loop :  0.03 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 775 
 TYR   0.006   0.001   TYR A1337 
 PHE   0.008   0.001   PHE A 657 
 TRP   0.007   0.001   TRP A1359 
 HIS   0.003   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5596)
  covalent geometry    : angle       0.91029 ( 7587)
  hydrogen bonds       : bond        0.03679 (  348)
  hydrogen bonds       : angle       4.04576 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  716 TYR cc_start: 0.8428 (t80) cc_final: 0.8119 (t80)
REVERT: A  784 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7620 (ptpt)
REVERT: A 1181 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7817 (mmtm)
REVERT: A 1228 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8696 (t70)
REVERT: A 1264 ASP cc_start: 0.7683 (m-30) cc_final: 0.6857 (t0)
REVERT: A 1270 MET cc_start: 0.8638 (tpt) cc_final: 0.8365 (tpt)
REVERT: A 1273 ASP cc_start: 0.9253 (p0) cc_final: 0.8915 (p0)
REVERT: A 1365 MET cc_start: 0.6267 (mmt) cc_final: 0.6005 (mmt)
  outliers start: 5
  outliers final: 3
  residues processed: 103
  average time/residue: 0.1308
  time to fit residues: 18.6677
Evaluate side-chains
  106 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  784 LYS
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1228 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 67 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.179090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.126555 restraints weight = 18488.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.34
r_work: 0.3126 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5596  Z= 0.092
  Angle     :  0.896  29.934   7587  Z= 0.352
  Chirality :  0.042   0.188    937
  Planarity :  0.003   0.035    940
  Dihedral  :  3.558  17.440    762
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.10 %
    Favored  : 86.24 %
  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:  2.56 (0.32), residues: 720
  helix:  2.71 (0.25), residues: 421
  sheet:  0.58 (0.44), residues: 125
  loop : -0.01 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 966 
 TYR   0.004   0.001   TYR A1390 
 PHE   0.007   0.001   PHE A 696 
 TRP   0.006   0.001   TRP A1359 
 HIS   0.002   0.000   HIS A1016 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 5596)
  covalent geometry    : angle       0.89598 ( 7587)
  hydrogen bonds       : bond        0.03279 (  348)
  hydrogen bonds       : angle       3.91796 ( 1008)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 1026 is missing expected H atoms. Skipping.
Residue LEU 1042 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7402 (tp30)
REVERT: A 1181 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7823 (mmtm)
REVERT: A 1228 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8672 (t70)
REVERT: A 1264 ASP cc_start: 0.7637 (m-30) cc_final: 0.6852 (t0)
REVERT: A 1270 MET cc_start: 0.8623 (tpt) cc_final: 0.8359 (tpt)
REVERT: A 1273 ASP cc_start: 0.9201 (p0) cc_final: 0.8842 (p0)
REVERT: A 1365 MET cc_start: 0.6186 (mmt) cc_final: 0.5982 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 106
  average time/residue: 0.1441
  time to fit residues: 21.1584
Evaluate side-chains
  109 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1228 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.176494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.123767 restraints weight = 18639.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.34
r_work: 0.3087 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5596  Z= 0.130
  Angle     :  0.904  31.377   7587  Z= 0.360
  Chirality :  0.043   0.188    937
  Planarity :  0.003   0.034    940
  Dihedral  :  3.622  17.948    762
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.27 %
    Favored  : 86.07 %
  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:  2.44 (0.32), residues: 720
  helix:  2.61 (0.25), residues: 421
  sheet:  0.56 (0.45), residues: 125
  loop : -0.05 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 775 
 TYR   0.009   0.001   TYR A 716 
 PHE   0.008   0.001   PHE A 657 
 TRP   0.006   0.001   TRP A 936 
 HIS   0.003   0.001   HIS A1213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5596)
  covalent geometry    : angle       0.90353 ( 7587)
  hydrogen bonds       : bond        0.03543 (  348)
  hydrogen bonds       : angle       3.99134 ( 1008)

===============================================================================
Job complete
usr+sys time: 2935.54 seconds
wall clock time: 50 minutes 24.18 seconds (3024.18 seconds total)