Starting phenix.real_space_refine
on Tue Mar  3 12:59:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oo9_17007/03_2026/8oo9_17007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oo9_17007/03_2026/8oo9_17007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oo9_17007/03_2026/8oo9_17007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oo9_17007/03_2026/8oo9_17007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oo9_17007/03_2026/8oo9_17007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oo9_17007/03_2026/8oo9_17007.cif"
  }
  resolution = 3.2
  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=   0.014
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
     P      44      5.49       5
     Mg      1      5.21       5
     S      24      5.16       5
     C    2737      2.51       5
     N     802      2.21       5
     O     903      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  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: 4516
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 3622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3622
          Classifications: {'peptide': 439}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425}
          Chain breaks: 3
    Chain: "K"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 431
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "L"
      Number of atoms: 430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 430
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "G"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.19, per 1000 atoms: 0.26
  Number of scatterers: 4516
  At special positions: 0
  Unit cell: (78.09, 78.912, 83.022, 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      24     16.00
     P      44     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O     903      8.00
     N     802      7.00
     C    2737      6.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 252.0 milliseconds
  

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  836

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 3 sheets defined
      54.2% alpha, 10.9% beta
      14 base pairs and 38 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'G' and resid 973 through 989
    Processing helix  chain 'G' and resid 1002 through 1019
      removed outlier: 3.602A  pdb=" N   GLN G1006 " --> pdb=" O   GLY G1002 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1029 through 1031
      No H-bonds generated for 'chain 'G' and resid 1029 through 1031'
    Processing helix  chain 'G' and resid 1032 through 1044
    Processing helix  chain 'G' and resid 1055 through 1063
    Processing helix  chain 'G' and resid 1064 through 1066
      No H-bonds generated for 'chain 'G' and resid 1064 through 1066'
    Processing helix  chain 'G' and resid 1087 through 1092
    Processing helix  chain 'G' and resid 1092 through 1097
    Processing helix  chain 'G' and resid 1108 through 1112
    Processing helix  chain 'G' and resid 1117 through 1125
    Processing helix  chain 'G' and resid 1142 through 1154
      removed outlier: 3.658A  pdb=" N   LEU G1149 " --> pdb=" O   GLU G1145 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1187 through 1194
      removed outlier: 3.707A  pdb=" N   MET G1192 " --> pdb=" O   LYS G1188 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1202 through 1207
    Processing helix  chain 'G' and resid 1223 through 1235
    Processing helix  chain 'G' and resid 1236 through 1239
    Processing helix  chain 'G' and resid 1257 through 1270
      removed outlier: 3.740A  pdb=" N   MET G1262 " --> pdb=" O   MET G1258 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1270 through 1275
      removed outlier: 3.945A  pdb=" N   PHE G1274 " --> pdb=" O   HIS G1270 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1544 through 1551
    Processing helix  chain 'G' and resid 1552 through 1568
      removed outlier: 3.730A  pdb=" N   GLU G1567 " --> pdb=" O   ARG G1563 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1578 through 1592
      removed outlier: 3.737A  pdb=" N   ILE G1582 " --> pdb=" O   MET G1578 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU G1586 " --> pdb=" O   ILE G1582 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1604 through 1618
    Processing helix  chain 'G' and resid 1651 through 1660
    Processing helix  chain 'G' and resid 1681 through 1700
      removed outlier: 3.866A  pdb=" N   ARG G1685 " --> pdb=" O   THR G1681 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS G1693 " --> pdb=" O   ARG G1689 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU G1694 " --> pdb=" O   ALA G1690 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU G1695 " --> pdb=" O   LEU G1691 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 1049 through 1052
      removed outlier: 4.751A  pdb=" N   SER G1085 " --> pdb=" O   TYR G1052 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   PHE G1024 " --> pdb=" O   MET G1082 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   THR G1084 " --> pdb=" O   PHE G1024 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL G1026 " --> pdb=" O   THR G1084 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU G1025 " --> pdb=" O   ILE G1105 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   MET G1104 " --> pdb=" O   LEU G1132 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   LEU G1134 " --> pdb=" O   MET G1104 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU G1106 " --> pdb=" O   LEU G1134 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY G 993 " --> pdb=" O   ARG G1131 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU G1133 " --> pdb=" O   GLY G 993 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ILE G 994 " --> pdb=" O   LEU G1199 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 1100 through 1101
    Processing sheet with id=AA3, first strand: chain 'G' and resid 1214 through 1220
      removed outlier: 6.257A  pdb=" N   ILE G1214 " --> pdb=" O   VAL G1673 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ARG G1675 " --> pdb=" O   ILE G1214 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE G1216 " --> pdb=" O   ARG G1675 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   ILE G1677 " --> pdb=" O   ILE G1216 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   VAL G1218 " --> pdb=" O   ILE G1677 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   VAL G1643 " --> pdb=" O   TYR G1674 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   LEU G1676 " --> pdb=" O   VAL G1643 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   PHE G1645 " --> pdb=" O   LEU G1676 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   THR G1678 " --> pdb=" O   PHE G1645 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LEU G1573 " --> pdb=" O   ILE G1644 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL G1572 " --> pdb=" O   PHE G1624 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU G1626 " --> pdb=" O   VAL G1572 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LEU G1574 " --> pdb=" O   LEU G1626 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   CYS G1597 " --> pdb=" O   LEU G1625 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   SER G1627 " --> pdb=" O   CYS G1597 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU G1599 " --> pdb=" O   SER G1627 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    143 hydrogen bonds defined for protein.
    420 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      38 stacking parallelities
  Total time for adding SS restraints: 0.88

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1330
        1.34 -     1.46: 1151
        1.46 -     1.58: 2088
        1.58 -     1.70: 78
        1.70 -     1.82: 46
  Bond restraints: 4693
  Sorted by residual:
  bond pdb=" F1  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.684  1.799 -0.115 2.00e-02 2.50e+03 3.33e+01
  bond pdb=" F3  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.685  1.795 -0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" F4  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.686  1.778 -0.092 2.00e-02 2.50e+03 2.09e+01
  bond pdb=" F2  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.685  1.775 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C4'  DG L -36 "
       pdb=" C3'  DG L -36 "
    ideal  model  delta    sigma   weight residual
    1.523  1.587 -0.064 2.00e-02 2.50e+03 1.04e+01
  ... (remaining 4688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.01: 6506
       14.01 -    28.02: 4
       28.02 -    42.04: 0
       42.04 -    56.05: 0
       56.05 -    70.06: 2
  Bond angle restraints: 6512
  Sorted by residual:
  angle pdb=" F3  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F4  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     109.63  179.69  -70.06 3.00e+00 1.11e-01 5.45e+02
  angle pdb=" F1  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F2  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     108.68  178.52  -69.84 3.00e+00 1.11e-01 5.42e+02
  angle pdb=" F1  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F4  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     109.02   88.48   20.54 3.00e+00 1.11e-01 4.69e+01
  angle pdb=" F2  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F4  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     110.21   90.04   20.17 3.00e+00 1.11e-01 4.52e+01
  angle pdb=" F2  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F3  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     109.59   89.92   19.67 3.00e+00 1.11e-01 4.30e+01
  ... (remaining 6507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.81: 2477
       32.81 -    65.62: 214
       65.62 -    98.43: 7
       98.43 -   131.25: 2
      131.25 -   164.06: 1
  Dihedral angle restraints: 2701
    sinusoidal: 1412
      harmonic: 1289
  Sorted by residual:
  dihedral pdb=" O1B ADP G2001 "
           pdb=" O3A ADP G2001 "
           pdb=" PB  ADP G2001 "
           pdb=" PA  ADP G2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  135.94  164.06     1      2.00e+01 2.50e-03 4.71e+01
  dihedral pdb=" C5' ADP G2001 "
           pdb=" O5' ADP G2001 "
           pdb=" PA  ADP G2001 "
           pdb=" O2A ADP G2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  169.04  130.97     1      2.00e+01 2.50e-03 3.97e+01
  dihedral pdb=" O2A ADP G2001 "
           pdb=" O3A ADP G2001 "
           pdb=" PA  ADP G2001 "
           pdb=" PB  ADP G2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   53.46 -113.46     1      2.00e+01 2.50e-03 3.36e+01
  ... (remaining 2698 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 442
       0.054 -    0.107: 219
       0.107 -    0.160: 49
       0.160 -    0.214: 8
       0.214 -    0.267: 2
  Chirality restraints: 720
  Sorted by residual:
  chirality pdb=" CB  ILE G1582 "
            pdb=" CA  ILE G1582 "
            pdb=" CG1 ILE G1582 "
            pdb=" CG2 ILE G1582 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C2' ADP G2001 "
            pdb=" C1' ADP G2001 "
            pdb=" C3' ADP G2001 "
            pdb=" O2' ADP G2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.73    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE G1701 "
            pdb=" CA  ILE G1701 "
            pdb=" CG1 ILE G1701 "
            pdb=" CG2 ILE G1701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 717 not shown)

  Planarity restraints: 667
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC K  33 "   -0.071 2.00e-02 2.50e+03   3.63e-02 2.97e+01
        pdb=" N1   DC K  33 "    0.077 2.00e-02 2.50e+03
        pdb=" C2   DC K  33 "    0.011 2.00e-02 2.50e+03
        pdb=" O2   DC K  33 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DC K  33 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC K  33 "   -0.009 2.00e-02 2.50e+03
        pdb=" N4   DC K  33 "   -0.020 2.00e-02 2.50e+03
        pdb=" C5   DC K  33 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC K  33 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC L -25 "    0.059 2.00e-02 2.50e+03   3.28e-02 2.43e+01
        pdb=" N1   DC L -25 "   -0.075 2.00e-02 2.50e+03
        pdb=" C2   DC L -25 "   -0.015 2.00e-02 2.50e+03
        pdb=" O2   DC L -25 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DC L -25 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DC L -25 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC L -25 "    0.013 2.00e-02 2.50e+03
        pdb=" C5   DC L -25 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DC L -25 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC L -28 "    0.048 2.00e-02 2.50e+03   2.77e-02 1.73e+01
        pdb=" N1   DC L -28 "   -0.066 2.00e-02 2.50e+03
        pdb=" C2   DC L -28 "   -0.011 2.00e-02 2.50e+03
        pdb=" O2   DC L -28 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DC L -28 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DC L -28 "    0.006 2.00e-02 2.50e+03
        pdb=" N4   DC L -28 "    0.010 2.00e-02 2.50e+03
        pdb=" C5   DC L -28 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DC L -28 "    0.002 2.00e-02 2.50e+03
  ... (remaining 664 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 13
        2.48 -     3.09: 3126
        3.09 -     3.69: 7057
        3.69 -     4.30: 11365
        4.30 -     4.90: 17524
  Nonbonded interactions: 39085
  Sorted by model distance:
  nonbonded pdb="MG    MG G2002 "
            pdb=" F3  ALF G2003 "
     model   vdw
     1.879 2.120
  nonbonded pdb=" O2B ADP G2001 "
            pdb="MG    MG G2002 "
     model   vdw
     2.007 2.170
  nonbonded pdb=" N2   DG K  40 "
            pdb=" O2   DC L -40 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" O   TYR G 975 "
            pdb=" NH1 ARG G1201 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" NH2 ARG G1608 "
            pdb=" OP2  DC L -28 "
     model   vdw
     2.366 3.120
  ... (remaining 39080 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.00 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:             4.040
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.760
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
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      :  0.013   0.534   4694  Z= 0.898
  Angle     :  1.701  70.061   6512  Z= 0.727
  Chirality :  0.064   0.267    720
  Planarity :  0.013   0.140    667
  Dihedral  : 20.609 164.056   1865
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -2.21 (0.37), residues: 431
  helix: -1.96 (0.28), residues: 215
  sheet: -0.20 (0.76), residues: 54
  loop : -0.88 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.004   ARG G1201 
 TYR   0.025   0.006   TYR G1588 
 PHE   0.039   0.005   PHE G1079 
 TRP   0.042   0.004   TRP G1650 
 HIS   0.011   0.002   HIS G1663 

Details of bonding type rmsd
  covalent geometry    : bond        0.01012 ( 4693)
  covalent geometry    : angle       1.70081 ( 6512)
  hydrogen bonds       : bond        0.22094 (  177)
  hydrogen bonds       : angle       8.94698 (  488)
  Misc. bond           : bond        0.53368 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: G 1001 LEU cc_start: 0.8600 (mt) cc_final: 0.8312 (mm)
REVERT: G 1020 ILE cc_start: 0.7443 (mm) cc_final: 0.7217 (mt)
REVERT: G 1143 MET cc_start: 0.8052 (mmp) cc_final: 0.7527 (mmt)
REVERT: G 1186 GLN cc_start: 0.5578 (pm20) cc_final: 0.5134 (tt0)
REVERT: G 1224 TYR cc_start: 0.7796 (p90) cc_final: 0.7327 (p90)
REVERT: G 1240 MET cc_start: 0.7127 (mmm) cc_final: 0.6864 (mmt)
REVERT: G 1585 MET cc_start: 0.8656 (tpt) cc_final: 0.8376 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1215
  time to fit residues: 16.4256
Evaluate side-chains
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0040
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
G1663 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.107987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.094066 restraints weight = 7646.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 0.87
r_work: 0.3330 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4694  Z= 0.183
  Angle     :  1.058  29.350   6512  Z= 0.445
  Chirality :  0.040   0.149    720
  Planarity :  0.005   0.065    667
  Dihedral  : 24.593 146.297    947
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.56 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.93 (0.39), residues: 431
  helix: -0.67 (0.31), residues: 227
  sheet: -0.18 (0.69), residues: 65
  loop : -0.36 (0.56), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G1201 
 TYR   0.010   0.001   TYR G 975 
 PHE   0.015   0.002   PHE G1615 
 TRP   0.011   0.002   TRP G1650 
 HIS   0.003   0.001   HIS G1663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 4693)
  covalent geometry    : angle       1.05756 ( 6512)
  hydrogen bonds       : bond        0.05659 (  177)
  hydrogen bonds       : angle       5.36889 (  488)
  Misc. bond           : bond        0.00019 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: G  999 MET cc_start: 0.7648 (mpp) cc_final: 0.7154 (mpp)
REVERT: G 1020 ILE cc_start: 0.7593 (mm) cc_final: 0.7393 (mt)
REVERT: G 1047 PHE cc_start: 0.8724 (m-10) cc_final: 0.8447 (m-80)
REVERT: G 1186 GLN cc_start: 0.5428 (pm20) cc_final: 0.4854 (pt0)
REVERT: G 1224 TYR cc_start: 0.7890 (p90) cc_final: 0.7624 (p90)
REVERT: G 1688 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6970 (tttp)
  outliers start: 3
  outliers final: 1
  residues processed: 75
  average time/residue: 0.0970
  time to fit residues: 8.7746
Evaluate side-chains
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1076 ASP
Chi-restraints excluded: chain G residue 1688 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0000
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0370
   chunk 4 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.3862

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

Flipped N/Q/H residues before XYZ refinement:
G1035 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.108112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.094248 restraints weight = 7538.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 0.88
r_work: 0.3338 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4694  Z= 0.155
  Angle     :  1.018  29.608   6512  Z= 0.417
  Chirality :  0.037   0.126    720
  Planarity :  0.004   0.042    667
  Dihedral  : 24.204 127.287    947
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.59 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.40 (0.40), residues: 431
  helix: -0.08 (0.33), residues: 225
  sheet: -0.13 (0.68), residues: 67
  loop : -0.31 (0.55), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G1679 
 TYR   0.010   0.001   TYR G 975 
 PHE   0.010   0.001   PHE G1615 
 TRP   0.009   0.001   TRP G1053 
 HIS   0.004   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4693)
  covalent geometry    : angle       1.01817 ( 6512)
  hydrogen bonds       : bond        0.04523 (  177)
  hydrogen bonds       : angle       4.91078 (  488)
  Misc. bond           : bond        0.00027 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: G 1047 PHE cc_start: 0.8754 (m-80) cc_final: 0.8510 (m-80)
REVERT: G 1157 LEU cc_start: 0.7588 (mp) cc_final: 0.7363 (mt)
REVERT: G 1224 TYR cc_start: 0.8052 (p90) cc_final: 0.7836 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 68
  average time/residue: 0.0967
  time to fit residues: 7.9429
Evaluate side-chains
  58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1076 ASP
Chi-restraints excluded: chain G residue 1100 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0670
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN
** G1692 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 = 0.3654 r_free = 0.3654 target = 0.106718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.093065 restraints weight = 7536.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 0.89
r_work: 0.3313 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4694  Z= 0.169
  Angle     :  1.023  29.917   6512  Z= 0.419
  Chirality :  0.037   0.124    720
  Planarity :  0.004   0.043    667
  Dihedral  : 24.052 112.602    947
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.35 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.47 (0.40), residues: 431
  helix: -0.01 (0.33), residues: 228
  sheet: -0.16 (0.67), residues: 67
  loop : -0.61 (0.54), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G1201 
 TYR   0.012   0.001   TYR G 975 
 PHE   0.009   0.001   PHE G1079 
 TRP   0.011   0.001   TRP G1650 
 HIS   0.003   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4693)
  covalent geometry    : angle       1.02292 ( 6512)
  hydrogen bonds       : bond        0.04413 (  177)
  hydrogen bonds       : angle       4.81604 (  488)
  Misc. bond           : bond        0.00023 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: G  999 MET cc_start: 0.7662 (mpp) cc_final: 0.7078 (mpp)
REVERT: G 1047 PHE cc_start: 0.8771 (m-80) cc_final: 0.8520 (m-80)
REVERT: G 1240 MET cc_start: 0.6620 (mmt) cc_final: 0.5990 (ttp)
  outliers start: 4
  outliers final: 4
  residues processed: 58
  average time/residue: 0.0795
  time to fit residues: 5.8957
Evaluate side-chains
  56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1076 ASP
Chi-restraints excluded: chain G residue 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN
G1140 GLN
** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.104658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.091410 restraints weight = 7623.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 0.90
r_work: 0.3281 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4694  Z= 0.199
  Angle     :  1.039  31.511   6512  Z= 0.429
  Chirality :  0.039   0.127    720
  Planarity :  0.004   0.048    667
  Dihedral  : 23.896 104.169    947
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.60 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.68 (0.40), residues: 431
  helix: -0.14 (0.33), residues: 228
  sheet: -0.43 (0.64), residues: 67
  loop : -0.68 (0.55), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G1201 
 TYR   0.011   0.001   TYR G 975 
 PHE   0.015   0.002   PHE G1047 
 TRP   0.009   0.002   TRP G1650 
 HIS   0.002   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 4693)
  covalent geometry    : angle       1.03870 ( 6512)
  hydrogen bonds       : bond        0.04830 (  177)
  hydrogen bonds       : angle       4.86851 (  488)
  Misc. bond           : bond        0.00045 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 5
  residues processed: 62
  average time/residue: 0.0927
  time to fit residues: 7.1160
Evaluate side-chains
  58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1076 ASP
Chi-restraints excluded: chain G residue 1100 LYS
Chi-restraints excluded: chain G residue 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0170
   chunk 39 optimal weight:    0.0870
   chunk 35 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.106557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.093214 restraints weight = 7649.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 0.90
r_work: 0.3316 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4694  Z= 0.146
  Angle     :  1.002  30.220   6512  Z= 0.404
  Chirality :  0.036   0.121    720
  Planarity :  0.004   0.033    667
  Dihedral  : 23.671 103.959    947
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.60 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.47 (0.40), residues: 431
  helix:  0.11 (0.34), residues: 228
  sheet: -0.35 (0.65), residues: 67
  loop : -0.74 (0.54), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.018   0.001   TYR G1591 
 PHE   0.008   0.001   PHE G1548 
 TRP   0.010   0.001   TRP G1650 
 HIS   0.002   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4693)
  covalent geometry    : angle       1.00196 ( 6512)
  hydrogen bonds       : bond        0.04122 (  177)
  hydrogen bonds       : angle       4.63738 (  488)
  Misc. bond           : bond        0.00002 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7839 (tptp)
REVERT: G  999 MET cc_start: 0.7679 (mpp) cc_final: 0.7062 (mpp)
REVERT: G 1131 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6966 (mtp85)
  outliers start: 7
  outliers final: 5
  residues processed: 61
  average time/residue: 0.1004
  time to fit residues: 7.3584
Evaluate side-chains
  58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1032 THR
Chi-restraints excluded: chain G residue 1100 LYS
Chi-restraints excluded: chain G residue 1131 ARG
Chi-restraints excluded: chain G residue 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0770
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN
** G1692 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 = 0.3630 r_free = 0.3630 target = 0.105392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.092268 restraints weight = 7625.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 0.89
r_work: 0.3295 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4694  Z= 0.175
  Angle     :  1.023  30.011   6512  Z= 0.415
  Chirality :  0.037   0.132    720
  Planarity :  0.004   0.037    667
  Dihedral  : 23.666 105.502    947
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.61 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.59 (0.40), residues: 431
  helix:  0.05 (0.34), residues: 228
  sheet: -0.50 (0.64), residues: 67
  loop : -0.82 (0.54), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.015   0.002   TYR G1591 
 PHE   0.011   0.001   PHE G1047 
 TRP   0.010   0.001   TRP G1650 
 HIS   0.002   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4693)
  covalent geometry    : angle       1.02264 ( 6512)
  hydrogen bonds       : bond        0.04459 (  177)
  hydrogen bonds       : angle       4.68133 (  488)
  Misc. bond           : bond        0.00029 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7851 (tptp)
REVERT: G  999 MET cc_start: 0.7702 (mpp) cc_final: 0.7069 (mpp)
REVERT: G 1131 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6934 (mtt90)
REVERT: G 1240 MET cc_start: 0.7343 (mpp) cc_final: 0.7116 (mpp)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0870
  time to fit residues: 6.1664
Evaluate side-chains
  57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1032 THR
Chi-restraints excluded: chain G residue 1076 ASP
Chi-restraints excluded: chain G residue 1100 LYS
Chi-restraints excluded: chain G residue 1131 ARG
Chi-restraints excluded: chain G residue 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0770
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.106490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.093307 restraints weight = 7706.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 0.90
r_work: 0.3315 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4694  Z= 0.147
  Angle     :  1.002  29.977   6512  Z= 0.402
  Chirality :  0.036   0.126    720
  Planarity :  0.004   0.037    667
  Dihedral  : 23.472 103.772    947
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.36 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.54 (0.40), residues: 431
  helix:  0.13 (0.34), residues: 228
  sheet: -0.40 (0.65), residues: 67
  loop : -0.92 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.012   0.001   TYR G1591 
 PHE   0.007   0.001   PHE G1548 
 TRP   0.008   0.001   TRP G1053 
 HIS   0.002   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4693)
  covalent geometry    : angle       1.00242 ( 6512)
  hydrogen bonds       : bond        0.04072 (  177)
  hydrogen bonds       : angle       4.57736 (  488)
  Misc. bond           : bond        0.00004 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7844 (tptp)
REVERT: G  999 MET cc_start: 0.7696 (mpp) cc_final: 0.7075 (mpp)
REVERT: G 1131 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6978 (mtp85)
  outliers start: 7
  outliers final: 4
  residues processed: 59
  average time/residue: 0.1068
  time to fit residues: 7.6368
Evaluate side-chains
  57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1032 THR
Chi-restraints excluded: chain G residue 1100 LYS
Chi-restraints excluded: chain G residue 1131 ARG
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0970
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0170
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.093828 restraints weight = 7630.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 0.90
r_work: 0.3324 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4694  Z= 0.142
  Angle     :  1.007  30.059   6512  Z= 0.404
  Chirality :  0.036   0.141    720
  Planarity :  0.004   0.038    667
  Dihedral  : 23.402 102.215    947
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.62 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.47 (0.40), residues: 431
  helix:  0.20 (0.34), residues: 228
  sheet: -0.29 (0.67), residues: 67
  loop : -0.97 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.018   0.001   TYR G1018 
 PHE   0.008   0.001   PHE G1548 
 TRP   0.034   0.002   TRP G1036 
 HIS   0.002   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4693)
  covalent geometry    : angle       1.00667 ( 6512)
  hydrogen bonds       : bond        0.03960 (  177)
  hydrogen bonds       : angle       4.55505 (  488)
  Misc. bond           : bond        0.00001 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7818 (tptp)
REVERT: G 1131 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6928 (mtp85)
REVERT: G 1240 MET cc_start: 0.7315 (mpp) cc_final: 0.6900 (ptm)
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.1025
  time to fit residues: 7.4819
Evaluate side-chains
  57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1032 THR
Chi-restraints excluded: chain G residue 1100 LYS
Chi-restraints excluded: chain G residue 1131 ARG
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN
G1692 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.105946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.093070 restraints weight = 7615.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 0.88
r_work: 0.3310 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4694  Z= 0.166
  Angle     :  1.019  30.047   6512  Z= 0.413
  Chirality :  0.037   0.158    720
  Planarity :  0.004   0.038    667
  Dihedral  : 23.393 102.072    947
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.62 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.60 (0.40), residues: 431
  helix:  0.09 (0.34), residues: 228
  sheet: -0.37 (0.67), residues: 67
  loop : -1.02 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.010   0.001   TYR G 987 
 PHE   0.010   0.001   PHE G1047 
 TRP   0.036   0.002   TRP G1036 
 HIS   0.002   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4693)
  covalent geometry    : angle       1.01875 ( 6512)
  hydrogen bonds       : bond        0.04244 (  177)
  hydrogen bonds       : angle       4.65622 (  488)
  Misc. bond           : bond        0.00016 (    1)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.160 
Fit side-chains
REVERT: G  966 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7827 (tptp)
REVERT: G  999 MET cc_start: 0.7769 (mpp) cc_final: 0.7200 (mpt)
REVERT: G 1131 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6987 (mtp85)
REVERT: G 1240 MET cc_start: 0.7379 (mpp) cc_final: 0.7020 (ptm)
  outliers start: 5
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1125
  time to fit residues: 8.5284
Evaluate side-chains
  60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1032 THR
Chi-restraints excluded: chain G residue 1100 LYS
Chi-restraints excluded: chain G residue 1131 ARG
Chi-restraints excluded: chain G residue 1648 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 21 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.106530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.093503 restraints weight = 7687.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 0.89
r_work: 0.3306 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4694  Z= 0.161
  Angle     :  1.016  30.132   6512  Z= 0.410
  Chirality :  0.037   0.131    720
  Planarity :  0.004   0.039    667
  Dihedral  : 23.291 101.096    947
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.62 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.63 (0.40), residues: 431
  helix:  0.10 (0.34), residues: 228
  sheet: -0.44 (0.67), residues: 67
  loop : -1.08 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.011   0.001   TYR G1224 
 PHE   0.009   0.001   PHE G1047 
 TRP   0.011   0.001   TRP G1036 
 HIS   0.002   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4693)
  covalent geometry    : angle       1.01601 ( 6512)
  hydrogen bonds       : bond        0.04197 (  177)
  hydrogen bonds       : angle       4.63187 (  488)
  Misc. bond           : bond        0.00016 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1294.22 seconds
wall clock time: 22 minutes 50.55 seconds (1370.55 seconds total)