Starting phenix.real_space_refine
on Fri Aug 22 15:09:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oo9_17007/08_2025/8oo9_17007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oo9_17007/08_2025/8oo9_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2025/8oo9_17007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2025/8oo9_17007.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2025/8oo9_17007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2025/8oo9_17007.map"
  }
  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-2.0-5787/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: 1.16, 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: 0.36
  Conformation dependent library (CDL) restraints added in 151.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.44
  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: 0.56

  Time building geometry restraints manager: 0.45 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:             2.810
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.630
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.390
-------------------------------------------------------------------------------
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 aren 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  : 0.092 
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: 0.1072
  time to fit residues: 14.4686
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  : 0.145 
-------------------------------------------------------------------------------
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 aren 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  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: G  999 MET cc_start: 0.7648 (mpp) cc_final: 0.7154 (mpp)
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: 0.0660
  time to fit residues: 6.0938
Evaluate side-chains
  62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 19 optimal weight:    0.0000
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.107291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.093500 restraints weight = 7537.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 0.89
r_work: 0.3326 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3432

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= 0.170
  Angle     :  1.029  29.518   6512  Z= 0.424
  Chirality :  0.038   0.127    720
  Planarity :  0.004   0.045    667
  Dihedral  : 24.250 127.248    947
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.09 %
    Favored  : 86.90 %
  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 aren not related in a simple way.
  whole: -0.50 (0.40), residues: 431
  helix: -0.15 (0.33), residues: 225
  sheet: -0.23 (0.67), residues: 67
  loop : -0.36 (0.54), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G1679 
 TYR   0.011   0.001   TYR G 975 
 PHE   0.010   0.001   PHE G1615 
 TRP   0.008   0.002   TRP G1650 
 HIS   0.007   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4693)
  covalent geometry    : angle       1.02853 ( 6512)
  hydrogen bonds       : bond        0.04708 (  177)
  hydrogen bonds       : angle       4.97200 (  488)
  Misc. bond           : bond        0.00045 (    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
  68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: G 1047 PHE cc_start: 0.8763 (m-80) cc_final: 0.8512 (m-80)
REVERT: G 1157 LEU cc_start: 0.7649 (mp) cc_final: 0.7396 (mt)
REVERT: G 1224 TYR cc_start: 0.8031 (p90) cc_final: 0.7800 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 66
  average time/residue: 0.0841
  time to fit residues: 6.8648
Evaluate side-chains
  57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.105647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.092130 restraints weight = 7530.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 0.88
r_work: 0.3295 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3817

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= 0.189
  Angle     :  1.033  30.035   6512  Z= 0.428
  Chirality :  0.038   0.123    720
  Planarity :  0.004   0.048    667
  Dihedral  : 24.134 113.055    947
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.85 %
    Favored  : 85.89 %
  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 aren not related in a simple way.
  whole: -0.64 (0.40), residues: 431
  helix: -0.15 (0.33), residues: 228
  sheet: -0.27 (0.67), residues: 67
  loop : -0.67 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G1201 
 TYR   0.013   0.001   TYR G 975 
 PHE   0.012   0.002   PHE G1047 
 TRP   0.011   0.002   TRP G1650 
 HIS   0.004   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 4693)
  covalent geometry    : angle       1.03316 ( 6512)
  hydrogen bonds       : bond        0.04750 (  177)
  hydrogen bonds       : angle       4.92907 (  488)
  Misc. bond           : bond        0.00016 (    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
  62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: G 1047 PHE cc_start: 0.8786 (m-80) cc_final: 0.8442 (m-80)
REVERT: G 1224 TYR cc_start: 0.8129 (p90) cc_final: 0.7917 (p90)
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0793
  time to fit residues: 6.0480
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  : 0.166 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0970
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
G1140 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 = 0.3624 r_free = 0.3624 target = 0.104961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.091737 restraints weight = 7565.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 0.88
r_work: 0.3291 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4694  Z= 0.191
  Angle     :  1.033  30.794   6512  Z= 0.425
  Chirality :  0.038   0.128    720
  Planarity :  0.004   0.041    667
  Dihedral  : 23.871 104.348    947
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.35 %
    Favored  : 84.89 %
  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 aren not related in a simple way.
  whole: -0.63 (0.40), residues: 431
  helix: -0.09 (0.33), residues: 227
  sheet: -0.43 (0.65), residues: 67
  loop : -0.67 (0.55), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1201 
 TYR   0.010   0.001   TYR G 975 
 PHE   0.014   0.002   PHE G1047 
 TRP   0.008   0.002   TRP G1650 
 HIS   0.002   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 4693)
  covalent geometry    : angle       1.03344 ( 6512)
  hydrogen bonds       : bond        0.04721 (  177)
  hydrogen bonds       : angle       4.84148 (  488)
  Misc. bond           : bond        0.00008 (    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
  64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0711
  time to fit residues: 5.6724
Evaluate side-chains
  59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.105881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.092568 restraints weight = 7628.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 0.90
r_work: 0.3302 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4694  Z= 0.165
  Angle     :  1.012  30.202   6512  Z= 0.412
  Chirality :  0.037   0.128    720
  Planarity :  0.004   0.034    667
  Dihedral  : 23.745 105.599    947
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.35 %
    Favored  : 84.38 %
  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 aren not related in a simple way.
  whole: -0.55 (0.40), residues: 431
  helix:  0.04 (0.33), residues: 227
  sheet: -0.40 (0.66), residues: 67
  loop : -0.76 (0.54), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.009   0.001   TYR G1224 
 PHE   0.010   0.001   PHE G1047 
 TRP   0.009   0.001   TRP G1650 
 HIS   0.002   0.001   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4693)
  covalent geometry    : angle       1.01215 ( 6512)
  hydrogen bonds       : bond        0.04374 (  177)
  hydrogen bonds       : angle       4.71463 (  488)
  Misc. bond           : bond        0.00003 (    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
  64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7841 (tptp)
REVERT: G 1240 MET cc_start: 0.7349 (mpp) cc_final: 0.7075 (mpp)
  outliers start: 9
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0742
  time to fit residues: 5.7388
Evaluate side-chains
  60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Chi-restraints excluded: chain G residue 1691 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
G1097 GLN
G1151 HIS
** 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 = 0.3608 r_free = 0.3608 target = 0.104158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.091105 restraints weight = 7596.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 0.89
r_work: 0.3275 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4694  Z= 0.206
  Angle     :  1.038  31.135   6512  Z= 0.427
  Chirality :  0.039   0.131    720
  Planarity :  0.004   0.043    667
  Dihedral  : 23.781 108.635    947
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.60 %
    Favored  : 84.13 %
  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 aren not related in a simple way.
  whole: -0.76 (0.40), residues: 431
  helix: -0.08 (0.33), residues: 227
  sheet: -0.62 (0.64), residues: 67
  loop : -0.87 (0.54), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1201 
 TYR   0.022   0.002   TYR G1591 
 PHE   0.014   0.002   PHE G1047 
 TRP   0.009   0.002   TRP G1650 
 HIS   0.002   0.001   HIS G1080 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 4693)
  covalent geometry    : angle       1.03794 ( 6512)
  hydrogen bonds       : bond        0.04877 (  177)
  hydrogen bonds       : angle       4.84855 (  488)
  Misc. bond           : bond        0.00055 (    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
  62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7872 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0826
  time to fit residues: 6.0024
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  : 0.185 
-------------------------------------------------------------------------------
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 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Chi-restraints excluded: chain G residue 1691 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 39 optimal weight:    0.1980
   chunk 9 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 41 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.105891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.092790 restraints weight = 7663.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 0.90
r_work: 0.3309 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.4512

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= 0.155
  Angle     :  1.006  30.157   6512  Z= 0.407
  Chirality :  0.036   0.127    720
  Planarity :  0.004   0.034    667
  Dihedral  : 23.508 105.070    947
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.60 %
    Favored  : 84.13 %
  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 aren not related in a simple way.
  whole: -0.57 (0.40), residues: 431
  helix:  0.14 (0.34), residues: 227
  sheet: -0.57 (0.65), residues: 67
  loop : -0.92 (0.54), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G1679 
 TYR   0.015   0.001   TYR G1591 
 PHE   0.009   0.001   PHE G1548 
 TRP   0.009   0.001   TRP G1650 
 HIS   0.001   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4693)
  covalent geometry    : angle       1.00570 ( 6512)
  hydrogen bonds       : bond        0.04271 (  177)
  hydrogen bonds       : angle       4.65521 (  488)
  Misc. bond           : bond        0.00006 (    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
  65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.179 
Fit side-chains
REVERT: G  966 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7864 (tptp)
REVERT: G 1001 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8166 (mm)
  outliers start: 9
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0960
  time to fit residues: 7.4427
Evaluate side-chains
  61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1001 LEU
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 1210 LEU
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:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.104268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.091434 restraints weight = 7608.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 0.88
r_work: 0.3283 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   4694  Z= 0.210
  Angle     :  1.038  30.262   6512  Z= 0.428
  Chirality :  0.039   0.153    720
  Planarity :  0.004   0.041    667
  Dihedral  : 23.599 106.474    947
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.36 %
    Favored  : 83.38 %
  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 aren not related in a simple way.
  whole: -0.80 (0.40), residues: 431
  helix: -0.07 (0.33), residues: 227
  sheet: -0.61 (0.66), residues: 67
  loop : -1.01 (0.53), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G1131 
 TYR   0.018   0.002   TYR G1018 
 PHE   0.014   0.002   PHE G1047 
 TRP   0.035   0.002   TRP G1036 
 HIS   0.002   0.001   HIS G1151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 4693)
  covalent geometry    : angle       1.03823 ( 6512)
  hydrogen bonds       : bond        0.04824 (  177)
  hydrogen bonds       : angle       4.81533 (  488)
  Misc. bond           : bond        0.00040 (    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
  63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: G  966 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7883 (tptp)
REVERT: G  999 MET cc_start: 0.7732 (mpp) cc_final: 0.7168 (mpt)
REVERT: G 1001 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8240 (mm)
  outliers start: 9
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0890
  time to fit residues: 6.7014
Evaluate side-chains
  59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  968 LEU
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1001 LEU
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 1210 LEU
Chi-restraints excluded: chain G residue 1648 SER
Chi-restraints excluded: chain G residue 1691 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 7 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
G1207 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 = 0.3643 r_free = 0.3643 target = 0.106227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.093386 restraints weight = 7528.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 0.89
r_work: 0.3321 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.4661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4694  Z= 0.151
  Angle     :  1.012  30.388   6512  Z= 0.412
  Chirality :  0.037   0.165    720
  Planarity :  0.004   0.036    667
  Dihedral  : 23.394 104.337    947
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.36 %
    Favored  : 83.38 %
  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 aren not related in a simple way.
  whole: -0.60 (0.40), residues: 431
  helix:  0.10 (0.33), residues: 228
  sheet: -0.43 (0.67), residues: 67
  loop : -0.99 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G1679 
 TYR   0.012   0.001   TYR G1591 
 PHE   0.009   0.001   PHE G1548 
 TRP   0.036   0.002   TRP G1036 
 HIS   0.001   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4693)
  covalent geometry    : angle       1.01245 ( 6512)
  hydrogen bonds       : bond        0.04209 (  177)
  hydrogen bonds       : angle       4.66969 (  488)
  Misc. bond           : bond        0.00003 (    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
  65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.168 
Fit side-chains
REVERT: G  966 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7850 (tptp)
REVERT: G  999 MET cc_start: 0.7728 (mpp) cc_final: 0.7176 (mpt)
REVERT: G 1001 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8174 (mm)
REVERT: G 1692 GLN cc_start: 0.7924 (pp30) cc_final: 0.7709 (pt0)
  outliers start: 9
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0880
  time to fit residues: 6.8384
Evaluate side-chains
  61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  991 ILE
Chi-restraints excluded: chain G residue 1001 LEU
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 1648 SER
Chi-restraints excluded: chain G residue 1691 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 29 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.106638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.093540 restraints weight = 7590.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 0.89
r_work: 0.3312 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4723

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= 0.160
  Angle     :  1.015  30.394   6512  Z= 0.412
  Chirality :  0.037   0.131    720
  Planarity :  0.004   0.038    667
  Dihedral  : 23.294 103.850    947
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.86 %
    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 aren not related in a simple way.
  whole: -0.61 (0.40), residues: 431
  helix:  0.12 (0.34), residues: 228
  sheet: -0.48 (0.67), residues: 67
  loop : -1.03 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G1679 
 TYR   0.012   0.001   TYR G1591 
 PHE   0.010   0.001   PHE G1047 
 TRP   0.009   0.001   TRP G1650 
 HIS   0.002   0.000   HIS G1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4693)
  covalent geometry    : angle       1.01479 ( 6512)
  hydrogen bonds       : bond        0.04269 (  177)
  hydrogen bonds       : angle       4.63609 (  488)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1143.96 seconds
wall clock time: 20 minutes 14.74 seconds (1214.74 seconds total)