Starting phenix.real_space_refine
on Wed Sep 17 07:58:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o0i_49973/09_2025/9o0i_49973.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o0i_49973/09_2025/9o0i_49973.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o0i_49973/09_2025/9o0i_49973.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o0i_49973/09_2025/9o0i_49973.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o0i_49973/09_2025/9o0i_49973.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o0i_49973/09_2025/9o0i_49973.map"
  }
  resolution = 3.86
  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=   0.002 sd=   0.013
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    4323      2.51       5
     N    1084      2.21       5
     O    1250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6677
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "G"
      Number of atoms: 1591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1591
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 5, 'TRANS': 189}
    Chain: "H"
      Number of atoms: 2543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2543
          Classifications: {'peptide': 315}
          Link IDs: {'PTRANS': 9, 'TRANS': 305}
    Chain: "J"
      Number of atoms: 2543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2543
          Classifications: {'peptide': 315}
          Link IDs: {'PTRANS': 9, 'TRANS': 305}
  Time building chain proxies: 1.65, per 1000 atoms: 0.25
  Number of scatterers: 6677
  At special positions: 0
  Unit cell: (75.166, 99.946, 133.812, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1250      8.00
     N    1084      7.00
     C    4323      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS G  33 " - pdb=" SG  CYS G  38 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 319.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1594

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 5 sheets defined
      43.9% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'G' and resid 3 through 16
    Processing helix  chain 'G' and resid 16 through 27
    Processing helix  chain 'G' and resid 42 through 50
    Processing helix  chain 'G' and resid 51 through 72
    Processing helix  chain 'G' and resid 95 through 102
    Processing helix  chain 'G' and resid 102 through 107
    Processing helix  chain 'G' and resid 112 through 132
      removed outlier: 4.390A  pdb=" N   LYS G 132 " --> pdb=" O   ILE G 128 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 139 through 145
      removed outlier: 3.653A  pdb=" N   PHE G 145 " --> pdb=" O   THR G 141 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 16
      removed outlier: 3.896A  pdb=" N   ASN H  16 " --> pdb=" O   LYS H  12 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 56
    Processing helix  chain 'H' and resid 66 through 70
    Processing helix  chain 'H' and resid 86 through 97
      removed outlier: 3.925A  pdb=" N   ALA H  97 " --> pdb=" O   THR H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 111
      removed outlier: 3.623A  pdb=" N   ASN H 110 " --> pdb=" O   ASN H 107 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS H 111 " --> pdb=" O   PRO H 108 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 107 through 111'
    Processing helix  chain 'H' and resid 186 through 192
    Processing helix  chain 'H' and resid 195 through 214
      removed outlier: 3.695A  pdb=" N   LEU H 214 " --> pdb=" O   LEU H 210 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 218 through 226
      removed outlier: 4.445A  pdb=" N   LEU H 222 " --> pdb=" O   ASP H 218 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 228 through 242
      removed outlier: 3.908A  pdb=" N   LYS H 234 " --> pdb=" O   SER H 230 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER H 242 " --> pdb=" O   ILE H 238 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 249 through 259
      removed outlier: 3.619A  pdb=" N   ILE H 253 " --> pdb=" O   ASP H 249 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 280 through 292
    Processing helix  chain 'J' and resid 2 through 16
      removed outlier: 3.698A  pdb=" N   ASN J  16 " --> pdb=" O   LYS J  12 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 37 through 57
    Processing helix  chain 'J' and resid 86 through 96
      removed outlier: 3.649A  pdb=" N   ASN J  90 " --> pdb=" O   PRO J  86 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 136 through 139
    Processing helix  chain 'J' and resid 185 through 192
      removed outlier: 3.769A  pdb=" N   LEU J 189 " --> pdb=" O   ASN J 185 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 195 through 212
    Processing helix  chain 'J' and resid 218 through 226
      removed outlier: 3.994A  pdb=" N   LEU J 222 " --> pdb=" O   ASP J 218 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 228 through 241
      removed outlier: 4.565A  pdb=" N   LYS J 234 " --> pdb=" O   SER J 230 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 249 through 260
    Processing helix  chain 'J' and resid 262 through 267
      removed outlier: 3.583A  pdb=" N   LEU J 267 " --> pdb=" O   LEU J 263 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 280 through 292
    Processing sheet with id=AA1, first strand: chain 'G' and resid 178 through 180
      removed outlier: 3.532A  pdb=" N   VAL G 179 " --> pdb=" O   VAL G  82 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ASN G 153 " --> pdb=" O   THR G  85 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   CYS G  87 " --> pdb=" O   ARG G 151 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ARG G 151 " --> pdb=" O   CYS G  87 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE G 166 " --> pdb=" O   PHE G 189 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA G 191 " --> pdb=" O   ILE G 166 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ILE G 168 " --> pdb=" O   ALA G 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 31 through 33
      removed outlier: 3.771A  pdb=" N   GLY H 117 " --> pdb=" O   THR H  25 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 268 through 269
      removed outlier: 4.513A  pdb=" N   GLN H 268 " --> pdb=" O   LEU H 277 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 295 through 297
      removed outlier: 6.636A  pdb=" N   ALA J 309 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   LYS H 310 " --> pdb=" O   SER J 307 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   SER J 307 " --> pdb=" O   LYS H 310 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   ARG H 312 " --> pdb=" O   TYR J 305 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   TYR J 305 " --> pdb=" O   ARG H 312 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 31 through 33
      removed outlier: 3.643A  pdb=" N   LYS J  32 " --> pdb=" O   PHE J  24 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   PHE J  17 " --> pdb=" O   GLY J 124 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLY J 124 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   GLY J  19 " --> pdb=" O   ILE J 122 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   ILE J 122 " --> pdb=" O   GLY J  19 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ARG J  21 " --> pdb=" O   ILE J 120 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   ILE J 120 " --> pdb=" O   ARG J  21 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   VAL J  23 " --> pdb=" O   ILE J 118 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   ILE J 118 " --> pdb=" O   VAL J  23 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   THR J  25 " --> pdb=" O   LYS J 116 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.73

  Time building geometry restraints manager: 0.55 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: 2097
        1.34 -     1.46: 1454
        1.46 -     1.58: 3211
        1.58 -     1.70: 0
        1.70 -     1.82: 34
  Bond restraints: 6796
  Sorted by residual:
  bond pdb=" C   VAL G  52 "
       pdb=" N   PRO G  53 "
    ideal  model  delta    sigma   weight residual
    1.335  1.401 -0.066 1.30e-02 5.92e+03 2.56e+01
  bond pdb=" CB  ASP H 169 "
       pdb=" CG  ASP H 169 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 2.50e-02 1.60e+03 4.29e+00
  bond pdb=" CB  LYS G  45 "
       pdb=" CG  LYS G  45 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.21e+00
  bond pdb=" CB  ARG G   3 "
       pdb=" CG  ARG G   3 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.13e+00
  bond pdb=" N   ARG G   3 "
       pdb=" CA  ARG G   3 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.021 1.29e-02 6.01e+03 2.55e+00
  ... (remaining 6791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 8950
        2.78 -     5.55: 169
        5.55 -     8.33: 31
        8.33 -    11.10: 7
       11.10 -    13.88: 7
  Bond angle restraints: 9164
  Sorted by residual:
  angle pdb=" CA  ARG G   3 "
        pdb=" CB  ARG G   3 "
        pdb=" CG  ARG G   3 "
      ideal   model   delta    sigma   weight residual
     114.10  126.21  -12.11 2.00e+00 2.50e-01 3.67e+01
  angle pdb=" CB  LYS G  45 "
        pdb=" CG  LYS G  45 "
        pdb=" CD  LYS G  45 "
      ideal   model   delta    sigma   weight residual
     111.30  123.32  -12.02 2.30e+00 1.89e-01 2.73e+01
  angle pdb=" C   LYS J  74 "
        pdb=" N   ASN J  75 "
        pdb=" CA  ASN J  75 "
      ideal   model   delta    sigma   weight residual
     121.54  130.99   -9.45 1.91e+00 2.74e-01 2.45e+01
  angle pdb=" CB  MET H 147 "
        pdb=" CG  MET H 147 "
        pdb=" SD  MET H 147 "
      ideal   model   delta    sigma   weight residual
     112.70  126.58  -13.88 3.00e+00 1.11e-01 2.14e+01
  angle pdb=" C   THR J 136 "
        pdb=" N   ASN J 137 "
        pdb=" CA  ASN J 137 "
      ideal   model   delta    sigma   weight residual
     122.61  129.68   -7.07 1.56e+00 4.11e-01 2.05e+01
  ... (remaining 9159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 3453
       17.93 -    35.86: 543
       35.86 -    53.79: 131
       53.79 -    71.72: 27
       71.72 -    89.65: 12
  Dihedral angle restraints: 4166
    sinusoidal: 1713
      harmonic: 2453
  Sorted by residual:
  dihedral pdb=" CB  CYS G  33 "
           pdb=" SG  CYS G  33 "
           pdb=" SG  CYS G  38 "
           pdb=" CB  CYS G  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    8.30   84.70     1      1.00e+01 1.00e-02 8.71e+01
  dihedral pdb=" CA  ALA J 139 "
           pdb=" C   ALA J 139 "
           pdb=" N   VAL J 140 "
           pdb=" CA  VAL J 140 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.34  -24.66     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  VAL H 140 "
           pdb=" C   VAL H 140 "
           pdb=" N   LEU H 141 "
           pdb=" CA  LEU H 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.59  -23.41     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 4163 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 977
       0.096 -    0.192: 78
       0.192 -    0.288: 5
       0.288 -    0.384: 0
       0.384 -    0.479: 1
  Chirality restraints: 1061
  Sorted by residual:
  chirality pdb=" CG  LEU H 235 "
            pdb=" CB  LEU H 235 "
            pdb=" CD1 LEU H 235 "
            pdb=" CD2 LEU H 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.75e+00
  chirality pdb=" CB  ILE H 177 "
            pdb=" CA  ILE H 177 "
            pdb=" CG1 ILE H 177 "
            pdb=" CG2 ILE H 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  ARG G   3 "
            pdb=" N   ARG G   3 "
            pdb=" C   ARG G   3 "
            pdb=" CB  ARG G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 1058 not shown)

  Planarity restraints: 1151
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP J 114 "    0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" CG  ASP J 114 "   -0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASP J 114 "    0.023 2.00e-02 2.50e+03
        pdb=" OD2 ASP J 114 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J 153 "   -0.050 5.00e-02 4.00e+02   7.66e-02 9.40e+00
        pdb=" N   PRO J 154 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO J 154 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO J 154 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  52 "    0.044 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO G  53 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO G  53 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G  53 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1148 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1658
        2.79 -     3.32: 5911
        3.32 -     3.85: 10982
        3.85 -     4.37: 11775
        4.37 -     4.90: 20872
  Nonbonded interactions: 51198
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN H 134 "
            pdb=" OG1 THR H 188 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OG  SER G  15 "
            pdb=" OD1 ASN G 139 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG  SER G 169 "
            pdb=" O   ASP G 171 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OE2 GLU G  90 "
            pdb=" OH  TYR G 137 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" O   SER H  64 "
            pdb=" OG  SER H  64 "
     model   vdw
     2.355 3.040
  ... (remaining 51193 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
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.870
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.880
  Find NCS groups from input model:        0.070
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
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      :  0.005   0.066   6797  Z= 0.217
  Angle     :  0.985  13.880   9166  Z= 0.509
  Chirality :  0.055   0.479   1061
  Planarity :  0.006   0.077   1151
  Dihedral  : 18.496  89.655   2569
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 32.50 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.62 (0.25), residues: 819
  helix: -1.01 (0.24), residues: 331
  sheet: -1.20 (0.44), residues: 143
  loop : -2.67 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 227 
 TYR   0.022   0.002   TYR G  76 
 PHE   0.034   0.002   PHE G 108 
 HIS   0.011   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 6796)
  covalent geometry    : angle       0.98502 ( 9164)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.28160 (    2)
  hydrogen bonds       : bond        0.15012 (  292)
  hydrogen bonds       : angle       6.82343 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 ARG cc_start: 0.8348 (mmt90) cc_final: 0.7777 (mmt-90)
REVERT: J  217 GLU cc_start: 0.6512 (mp0) cc_final: 0.3891 (pt0)
  outliers start: 1
  outliers final: 1
  residues processed: 111
  average time/residue: 0.0940
  time to fit residues: 13.6467
Evaluate side-chains
  103 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  128 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
G 139 ASN
J 137 ASN
J 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104438 restraints weight = 11727.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.106492 restraints weight = 7805.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.107949 restraints weight = 5822.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.108852 restraints weight = 4776.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.109269 restraints weight = 4192.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6797  Z= 0.116
  Angle     :  0.546   7.909   9166  Z= 0.292
  Chirality :  0.043   0.258   1061
  Planarity :  0.004   0.052   1151
  Dihedral  :  4.740  26.421    884
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 29.33 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.28), residues: 819
  helix:  0.05 (0.27), residues: 353
  sheet: -1.05 (0.44), residues: 147
  loop : -2.52 (0.30), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG J 167 
 TYR   0.013   0.001   TYR G  76 
 PHE   0.017   0.001   PHE J 287 
 HIS   0.004   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6796)
  covalent geometry    : angle       0.54602 ( 9164)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.54925 (    2)
  hydrogen bonds       : bond        0.03723 (  292)
  hydrogen bonds       : angle       4.99233 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   69 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8031 (ttp80)
REVERT: H  157 TYR cc_start: 0.4943 (OUTLIER) cc_final: 0.2029 (t80)
REVERT: J  105 TYR cc_start: 0.5431 (OUTLIER) cc_final: 0.4101 (t80)
REVERT: J  256 TYR cc_start: 0.8237 (t80) cc_final: 0.7970 (t80)
  outliers start: 24
  outliers final: 12
  residues processed: 128
  average time/residue: 0.0806
  time to fit residues: 13.8527
Evaluate side-chains
  116 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain G residue  172 VAL
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   23 VAL
Chi-restraints excluded: chain J residue   33 LEU
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  165 ILE
Chi-restraints excluded: chain J residue  169 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0370
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
J 284 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.127753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.104523 restraints weight = 11757.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106264 restraints weight = 8095.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.106699 restraints weight = 5590.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.106913 restraints weight = 5225.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107018 restraints weight = 4849.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6797  Z= 0.111
  Angle     :  0.545   9.514   9166  Z= 0.286
  Chirality :  0.042   0.203   1061
  Planarity :  0.004   0.043   1151
  Dihedral  :  4.422  17.224    883
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 29.06 %
    Favored  : 67.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.29), residues: 819
  helix:  0.54 (0.28), residues: 353
  sheet: -0.98 (0.47), residues: 135
  loop : -2.37 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.014   0.001   TYR G 181 
 PHE   0.023   0.001   PHE J 287 
 HIS   0.004   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6796)
  covalent geometry    : angle       0.54527 ( 9164)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.44028 (    2)
  hydrogen bonds       : bond        0.03470 (  292)
  hydrogen bonds       : angle       4.67927 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: G   69 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8069 (ttp80)
REVERT: H  128 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7836 (p)
REVERT: H  157 TYR cc_start: 0.4774 (OUTLIER) cc_final: 0.1971 (t80)
REVERT: J  105 TYR cc_start: 0.5448 (OUTLIER) cc_final: 0.4082 (t80)
  outliers start: 29
  outliers final: 13
  residues processed: 129
  average time/residue: 0.0770
  time to fit residues: 13.7193
Evaluate side-chains
  114 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  166 LEU
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  252 THR
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   23 VAL
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 3 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0170
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 28 optimal weight:    0.4980
   chunk 53 optimal weight:    0.0470
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.1916

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

Flipped N/Q/H residues before XYZ refinement:
H  16 ASN
** J 284 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 = 0.3567 r_free = 0.3567 target = 0.129080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.105845 restraints weight = 11879.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.107732 restraints weight = 8218.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.107931 restraints weight = 5725.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.108351 restraints weight = 5498.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.108552 restraints weight = 4779.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6797  Z= 0.098
  Angle     :  0.539   8.640   9166  Z= 0.279
  Chirality :  0.042   0.198   1061
  Planarity :  0.003   0.040   1151
  Dihedral  :  4.245  16.595    883
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.25 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 29.46 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.29), residues: 819
  helix:  1.12 (0.29), residues: 339
  sheet: -0.98 (0.47), residues: 135
  loop : -2.29 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.014   0.001   TYR G 181 
 PHE   0.017   0.001   PHE J 287 
 HIS   0.004   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6796)
  covalent geometry    : angle       0.53925 ( 9164)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.35250 (    2)
  hydrogen bonds       : bond        0.03152 (  292)
  hydrogen bonds       : angle       4.46593 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7870 (p)
REVERT: H  157 TYR cc_start: 0.4568 (OUTLIER) cc_final: 0.1730 (t80)
REVERT: J  105 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.3877 (t80)
REVERT: J  147 MET cc_start: 0.6574 (pmm) cc_final: 0.6162 (pmm)
REVERT: J  291 MET cc_start: 0.7910 (mtp) cc_final: 0.7710 (mtp)
  outliers start: 25
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0707
  time to fit residues: 12.2522
Evaluate side-chains
  115 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  229 ILE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   23 VAL
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  267 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H 284 GLN
J 241 HIS
** J 284 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 = 0.3538 r_free = 0.3538 target = 0.126851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.103392 restraints weight = 11870.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.105273 restraints weight = 8264.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105458 restraints weight = 5900.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.105815 restraints weight = 5421.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.105880 restraints weight = 4894.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6797  Z= 0.127
  Angle     :  0.554   8.841   9166  Z= 0.285
  Chirality :  0.043   0.192   1061
  Planarity :  0.003   0.040   1151
  Dihedral  :  4.179  16.324    883
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.74 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.93 %
    Favored  : 66.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.30), residues: 819
  helix:  1.31 (0.29), residues: 339
  sheet: -1.00 (0.46), residues: 135
  loop : -2.23 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 167 
 TYR   0.019   0.001   TYR G  12 
 PHE   0.015   0.001   PHE J 287 
 HIS   0.005   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6796)
  covalent geometry    : angle       0.55429 ( 9164)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.37453 (    2)
  hydrogen bonds       : bond        0.03251 (  292)
  hydrogen bonds       : angle       4.42940 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7843 (p)
REVERT: H  157 TYR cc_start: 0.4658 (OUTLIER) cc_final: 0.1896 (t80)
REVERT: J  105 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.3941 (t80)
REVERT: J  147 MET cc_start: 0.6533 (pmm) cc_final: 0.6047 (pmm)
REVERT: J  291 MET cc_start: 0.7945 (mtp) cc_final: 0.7743 (mtp)
  outliers start: 34
  outliers final: 23
  residues processed: 129
  average time/residue: 0.0704
  time to fit residues: 12.7127
Evaluate side-chains
  122 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   64 ILE
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain G residue  172 VAL
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   96 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  145 ARG
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  166 LEU
Chi-restraints excluded: chain H residue  229 ILE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  252 THR
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   23 VAL
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  239 SER
Chi-restraints excluded: chain J residue  267 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0770
   chunk 38 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 284 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 = 0.3531 r_free = 0.3531 target = 0.126507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.102907 restraints weight = 11898.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.104815 restraints weight = 8158.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.104978 restraints weight = 6038.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.105167 restraints weight = 5384.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105399 restraints weight = 4969.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6797  Z= 0.124
  Angle     :  0.567   9.067   9166  Z= 0.289
  Chirality :  0.043   0.188   1061
  Planarity :  0.003   0.036   1151
  Dihedral  :  4.161  16.712    883
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.23 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 29.46 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.30), residues: 819
  helix:  1.34 (0.29), residues: 341
  sheet: -1.02 (0.46), residues: 135
  loop : -2.20 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 167 
 TYR   0.019   0.001   TYR G  12 
 PHE   0.015   0.001   PHE J 287 
 HIS   0.005   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6796)
  covalent geometry    : angle       0.56715 ( 9164)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.40021 (    2)
  hydrogen bonds       : bond        0.03158 (  292)
  hydrogen bonds       : angle       4.40225 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7848 (p)
REVERT: H  157 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.1903 (t80)
REVERT: H  231 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8414 (t80)
REVERT: J  105 TYR cc_start: 0.5598 (OUTLIER) cc_final: 0.3723 (t80)
REVERT: J  147 MET cc_start: 0.6433 (pmm) cc_final: 0.5997 (pmm)
REVERT: J  227 ARG cc_start: 0.8220 (ptp90) cc_final: 0.8000 (ptp-110)
  outliers start: 33
  outliers final: 23
  residues processed: 126
  average time/residue: 0.0773
  time to fit residues: 13.3703
Evaluate side-chains
  120 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   64 ILE
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   96 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  145 ARG
Chi-restraints excluded: chain H residue  155 ASP
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  229 ILE
Chi-restraints excluded: chain H residue  231 PHE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  252 THR
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   23 VAL
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  239 SER
Chi-restraints excluded: chain J residue  267 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 284 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 = 0.3501 r_free = 0.3501 target = 0.124247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.100631 restraints weight = 11728.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.102002 restraints weight = 7935.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.102082 restraints weight = 5772.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.102405 restraints weight = 5704.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.102546 restraints weight = 5216.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6797  Z= 0.152
  Angle     :  0.586   9.123   9166  Z= 0.300
  Chirality :  0.043   0.181   1061
  Planarity :  0.003   0.036   1151
  Dihedral  :  4.209  17.179    883
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.84 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 29.85 %
    Favored  : 66.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.30), residues: 819
  helix:  1.39 (0.30), residues: 340
  sheet: -1.10 (0.46), residues: 135
  loop : -2.23 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.017   0.001   TYR G  76 
 PHE   0.014   0.001   PHE J 287 
 HIS   0.006   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6796)
  covalent geometry    : angle       0.58626 ( 9164)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.45477 (    2)
  hydrogen bonds       : bond        0.03357 (  292)
  hydrogen bonds       : angle       4.46014 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7884 (p)
REVERT: H  157 TYR cc_start: 0.4758 (OUTLIER) cc_final: 0.1936 (t80)
REVERT: H  231 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8409 (t80)
REVERT: J  105 TYR cc_start: 0.5766 (OUTLIER) cc_final: 0.3726 (t80)
REVERT: J  147 MET cc_start: 0.6520 (pmm) cc_final: 0.6053 (pmm)
REVERT: J  227 ARG cc_start: 0.8252 (ptp90) cc_final: 0.7992 (ptp-110)
  outliers start: 29
  outliers final: 23
  residues processed: 125
  average time/residue: 0.0702
  time to fit residues: 12.1075
Evaluate side-chains
  127 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   24 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   64 ILE
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   96 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  155 ASP
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  166 LEU
Chi-restraints excluded: chain H residue  229 ILE
Chi-restraints excluded: chain H residue  231 PHE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  252 THR
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   23 VAL
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  239 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 33 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 286 HIS
J  75 ASN
** J 284 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 = 0.3502 r_free = 0.3502 target = 0.124381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.100797 restraints weight = 11942.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.102332 restraints weight = 8107.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.102544 restraints weight = 5748.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.102782 restraints weight = 5678.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.103026 restraints weight = 5162.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6797  Z= 0.145
  Angle     :  0.593  10.186   9166  Z= 0.303
  Chirality :  0.044   0.182   1061
  Planarity :  0.003   0.036   1151
  Dihedral  :  4.233  17.839    883
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.47 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 30.91 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.30), residues: 819
  helix:  1.44 (0.30), residues: 340
  sheet: -1.12 (0.46), residues: 135
  loop : -2.25 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 167 
 TYR   0.023   0.001   TYR J 262 
 PHE   0.015   0.001   PHE J 287 
 HIS   0.008   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6796)
  covalent geometry    : angle       0.59323 ( 9164)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.44389 (    2)
  hydrogen bonds       : bond        0.03307 (  292)
  hydrogen bonds       : angle       4.43647 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7896 (p)
REVERT: H  157 TYR cc_start: 0.4766 (OUTLIER) cc_final: 0.1964 (t80)
REVERT: H  231 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8378 (t80)
REVERT: J  105 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.3704 (t80)
REVERT: J  132 TYR cc_start: 0.8653 (t80) cc_final: 0.8086 (t80)
REVERT: J  147 MET cc_start: 0.6557 (pmm) cc_final: 0.6035 (pmm)
REVERT: J  227 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7987 (ptp-110)
  outliers start: 30
  outliers final: 22
  residues processed: 122
  average time/residue: 0.0751
  time to fit residues: 12.5662
Evaluate side-chains
  123 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   24 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   64 ILE
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   96 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  155 ASP
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  229 ILE
Chi-restraints excluded: chain H residue  231 PHE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   31 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  163 ASN
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  239 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0980
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  75 ASN
** J 284 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 = 0.3465 r_free = 0.3465 target = 0.121400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.097613 restraints weight = 11982.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.099243 restraints weight = 8319.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.099465 restraints weight = 5858.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.099628 restraints weight = 5710.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.099834 restraints weight = 5249.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6797  Z= 0.122
  Angle     :  0.588  10.158   9166  Z= 0.297
  Chirality :  0.043   0.182   1061
  Planarity :  0.003   0.035   1151
  Dihedral  :  4.164  17.326    883
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.84 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 30.91 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.30), residues: 819
  helix:  1.48 (0.30), residues: 340
  sheet: -1.11 (0.47), residues: 135
  loop : -2.24 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 142 
 TYR   0.015   0.001   TYR G  76 
 PHE   0.015   0.001   PHE J 287 
 HIS   0.006   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6796)
  covalent geometry    : angle       0.58780 ( 9164)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.42063 (    2)
  hydrogen bonds       : bond        0.03186 (  292)
  hydrogen bonds       : angle       4.37723 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7914 (p)
REVERT: H  157 TYR cc_start: 0.4834 (OUTLIER) cc_final: 0.2028 (t80)
REVERT: H  231 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8370 (t80)
REVERT: J  105 TYR cc_start: 0.5760 (OUTLIER) cc_final: 0.4949 (t80)
REVERT: J  132 TYR cc_start: 0.8618 (t80) cc_final: 0.8032 (t80)
REVERT: J  147 MET cc_start: 0.6546 (pmm) cc_final: 0.6069 (pmm)
  outliers start: 28
  outliers final: 22
  residues processed: 122
  average time/residue: 0.0772
  time to fit residues: 12.9644
Evaluate side-chains
  124 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   24 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   64 ILE
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   96 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  155 ASP
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  229 ILE
Chi-restraints excluded: chain H residue  231 PHE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   31 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  163 ASN
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  239 SER
Chi-restraints excluded: chain J residue  267 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0470
   chunk 64 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0670
   chunk 57 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0470
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.2114

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

Flipped N/Q/H residues before XYZ refinement:
H 284 GLN
J  75 ASN
** J 284 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 = 0.3536 r_free = 0.3536 target = 0.127005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.103868 restraints weight = 11873.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105613 restraints weight = 7957.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.105909 restraints weight = 5371.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106201 restraints weight = 5290.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.106397 restraints weight = 4757.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6797  Z= 0.102
  Angle     :  0.580  10.034   9166  Z= 0.294
  Chirality :  0.042   0.182   1061
  Planarity :  0.003   0.036   1151
  Dihedral  :  4.108  17.374    883
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.74 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 31.97 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.30), residues: 819
  helix:  1.57 (0.30), residues: 339
  sheet: -1.10 (0.46), residues: 135
  loop : -2.17 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 142 
 TYR   0.023   0.001   TYR J 262 
 PHE   0.017   0.001   PHE J 287 
 HIS   0.006   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6796)
  covalent geometry    : angle       0.58009 ( 9164)
  SS BOND              : bond        0.00032 (    1)
  SS BOND              : angle       0.33249 (    2)
  hydrogen bonds       : bond        0.03007 (  292)
  hydrogen bonds       : angle       4.27231 (  837)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: H  128 CYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7930 (p)
REVERT: H  157 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.2015 (t80)
REVERT: H  231 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8311 (t80)
REVERT: J  105 TYR cc_start: 0.5619 (OUTLIER) cc_final: 0.4781 (t80)
REVERT: J  147 MET cc_start: 0.6538 (pmm) cc_final: 0.6123 (pmm)
  outliers start: 23
  outliers final: 15
  residues processed: 124
  average time/residue: 0.0806
  time to fit residues: 13.4030
Evaluate side-chains
  118 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   24 ILE
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue  123 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  128 CYS
Chi-restraints excluded: chain H residue  155 ASP
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  231 PHE
Chi-restraints excluded: chain H residue  235 LEU
Chi-restraints excluded: chain H residue  304 ILE
Chi-restraints excluded: chain J residue   20 ILE
Chi-restraints excluded: chain J residue   31 LEU
Chi-restraints excluded: chain J residue   63 THR
Chi-restraints excluded: chain J residue  105 TYR
Chi-restraints excluded: chain J residue  115 VAL
Chi-restraints excluded: chain J residue  169 ASP
Chi-restraints excluded: chain J residue  239 SER
Chi-restraints excluded: chain J residue  267 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0030
   chunk 51 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  75 ASN
** J 284 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 = 0.3520 r_free = 0.3520 target = 0.125700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102439 restraints weight = 11917.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104012 restraints weight = 8024.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104237 restraints weight = 5657.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.104445 restraints weight = 5638.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.104759 restraints weight = 5091.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6797  Z= 0.123
  Angle     :  0.592  10.024   9166  Z= 0.297
  Chirality :  0.043   0.177   1061
  Planarity :  0.003   0.035   1151
  Dihedral  :  4.067  16.842    883
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.84 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 31.84 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.30), residues: 819
  helix:  1.54 (0.30), residues: 340
  sheet: -1.05 (0.46), residues: 135
  loop : -2.20 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.017   0.001   TYR G  12 
 PHE   0.016   0.001   PHE J 287 
 HIS   0.004   0.001   HIS H 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6796)
  covalent geometry    : angle       0.59200 ( 9164)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.36461 (    2)
  hydrogen bonds       : bond        0.03078 (  292)
  hydrogen bonds       : angle       4.29623 (  837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.09 seconds
wall clock time: 23 minutes 12.37 seconds (1392.37 seconds total)