Starting phenix.real_space_refine
on Sat Aug 23 08:58:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8til_41295/08_2025/8til_41295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8til_41295/08_2025/8til_41295.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8til_41295/08_2025/8til_41295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8til_41295/08_2025/8til_41295.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8til_41295/08_2025/8til_41295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8til_41295/08_2025/8til_41295.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      21      5.16       5
     C    3512      2.51       5
     N     931      2.21       5
     O    1045      1.98       5
     H    5472      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10983
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 3182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3182
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 3115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 3115
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 121
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "A"
      Number of atoms: 4565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 4565
          Classifications: {'peptide': 282}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 263}
          Chain breaks: 9
  Time building chain proxies: 1.45, per 1000 atoms: 0.13
  Number of scatterers: 10983
  At special positions: 0
  Unit cell: (57.97, 102.238, 118.048, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P       2     15.00
     O    1045      8.00
     N     931      7.00
     C    3512      6.00
     H    5472      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.04

  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: 0.86
  Conformation dependent library (CDL) restraints added in 168.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1336

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 18 sheets defined
      5.0% alpha, 44.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'H' and resid 204 through 208
    Processing helix  chain 'L' and resid 122 through 129
      removed outlier: 3.511A  pdb=" N   SER L 128 " --> pdb=" O   SER L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 190
      removed outlier: 3.632A  pdb=" N   HIS L 190 " --> pdb=" O   ASP L 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.869A  pdb=" N   LEU A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
      removed outlier: 3.637A  pdb=" N   LYS A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63
      removed outlier: 5.367A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR H 121 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63
      removed outlier: 5.367A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.933A  pdb=" N   TYR H 195 " --> pdb=" O   ASP H 163 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL H 200 " --> pdb=" O   HIS H 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.933A  pdb=" N   TYR H 195 " --> pdb=" O   ASP H 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 172 through 173
    Processing sheet with id=AA7, first strand: chain 'L' and resid 6 through 8
      removed outlier: 3.663A  pdb=" N   VAL L  20 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 12
    Processing sheet with id=AA9, first strand: chain 'L' and resid 35 through 39
      removed outlier: 3.887A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 49 through 50
    Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.840A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 150
    Processing sheet with id=AB4, first strand: chain 'R' and resid 353 through 355
      removed outlier: 3.843A  pdb=" N   LYS A  11 " --> pdb=" O   GLY R 353 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TPO R 355 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL A   9 " --> pdb=" O   TPO R 355 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.004A  pdb=" N   PHE A  28 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'A' and resid 78 through 88
      removed outlier: 4.643A  pdb=" N   ASP A  79 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE A  62 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   PHE A  81 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 128 through 130
    Processing sheet with id=AB8, first strand: chain 'A' and resid 184 through 188
    Processing sheet with id=AB9, first strand: chain 'A' and resid 253 through 259
      removed outlier: 6.887A  pdb=" N   GLN A 238 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ALA A 255 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 234 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS A 231 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    615 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5456
        1.03 -     1.23: 56
        1.23 -     1.43: 2317
        1.43 -     1.62: 3247
        1.62 -     1.82: 26
  Bond restraints: 11102
  Sorted by residual:
  bond pdb=" CG2 TPO R 355 "
       pdb="HG21 TPO R 355 "
    ideal  model  delta    sigma   weight residual
    0.970  1.091 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG23 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.61e+01
  bond pdb=" CG2 TPO R 355 "
       pdb="HG23 TPO R 355 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG21 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" CB  TPO R 355 "
       pdb=" HB  TPO R 355 "
    ideal  model  delta    sigma   weight residual
    0.970  1.088 -0.118 2.00e-02 2.50e+03 3.50e+01
  ... (remaining 11097 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 19927
        2.15 -     4.30: 96
        4.30 -     6.45: 9
        6.45 -     8.60: 1
        8.60 -    10.75: 4
  Bond angle restraints: 20037
  Sorted by residual:
  angle pdb=" OG1 TPO R 355 "
        pdb=" P   TPO R 355 "
        pdb=" O1P TPO R 355 "
      ideal   model   delta    sigma   weight residual
     100.43  111.18  -10.75 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" CB  TPO R 352 "
        pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
      ideal   model   delta    sigma   weight residual
     119.31  108.62   10.69 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" CB  TPO R 355 "
        pdb=" OG1 TPO R 355 "
        pdb=" P   TPO R 355 "
      ideal   model   delta    sigma   weight residual
     119.31  109.12   10.19 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" N   LEU A  32 "
        pdb=" CA  LEU A  32 "
        pdb=" CB  LEU A  32 "
      ideal   model   delta    sigma   weight residual
     114.17  110.79    3.38 1.14e+00 7.69e-01 8.77e+00
  angle pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
        pdb=" O1P TPO R 352 "
      ideal   model   delta    sigma   weight residual
     100.43  109.25   -8.82 3.00e+00 1.11e-01 8.65e+00
  ... (remaining 20032 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4875
       17.94 -    35.88: 306
       35.88 -    53.82: 91
       53.82 -    71.76: 17
       71.76 -    89.70: 3
  Dihedral angle restraints: 5292
    sinusoidal: 2847
      harmonic: 2445
  Sorted by residual:
  dihedral pdb=" CA  ALA H  95 "
           pdb=" C   ALA H  95 "
           pdb=" N   VAL H  96 "
           pdb=" CA  VAL H  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.52   22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ASP L 171 "
           pdb=" C   ASP L 171 "
           pdb=" N   SER L 172 "
           pdb=" CA  SER L 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  TRP H 111 "
           pdb=" CB  TRP H 111 "
           pdb=" CG  TRP H 111 "
           pdb=" CD1 TRP H 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -179.70   89.70     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 5289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 467
       0.027 -    0.054: 266
       0.054 -    0.082: 56
       0.082 -    0.109: 54
       0.109 -    0.136: 32
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" CA  VAL H 203 "
            pdb=" N   VAL H 203 "
            pdb=" C   VAL H 203 "
            pdb=" CB  VAL H 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  ILE A 147 "
            pdb=" N   ILE A 147 "
            pdb=" C   ILE A 147 "
            pdb=" CB  ILE A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  VAL A 165 "
            pdb=" N   VAL A 165 "
            pdb=" C   VAL A 165 "
            pdb=" CB  VAL A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 872 not shown)

  Planarity restraints: 1583
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 167 "   -0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO H 168 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H 168 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO H 168 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 141 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO H 142 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO H 142 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H 142 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 220 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO H 221 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO H 221 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H 221 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1580 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 364
        2.14 -     2.75: 20960
        2.75 -     3.37: 29451
        3.37 -     3.98: 39898
        3.98 -     4.60: 61426
  Nonbonded interactions: 152099
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN H  42 "
            pdb="HE22 GLN L  39 "
     model   vdw
     1.521 2.450
  nonbonded pdb=" HE1 TRP H  50 "
            pdb=" OG  SER H  53 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" OE2 GLU H   9 "
            pdb=" H   CYS H  99 "
     model   vdw
     1.564 2.450
  nonbonded pdb=" H   ASP L 168 "
            pdb=" O   THR L 173 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" OE1 GLU H   9 "
            pdb=" H   GLY H 125 "
     model   vdw
     1.590 2.450
  ... (remaining 152094 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.590
  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:             0.070
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.960
  Find NCS groups from input model:        0.030
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
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   0.106   5634  Z= 0.233
  Angle     :  0.679  10.751   7644  Z= 0.358
  Chirality :  0.045   0.136    875
  Planarity :  0.004   0.040    951
  Dihedral  : 12.238  89.701   2034
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  :  8.35 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.91 (0.33), residues: 666
  helix: -0.97 (0.97), residues: 29
  sheet: -1.04 (0.28), residues: 350
  loop : -1.43 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 101 
 TYR   0.012   0.001   TYR H  36 
 PHE   0.013   0.002   PHE A 145 
 TRP   0.012   0.002   TRP H  50 
 HIS   0.004   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 5630)
  covalent geometry    : angle       0.67898 ( 7636)
  SS BOND              : bond        0.00276 (    4)
  SS BOND              : angle       0.81007 (    8)
  hydrogen bonds       : bond        0.14898 (  204)
  hydrogen bonds       : angle       7.05742 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  157 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4792 (pp)
REVERT: L  136 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7891 (tp)
REVERT: L  166 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6375 (tp30)
REVERT: A  284 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6911 (pp20)
REVERT: A  291 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7412 (m-30)
REVERT: A  318 ILE cc_start: 0.5436 (mt) cc_final: 0.5189 (tt)
  outliers start: 40
  outliers final: 23
  residues processed: 156
  average time/residue: 0.1649
  time to fit residues: 32.6162
Evaluate side-chains
  112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
A 182 GLN
** A 300 ASN ** 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 = 0.4456 r_free = 0.4456 target = 0.192347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.161511 restraints weight = 17802.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.168179 restraints weight = 10236.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.172712 restraints weight = 6611.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.175998 restraints weight = 4705.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.178034 restraints weight = 3571.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5972
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5634  Z= 0.144
  Angle     :  0.566   4.604   7644  Z= 0.296
  Chirality :  0.046   0.153    875
  Planarity :  0.005   0.046    951
  Dihedral  :  9.229  89.603    807
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 15.09 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.62 (0.33), residues: 666
  helix: -1.00 (0.91), residues: 31
  sheet: -0.79 (0.28), residues: 342
  loop : -1.29 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  26 
 TYR   0.010   0.001   TYR H  36 
 PHE   0.013   0.002   PHE A 116 
 TRP   0.012   0.002   TRP H  50 
 HIS   0.009   0.002   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5630)
  covalent geometry    : angle       0.56524 ( 7636)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       0.81733 (    8)
  hydrogen bonds       : bond        0.03439 (  204)
  hydrogen bonds       : angle       5.77431 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 86
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  157 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4445 (pp)
REVERT: L   92 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7460 (t)
REVERT: L   93 TYR cc_start: 0.7694 (t80) cc_final: 0.7438 (t80)
REVERT: L  136 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7765 (tp)
REVERT: L  164 VAL cc_start: 0.9180 (t) cc_final: 0.8846 (p)
REVERT: L  166 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6309 (tp30)
REVERT: A  284 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6898 (pp20)
  outliers start: 33
  outliers final: 22
  residues processed: 111
  average time/residue: 0.1703
  time to fit residues: 25.0853
Evaluate side-chains
  108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  338 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0770
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
L 211 ASN
A  86 GLN
A 182 GLN
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.190492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.159951 restraints weight = 18217.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.166256 restraints weight = 10680.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.170681 restraints weight = 7041.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.173687 restraints weight = 5069.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.175914 restraints weight = 3914.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6049
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5634  Z= 0.163
  Angle     :  0.584   9.117   7644  Z= 0.306
  Chirality :  0.046   0.154    875
  Planarity :  0.005   0.043    951
  Dihedral  :  8.737  89.373    793
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 16.05 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.65 (0.33), residues: 666
  helix: -1.04 (0.86), residues: 31
  sheet: -0.75 (0.28), residues: 344
  loop : -1.39 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.012   0.001   TYR A  22 
 PHE   0.013   0.002   PHE A 116 
 TRP   0.013   0.002   TRP H  50 
 HIS   0.007   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5630)
  covalent geometry    : angle       0.57942 ( 7636)
  SS BOND              : bond        0.00814 (    4)
  SS BOND              : angle       2.30746 (    8)
  hydrogen bonds       : bond        0.03543 (  204)
  hydrogen bonds       : angle       5.76574 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 80
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  157 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4542 (pp)
REVERT: H  164 TYR cc_start: 0.7707 (p90) cc_final: 0.7324 (p90)
REVERT: L   92 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7481 (t)
REVERT: L  137 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7569 (mp)
REVERT: L  164 VAL cc_start: 0.9204 (t) cc_final: 0.8891 (p)
REVERT: L  166 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6251 (tp30)
REVERT: A  284 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6883 (pp20)
  outliers start: 39
  outliers final: 29
  residues processed: 108
  average time/residue: 0.1770
  time to fit residues: 25.0139
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0020
   chunk 0 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 ASN ** 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 = 0.4411 r_free = 0.4411 target = 0.188777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.159456 restraints weight = 17988.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.166037 restraints weight = 10363.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.170638 restraints weight = 6741.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.173673 restraints weight = 4749.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.175614 restraints weight = 3592.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6010
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5634  Z= 0.139
  Angle     :  0.555   7.518   7644  Z= 0.290
  Chirality :  0.045   0.145    875
  Planarity :  0.004   0.040    951
  Dihedral  :  8.576  88.855    792
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 16.37 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.52 (0.33), residues: 666
  helix: -0.95 (0.84), residues: 31
  sheet: -0.63 (0.29), residues: 343
  loop : -1.35 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  22 
 TYR   0.010   0.001   TYR A  22 
 PHE   0.011   0.002   PHE A 116 
 TRP   0.012   0.002   TRP H  50 
 HIS   0.008   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5630)
  covalent geometry    : angle       0.55289 ( 7636)
  SS BOND              : bond        0.00409 (    4)
  SS BOND              : angle       1.75096 (    8)
  hydrogen bonds       : bond        0.03170 (  204)
  hydrogen bonds       : angle       5.55001 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 75
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  139 SER cc_start: 0.6027 (OUTLIER) cc_final: 0.5786 (m)
REVERT: H  157 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4572 (pp)
REVERT: H  164 TYR cc_start: 0.7714 (p90) cc_final: 0.7367 (p90)
REVERT: L   92 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7458 (t)
REVERT: L  166 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6422 (tp30)
REVERT: L  168 ASP cc_start: 0.8644 (t0) cc_final: 0.8328 (m-30)
REVERT: A  284 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6830 (pp20)
  outliers start: 40
  outliers final: 29
  residues processed: 103
  average time/residue: 0.1733
  time to fit residues: 23.5287
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
L  39 GLN
** A 300 ASN ** 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 = 0.4389 r_free = 0.4389 target = 0.186765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.158623 restraints weight = 17993.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.164818 restraints weight = 10518.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.169236 restraints weight = 6898.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.171795 restraints weight = 4880.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.173969 restraints weight = 3793.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6075
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5634  Z= 0.165
  Angle     :  0.573   7.567   7644  Z= 0.301
  Chirality :  0.046   0.149    875
  Planarity :  0.005   0.061    951
  Dihedral  :  8.648  88.840    790
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 17.50 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.60 (0.33), residues: 666
  helix: -0.97 (0.84), residues: 31
  sheet: -0.68 (0.29), residues: 344
  loop : -1.42 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  62 
 TYR   0.010   0.001   TYR H  36 
 PHE   0.015   0.002   PHE A 116 
 TRP   0.011   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5630)
  covalent geometry    : angle       0.57098 ( 7636)
  SS BOND              : bond        0.00609 (    4)
  SS BOND              : angle       1.46054 (    8)
  hydrogen bonds       : bond        0.03327 (  204)
  hydrogen bonds       : angle       5.64605 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 75
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  139 SER cc_start: 0.6155 (OUTLIER) cc_final: 0.5926 (m)
REVERT: H  157 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4550 (pp)
REVERT: H  164 TYR cc_start: 0.7822 (p90) cc_final: 0.7584 (p90)
REVERT: L   92 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7473 (t)
REVERT: L  166 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6401 (tp30)
REVERT: L  168 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8218 (m-30)
REVERT: A  284 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6833 (pp20)
  outliers start: 38
  outliers final: 30
  residues processed: 101
  average time/residue: 0.1738
  time to fit residues: 23.1716
Evaluate side-chains
  111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 75
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0870
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0770
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 ASN ** 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 = 0.4419 r_free = 0.4419 target = 0.189872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.162278 restraints weight = 17912.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.168532 restraints weight = 10307.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.172855 restraints weight = 6653.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.175804 restraints weight = 4672.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.177731 restraints weight = 3531.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6008
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5634  Z= 0.122
  Angle     :  0.529   6.673   7644  Z= 0.276
  Chirality :  0.045   0.142    875
  Planarity :  0.004   0.041    951
  Dihedral  :  8.242  87.816    788
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 17.66 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.34 (0.33), residues: 666
  helix: -0.81 (0.84), residues: 31
  sheet: -0.44 (0.29), residues: 341
  loop : -1.34 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  22 
 TYR   0.007   0.001   TYR H  36 
 PHE   0.009   0.001   PHE A 116 
 TRP   0.010   0.001   TRP H  50 
 HIS   0.008   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5630)
  covalent geometry    : angle       0.52810 ( 7636)
  SS BOND              : bond        0.00493 (    4)
  SS BOND              : angle       1.18688 (    8)
  hydrogen bonds       : bond        0.02910 (  204)
  hydrogen bonds       : angle       5.35808 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 74
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  139 SER cc_start: 0.6139 (OUTLIER) cc_final: 0.5918 (m)
REVERT: H  157 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4749 (pp)
REVERT: L   92 SER cc_start: 0.7724 (OUTLIER) cc_final: 0.7504 (t)
REVERT: L   99 PHE cc_start: 0.5221 (m-80) cc_final: 0.4625 (m-80)
REVERT: L  166 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6469 (tp30)
REVERT: L  168 ASP cc_start: 0.8614 (t0) cc_final: 0.8320 (m-30)
REVERT: A   63 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6330 (mpt90)
REVERT: A  284 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6767 (pp20)
  outliers start: 36
  outliers final: 28
  residues processed: 98
  average time/residue: 0.1834
  time to fit residues: 23.3779
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 ASN ** 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 = 0.4399 r_free = 0.4399 target = 0.188046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.159372 restraints weight = 18090.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.165640 restraints weight = 10576.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.170103 restraints weight = 6918.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.173103 restraints weight = 4908.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.175083 restraints weight = 3730.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6063
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5634  Z= 0.159
  Angle     :  0.560   7.182   7644  Z= 0.293
  Chirality :  0.045   0.149    875
  Planarity :  0.005   0.046    951
  Dihedral  :  8.366  87.914    786
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 17.98 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.45 (0.33), residues: 666
  helix: -0.84 (0.84), residues: 31
  sheet: -0.52 (0.28), residues: 348
  loop : -1.43 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  22 
 TYR   0.016   0.001   TYR H 164 
 PHE   0.013   0.002   PHE A 116 
 TRP   0.011   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5630)
  covalent geometry    : angle       0.55924 ( 7636)
  SS BOND              : bond        0.00602 (    4)
  SS BOND              : angle       1.25039 (    8)
  hydrogen bonds       : bond        0.03192 (  204)
  hydrogen bonds       : angle       5.54498 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 72
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  139 SER cc_start: 0.6152 (OUTLIER) cc_final: 0.5903 (m)
REVERT: H  157 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4632 (pp)
REVERT: L   92 SER cc_start: 0.7780 (OUTLIER) cc_final: 0.7453 (t)
REVERT: L  166 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6361 (tp30)
REVERT: L  168 ASP cc_start: 0.8584 (t0) cc_final: 0.8251 (m-30)
REVERT: A  284 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6804 (pp20)
  outliers start: 37
  outliers final: 31
  residues processed: 97
  average time/residue: 0.1783
  time to fit residues: 22.6600
Evaluate side-chains
  104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 68
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 25 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** 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 = 0.4395 r_free = 0.4395 target = 0.187466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.159674 restraints weight = 17972.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.165778 restraints weight = 10607.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.170047 restraints weight = 6967.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.172873 restraints weight = 4968.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.174953 restraints weight = 3791.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6084
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5634  Z= 0.158
  Angle     :  0.562   6.815   7644  Z= 0.293
  Chirality :  0.046   0.147    875
  Planarity :  0.005   0.047    951
  Dihedral  :  8.419  87.427    786
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 18.14 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.50 (0.33), residues: 666
  helix: -0.79 (0.86), residues: 31
  sheet: -0.60 (0.29), residues: 343
  loop : -1.39 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  22 
 TYR   0.013   0.001   TYR H 164 
 PHE   0.012   0.002   PHE A 116 
 TRP   0.011   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5630)
  covalent geometry    : angle       0.56119 ( 7636)
  SS BOND              : bond        0.00575 (    4)
  SS BOND              : angle       1.16655 (    8)
  hydrogen bonds       : bond        0.03140 (  204)
  hydrogen bonds       : angle       5.55182 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 69
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  139 SER cc_start: 0.6230 (OUTLIER) cc_final: 0.6011 (m)
REVERT: H  157 LEU cc_start: 0.5130 (OUTLIER) cc_final: 0.4723 (pp)
REVERT: L    4 GLN cc_start: 0.7201 (mp10) cc_final: 0.6914 (mm-40)
REVERT: L  166 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6332 (tp30)
REVERT: L  168 ASP cc_start: 0.8519 (t0) cc_final: 0.8184 (m-30)
REVERT: A  284 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6825 (pp20)
  outliers start: 40
  outliers final: 33
  residues processed: 96
  average time/residue: 0.1724
  time to fit residues: 21.7862
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 68
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** 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 = 0.4389 r_free = 0.4389 target = 0.186998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.159517 restraints weight = 17830.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.165668 restraints weight = 10479.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.169796 restraints weight = 6848.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.172603 restraints weight = 4883.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.174595 restraints weight = 3724.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6088
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5634  Z= 0.156
  Angle     :  0.559   6.810   7644  Z= 0.292
  Chirality :  0.046   0.146    875
  Planarity :  0.005   0.045    951
  Dihedral  :  8.488  87.451    786
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 18.46 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.45 (0.33), residues: 666
  helix: -0.72 (0.87), residues: 31
  sheet: -0.55 (0.29), residues: 342
  loop : -1.38 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  22 
 TYR   0.015   0.001   TYR A  48 
 PHE   0.012   0.002   PHE A 116 
 TRP   0.011   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5630)
  covalent geometry    : angle       0.55756 ( 7636)
  SS BOND              : bond        0.00551 (    4)
  SS BOND              : angle       1.17229 (    8)
  hydrogen bonds       : bond        0.03155 (  204)
  hydrogen bonds       : angle       5.57621 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 71
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  157 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4841 (pp)
REVERT: L    4 GLN cc_start: 0.7181 (mp10) cc_final: 0.6929 (mm-40)
REVERT: L  166 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6288 (tp30)
REVERT: L  168 ASP cc_start: 0.8543 (t0) cc_final: 0.8202 (m-30)
  outliers start: 38
  outliers final: 34
  residues processed: 97
  average time/residue: 0.1673
  time to fit residues: 21.6572
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 70
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** 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 = 0.4416 r_free = 0.4416 target = 0.189253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.160688 restraints weight = 18062.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.167140 restraints weight = 10398.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.171511 restraints weight = 6728.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.174523 restraints weight = 4742.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.176385 restraints weight = 3601.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6033
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5634  Z= 0.128
  Angle     :  0.541   6.391   7644  Z= 0.279
  Chirality :  0.045   0.144    875
  Planarity :  0.004   0.044    951
  Dihedral  :  8.343  86.940    786
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 19.10 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.29 (0.33), residues: 666
  helix: -0.54 (0.88), residues: 31
  sheet: -0.44 (0.29), residues: 335
  loop : -1.28 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  22 
 TYR   0.012   0.001   TYR A  48 
 PHE   0.009   0.001   PHE A 116 
 TRP   0.010   0.001   TRP H  50 
 HIS   0.007   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5630)
  covalent geometry    : angle       0.53985 ( 7636)
  SS BOND              : bond        0.00522 (    4)
  SS BOND              : angle       1.06542 (    8)
  hydrogen bonds       : bond        0.02912 (  204)
  hydrogen bonds       : angle       5.38630 (  615)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 69
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  157 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4846 (pp)
REVERT: L    4 GLN cc_start: 0.7201 (mp10) cc_final: 0.6937 (mm-40)
REVERT: L  166 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6496 (tp30)
REVERT: L  168 ASP cc_start: 0.8577 (t0) cc_final: 0.8254 (m-30)
REVERT: A  284 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6893 (pp20)
  outliers start: 35
  outliers final: 31
  residues processed: 92
  average time/residue: 0.1731
  time to fit residues: 21.1341
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.4980
   chunk 65 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** 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 = 0.4404 r_free = 0.4404 target = 0.188109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.160386 restraints weight = 18176.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.166371 restraints weight = 10603.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.170578 restraints weight = 7000.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.173403 restraints weight = 4994.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.175442 restraints weight = 3833.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6081
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5634  Z= 0.143
  Angle     :  0.549   6.527   7644  Z= 0.285
  Chirality :  0.045   0.145    875
  Planarity :  0.004   0.045    951
  Dihedral  :  8.419  87.042    786
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 19.10 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    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: -1.31 (0.33), residues: 666
  helix: -0.38 (0.89), residues: 31
  sheet: -0.45 (0.29), residues: 341
  loop : -1.32 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  22 
 TYR   0.013   0.001   TYR A  48 
 PHE   0.011   0.002   PHE A 116 
 TRP   0.010   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5630)
  covalent geometry    : angle       0.54838 ( 7636)
  SS BOND              : bond        0.00547 (    4)
  SS BOND              : angle       1.10542 (    8)
  hydrogen bonds       : bond        0.03027 (  204)
  hydrogen bonds       : angle       5.46482 (  615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2617.98 seconds
wall clock time: 45 minutes 30.90 seconds (2730.90 seconds total)