Starting phenix.real_space_refine
on Tue Jan 14 06:28:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yo1_39433/01_2025/8yo1_39433.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yo1_39433/01_2025/8yo1_39433.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yo1_39433/01_2025/8yo1_39433.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yo1_39433/01_2025/8yo1_39433.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yo1_39433/01_2025/8yo1_39433.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yo1_39433/01_2025/8yo1_39433.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.000 sd=   0.051
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       6      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    3744      2.51       5
     N    1048      2.21       5
     O    1134      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5969
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2953
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 13, 'TRANS': 359}
    Chain: "D"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2953
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 13, 'TRANS': 359}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.91, per 1000 atoms: 0.66
  Number of scatterers: 5969
  At special positions: 0
  Unit cell: (64.48, 86.32, 94.64, 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      36     16.00
     P       6     15.00
     Mg      1     11.99
     O    1134      8.00
     N    1048      7.00
     C    3744      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 796.8 milliseconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      39.4% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'C' and resid 10 through 18
    Processing helix  chain 'C' and resid 18 through 24
      removed outlier: 4.082A  pdb=" N   TYR C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 66
      removed outlier: 3.551A  pdb=" N   VAL C  49 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR C  66 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 114
    Processing helix  chain 'C' and resid 136 through 143
      removed outlier: 3.641A  pdb=" N   ASN C 141 " --> pdb=" O   SER C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 216
      removed outlier: 3.663A  pdb=" N   LEU C 202 " --> pdb=" O   SER C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 240
      removed outlier: 3.759A  pdb=" N   TYR C 239 " --> pdb=" O   TYR C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 300
      removed outlier: 3.604A  pdb=" N   ASP C 290 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      Proline residue:  C 293  - end of helix
    Processing helix  chain 'C' and resid 304 through 310
      removed outlier: 3.503A  pdb=" N   VAL C 308 " --> pdb=" O   THR C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 345
    Processing helix  chain 'C' and resid 348 through 359
      removed outlier: 3.597A  pdb=" N   ILE C 352 " --> pdb=" O   ASP C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 373
      removed outlier: 3.811A  pdb=" N   LEU C 363 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET C 364 " --> pdb=" O   GLU C 360 " (cutoff:3.500A)
      Proline residue:  C 365  - end of helix
    Processing helix  chain 'D' and resid 10 through 18
    Processing helix  chain 'D' and resid 19 through 22
    Processing helix  chain 'D' and resid 45 through 66
      removed outlier: 3.637A  pdb=" N   VAL D  49 " --> pdb=" O   VAL D  45 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE D  55 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 114
      removed outlier: 3.785A  pdb=" N   ILE D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 143
    Processing helix  chain 'D' and resid 198 through 216
      removed outlier: 3.501A  pdb=" N   LEU D 202 " --> pdb=" O   SER D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 240
      removed outlier: 3.794A  pdb=" N   TYR D 239 " --> pdb=" O   TYR D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 300
      removed outlier: 3.724A  pdb=" N   ASP D 290 " --> pdb=" O   ASP D 286 " (cutoff:3.500A)
      Proline residue:  D 293  - end of helix
    Processing helix  chain 'D' and resid 304 through 310
    Processing helix  chain 'D' and resid 337 through 345
    Processing helix  chain 'D' and resid 348 through 358
      removed outlier: 3.804A  pdb=" N   ILE D 352 " --> pdb=" O   ASP D 348 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 362 through 373
      removed outlier: 3.824A  pdb=" N   ILE D 366 " --> pdb=" O   ILE D 362 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 8
    Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 31
    Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 35
    Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 175
      removed outlier: 5.219A  pdb=" N   ASN C 156 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   MET C 146 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98
      removed outlier: 3.851A  pdb=" N   VAL C  97 " --> pdb=" O   ILE C 105 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA7, first strand: chain 'C' and resid 244 through 247
      removed outlier: 7.106A  pdb=" N   ARG C 263 " --> pdb=" O   ILE C 314 " (cutoff:3.500A)
      removed outlier: 8.624A  pdb=" N   MET C 316 " --> pdb=" O   ARG C 263 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LEU C 265 " --> pdb=" O   MET C 316 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   VAL C 318 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   TYR C 267 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 35
    Processing sheet with id=AA9, first strand: chain 'D' and resid 168 through 175
      removed outlier: 5.734A  pdb=" N   ASN D 156 " --> pdb=" O   ASP D 153 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP D 153 " --> pdb=" O   ASN D 156 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET D 146 " --> pdb=" O   ILE D 186 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 97 through 98
    Processing sheet with id=AB2, first strand: chain 'D' and resid 244 through 247
      removed outlier: 7.245A  pdb=" N   ARG D 263 " --> pdb=" O   ILE D 314 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   MET D 316 " --> pdb=" O   ARG D 263 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU D 265 " --> pdb=" O   MET D 316 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   VAL D 318 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   TYR D 267 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    777 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: 1.81

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1015
        1.31 -     1.44: 1513
        1.44 -     1.56: 3475
        1.56 -     1.69: 7
        1.69 -     1.81: 66
  Bond restraints: 6076
  Sorted by residual:
  bond pdb=" N   ASN C 141 "
       pdb=" CA  ASN C 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.381  0.077 1.16e-02 7.43e+03 4.45e+01
  bond pdb=" CA  ASN C 141 "
       pdb=" C   ASN C 141 "
    ideal  model  delta    sigma   weight residual
    1.524  1.450  0.074 1.28e-02 6.10e+03 3.36e+01
  bond pdb=" O3A ANP D 701 "
       pdb=" PB  ANP D 701 "
    ideal  model  delta    sigma   weight residual
    1.700  1.586  0.114 2.00e-02 2.50e+03 3.27e+01
  bond pdb=" O3A ANP C 701 "
       pdb=" PB  ANP C 701 "
    ideal  model  delta    sigma   weight residual
    1.700  1.611  0.089 2.00e-02 2.50e+03 1.97e+01
  bond pdb=" CA  SER C 138 "
       pdb=" C   SER C 138 "
    ideal  model  delta    sigma   weight residual
    1.524  1.462  0.062 1.44e-02 4.82e+03 1.83e+01
  ... (remaining 6071 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.50: 8118
        3.50 -     7.00: 69
        7.00 -    10.49: 11
       10.49 -    13.99: 1
       13.99 -    17.49: 1
  Bond angle restraints: 8200
  Sorted by residual:
  angle pdb=" N   SER C 137 "
        pdb=" CA  SER C 137 "
        pdb=" C   SER C 137 "
      ideal   model   delta    sigma   weight residual
     111.07   97.72   13.35 1.07e+00 8.73e-01 1.56e+02
  angle pdb=" N   GLY C 136 "
        pdb=" CA  GLY C 136 "
        pdb=" C   GLY C 136 "
      ideal   model   delta    sigma   weight residual
     113.18  130.67  -17.49 2.37e+00 1.78e-01 5.45e+01
  angle pdb=" N   LEU C 139 "
        pdb=" CA  LEU C 139 "
        pdb=" C   LEU C 139 "
      ideal   model   delta    sigma   weight residual
     111.28  118.77   -7.49 1.09e+00 8.42e-01 4.73e+01
  angle pdb=" N   ASN C 141 "
        pdb=" CA  ASN C 141 "
        pdb=" C   ASN C 141 "
      ideal   model   delta    sigma   weight residual
     111.02  103.35    7.67 1.22e+00 6.72e-01 3.95e+01
  angle pdb=" N   VAL D 128 "
        pdb=" CA  VAL D 128 "
        pdb=" C   VAL D 128 "
      ideal   model   delta    sigma   weight residual
     112.17  106.49    5.68 9.50e-01 1.11e+00 3.58e+01
  ... (remaining 8195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.82: 3542
       29.82 -    59.64: 167
       59.64 -    89.45: 13
       89.45 -   119.27: 1
      119.27 -   149.09: 1
  Dihedral angle restraints: 3724
    sinusoidal: 1590
      harmonic: 2134
  Sorted by residual:
  dihedral pdb=" O1B ANP C 701 "
           pdb=" N3B ANP C 701 "
           pdb=" PB  ANP C 701 "
           pdb=" PG  ANP C 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15 -175.76 -149.09     1      3.00e+01 1.11e-03 1.98e+01
  dihedral pdb=" C   ASN C 141 "
           pdb=" N   ASN C 141 "
           pdb=" CA  ASN C 141 "
           pdb=" CB  ASN C 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.18   -9.42     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" O1A ANP C 701 "
           pdb=" O3A ANP C 701 "
           pdb=" PA  ANP C 701 "
           pdb=" PB  ANP C 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  178.40  -95.29     1      3.00e+01 1.11e-03 1.16e+01
  ... (remaining 3721 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 739
       0.060 -    0.121: 144
       0.121 -    0.181: 18
       0.181 -    0.241: 4
       0.241 -    0.302: 1
  Chirality restraints: 906
  Sorted by residual:
  chirality pdb=" CA  LEU C 139 "
            pdb=" N   LEU C 139 "
            pdb=" C   LEU C 139 "
            pdb=" CB  LEU C 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  SER C 137 "
            pdb=" N   SER C 137 "
            pdb=" C   SER C 137 "
            pdb=" CB  SER C 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  VAL C 135 "
            pdb=" N   VAL C 135 "
            pdb=" C   VAL C 135 "
            pdb=" CB  VAL C 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 903 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 136 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   GLY C 136 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   GLY C 136 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER C 137 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 134 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.07e+00
        pdb=" C   GLY C 134 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLY C 134 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL C 135 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 105 "   -0.036 5.00e-02 4.00e+02   5.42e-02 4.70e+00
        pdb=" N   PRO D 106 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D 106 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 106 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 136
        2.67 -     3.23: 5828
        3.23 -     3.79: 9495
        3.79 -     4.34: 12765
        4.34 -     4.90: 21016
  Nonbonded interactions: 49240
  Sorted by model distance:
  nonbonded pdb=" O   THR D 140 "
            pdb=" OG  SER D 144 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   VAL C 109 "
            pdb=" OG1 THR C 113 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OH  TYR C  22 "
            pdb=" OH  TYR D  22 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   TRP D 112 "
            pdb=" ND2 ASN D 141 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" ND2 ASN D  28 "
            pdb=" O   GLU D 193 "
     model   vdw
     2.221 3.120
  ... (remaining 49235 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 1 through 373 or resid 701))
  selection = chain 'D'
}

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:             0.430
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.800
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
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      :  0.006   0.114   6076  Z= 0.396
  Angle     :  0.807  17.490   8200  Z= 0.432
  Chirality :  0.050   0.302    906
  Planarity :  0.005   0.054   1056
  Dihedral  : 16.112 149.087   2348
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 20.49 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.31), residues: 742
  helix:  0.92 (0.32), residues: 254
  sheet:  0.16 (0.43), residues: 130
  loop : -1.21 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.026   0.001   PHE D 221 
 TYR   0.004   0.001   TYR D  44 
 ARG   0.003   0.000   ARG C 182 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.669 
Fit side-chains
REVERT: C  142 ILE cc_start: 0.4883 (OUTLIER) cc_final: 0.4446 (tt)
REVERT: C  310 GLU cc_start: 0.5848 (pt0) cc_final: 0.5362 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 100
  average time/residue: 0.1886
  time to fit residues: 24.7197
Evaluate side-chains
  96 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain D residue  156 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 22 optimal weight:    0.1980
   chunk 35 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
D  75 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.226226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.188905 restraints weight = 5565.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.190305 restraints weight = 4801.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.192335 restraints weight = 4283.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6764
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   6076  Z= 0.422
  Angle     :  0.703   7.742   8200  Z= 0.369
  Chirality :  0.054   0.234    906
  Planarity :  0.006   0.062   1056
  Dihedral  : 10.000 104.840    866
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.18 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.30), residues: 742
  helix:  0.19 (0.31), residues: 258
  sheet: -0.12 (0.44), residues: 116
  loop : -1.29 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  39 
 HIS   0.005   0.002   HIS D 279 
 PHE   0.025   0.002   PHE D 147 
 TYR   0.016   0.003   TYR D 267 
 ARG   0.005   0.001   ARG C 208 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.662 
Fit side-chains
REVERT: C  182 ARG cc_start: 0.6935 (mmt180) cc_final: 0.6452 (mtp85)
REVERT: C  237 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7106 (mtm110)
REVERT: C  366 ILE cc_start: 0.7119 (mt) cc_final: 0.6916 (pt)
REVERT: D   34 PHE cc_start: 0.5532 (OUTLIER) cc_final: 0.4429 (m-10)
REVERT: D   57 ASP cc_start: 0.6612 (t70) cc_final: 0.6408 (t0)
REVERT: D   96 MET cc_start: 0.6339 (mmt) cc_final: 0.6032 (mmt)
  outliers start: 23
  outliers final: 12
  residues processed: 122
  average time/residue: 0.2093
  time to fit residues: 32.8496
Evaluate side-chains
  111 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain D residue    6 ILE
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  287 ILE
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0970
   chunk 61 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0870
   chunk 57 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
D  80 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.236310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.198982 restraints weight = 5537.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.202605 restraints weight = 4825.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.205187 restraints weight = 3355.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6076  Z= 0.163
  Angle     :  0.522   7.009   8200  Z= 0.276
  Chirality :  0.047   0.152    906
  Planarity :  0.004   0.058   1056
  Dihedral  :  8.236  88.422    860
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.10 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.30), residues: 742
  helix:  0.62 (0.32), residues: 248
  sheet:  0.07 (0.43), residues: 128
  loop : -0.95 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  39 
 HIS   0.003   0.001   HIS D  31 
 PHE   0.020   0.001   PHE D 221 
 TYR   0.007   0.001   TYR C  22 
 ARG   0.003   0.000   ARG D  65 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.700 
Fit side-chains
REVERT: C   92 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5689 (mm)
REVERT: C  237 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.6922 (mtm110)
REVERT: C  356 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7319 (tp)
REVERT: D   34 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4524 (m-10)
REVERT: D   96 MET cc_start: 0.6341 (mmt) cc_final: 0.6097 (mmt)
REVERT: D  104 GLU cc_start: 0.5901 (mm-30) cc_final: 0.5549 (mm-30)
REVERT: D  313 THR cc_start: 0.6406 (OUTLIER) cc_final: 0.6172 (t)
REVERT: D  321 MET cc_start: 0.7432 (tpt) cc_final: 0.6653 (ttm)
  outliers start: 21
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1945
  time to fit residues: 29.3843
Evaluate side-chains
  106 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  311 CYS
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 70 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
D  58 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.231212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.193071 restraints weight = 5731.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.193623 restraints weight = 4778.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.197184 restraints weight = 3882.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6076  Z= 0.256
  Angle     :  0.582   9.338   8200  Z= 0.302
  Chirality :  0.050   0.325    906
  Planarity :  0.005   0.057   1056
  Dihedral  :  8.145  88.694    860
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.64 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.30), residues: 742
  helix:  0.44 (0.31), residues: 262
  sheet:  0.08 (0.43), residues: 128
  loop : -1.10 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.018   0.002   PHE D 147 
 TYR   0.008   0.001   TYR C 267 
 ARG   0.003   0.000   ARG D 127 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.765 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7138 (mmm) cc_final: 0.6450 (ttt)
REVERT: C   92 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5778 (mm)
REVERT: C  182 ARG cc_start: 0.7085 (tpt90) cc_final: 0.6572 (mtp85)
REVERT: C  237 ARG cc_start: 0.7401 (ttm-80) cc_final: 0.6986 (mtm110)
REVERT: C  271 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (mt)
REVERT: D   34 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4542 (m-10)
REVERT: D  313 THR cc_start: 0.6310 (OUTLIER) cc_final: 0.6078 (t)
REVERT: D  321 MET cc_start: 0.7422 (tpt) cc_final: 0.6634 (ttm)
REVERT: D  358 ASN cc_start: 0.7186 (m-40) cc_final: 0.6957 (m-40)
  outliers start: 25
  outliers final: 12
  residues processed: 118
  average time/residue: 0.2459
  time to fit residues: 38.1002
Evaluate side-chains
  114 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0170
   chunk 9 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.234632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.197441 restraints weight = 5578.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.202197 restraints weight = 4676.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.204515 restraints weight = 3124.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6076  Z= 0.188
  Angle     :  0.559  15.793   8200  Z= 0.286
  Chirality :  0.047   0.145    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.811  89.194    860
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 20.49 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.30), residues: 742
  helix:  0.64 (0.31), residues: 262
  sheet:  0.30 (0.44), residues: 128
  loop : -1.07 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.017   0.001   PHE D 221 
 TYR   0.004   0.001   TYR C 267 
 ARG   0.003   0.000   ARG D  65 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.622 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7055 (mmm) cc_final: 0.6427 (ttt)
REVERT: C   92 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5800 (mm)
REVERT: C  237 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.6997 (mtm110)
REVERT: D    1 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6372 (ttt)
REVERT: D   34 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.4579 (m-10)
REVERT: D  313 THR cc_start: 0.6310 (OUTLIER) cc_final: 0.6089 (t)
REVERT: D  321 MET cc_start: 0.7370 (tpt) cc_final: 0.6661 (ttm)
REVERT: D  344 HIS cc_start: 0.7170 (t-90) cc_final: 0.6451 (t-170)
  outliers start: 24
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1798
  time to fit residues: 28.3887
Evaluate side-chains
  109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
D  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.234541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.198751 restraints weight = 5495.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.201990 restraints weight = 4175.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.204057 restraints weight = 3103.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6583
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6076  Z= 0.194
  Angle     :  0.571  15.703   8200  Z= 0.292
  Chirality :  0.047   0.142    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.739  89.570    860
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.80 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.30), residues: 742
  helix:  0.67 (0.31), residues: 262
  sheet:  0.34 (0.44), residues: 128
  loop : -1.07 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  39 
 HIS   0.005   0.001   HIS C 279 
 PHE   0.018   0.001   PHE C 232 
 TYR   0.005   0.001   TYR C 267 
 ARG   0.002   0.000   ARG D 127 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.653 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7067 (mmm) cc_final: 0.6449 (ttt)
REVERT: C   92 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5852 (mm)
REVERT: C  237 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.6996 (mtm110)
REVERT: D    1 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6293 (ttt)
REVERT: D   34 PHE cc_start: 0.5425 (OUTLIER) cc_final: 0.4574 (m-10)
REVERT: D  313 THR cc_start: 0.6351 (OUTLIER) cc_final: 0.6093 (t)
REVERT: D  321 MET cc_start: 0.7388 (tpt) cc_final: 0.6616 (ttm)
REVERT: D  324 MET cc_start: 0.6196 (ptt) cc_final: 0.5878 (ptt)
REVERT: D  344 HIS cc_start: 0.7216 (t-90) cc_final: 0.6485 (t-170)
  outliers start: 23
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1738
  time to fit residues: 26.6880
Evaluate side-chains
  109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 10 optimal weight:    0.0470
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 56 optimal weight:    0.2980
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.8082

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN
D 323 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.234327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.198466 restraints weight = 5552.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.201446 restraints weight = 4206.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.204059 restraints weight = 3135.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6076  Z= 0.190
  Angle     :  0.549  15.866   8200  Z= 0.282
  Chirality :  0.047   0.142    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.673  88.810    860
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.10 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.30), residues: 742
  helix:  0.72 (0.31), residues: 262
  sheet:  0.40 (0.44), residues: 128
  loop : -1.08 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  39 
 HIS   0.005   0.001   HIS D  31 
 PHE   0.017   0.002   PHE D 221 
 TYR   0.005   0.001   TYR C 267 
 ARG   0.002   0.000   ARG D 127 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.677 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7122 (mmm) cc_final: 0.6500 (ttt)
REVERT: C   92 ILE cc_start: 0.6315 (OUTLIER) cc_final: 0.5874 (mm)
REVERT: C  237 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.6989 (mtm110)
REVERT: C  356 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7223 (tp)
REVERT: D    1 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6483 (ttt)
REVERT: D   34 PHE cc_start: 0.5446 (OUTLIER) cc_final: 0.4559 (m-10)
REVERT: D  313 THR cc_start: 0.6347 (OUTLIER) cc_final: 0.6107 (t)
REVERT: D  324 MET cc_start: 0.6164 (ptt) cc_final: 0.5893 (ptt)
  outliers start: 22
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1879
  time to fit residues: 27.8974
Evaluate side-chains
  111 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 59 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.235325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.199567 restraints weight = 5473.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.202906 restraints weight = 4202.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.204886 restraints weight = 3431.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6076  Z= 0.189
  Angle     :  0.563  16.798   8200  Z= 0.288
  Chirality :  0.047   0.141    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.598  88.027    860
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.56 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.31), residues: 742
  helix:  0.90 (0.32), residues: 256
  sheet:  0.47 (0.45), residues: 128
  loop : -0.98 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.015   0.001   PHE D 221 
 TYR   0.005   0.001   TYR D 267 
 ARG   0.002   0.000   ARG D 127 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.644 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7080 (mmm) cc_final: 0.6532 (ttt)
REVERT: C   92 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.5899 (mm)
REVERT: C  237 ARG cc_start: 0.7476 (ttm-80) cc_final: 0.7046 (mtm110)
REVERT: C  356 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7178 (tp)
REVERT: D    1 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6544 (ttt)
REVERT: D   34 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4573 (m-10)
REVERT: D  313 THR cc_start: 0.6337 (OUTLIER) cc_final: 0.6103 (t)
REVERT: D  324 MET cc_start: 0.6174 (ptt) cc_final: 0.5929 (ptt)
  outliers start: 22
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1952
  time to fit residues: 28.4325
Evaluate side-chains
  108 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.237048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.201385 restraints weight = 5483.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.204457 restraints weight = 4163.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.207231 restraints weight = 3071.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6076  Z= 0.172
  Angle     :  0.551  16.735   8200  Z= 0.283
  Chirality :  0.046   0.141    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.470  87.521    860
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.32 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.31), residues: 742
  helix:  0.96 (0.32), residues: 258
  sheet:  0.59 (0.46), residues: 128
  loop : -0.97 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.017   0.001   PHE D 221 
 TYR   0.005   0.001   TYR C  22 
 ARG   0.004   0.000   ARG C 333 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.656 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7075 (mmm) cc_final: 0.6529 (ttt)
REVERT: C   92 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.5892 (mm)
REVERT: D    1 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6586 (ttt)
REVERT: D   34 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.4644 (m-10)
REVERT: D  324 MET cc_start: 0.6133 (ptt) cc_final: 0.5861 (ptt)
  outliers start: 19
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1644
  time to fit residues: 23.8839
Evaluate side-chains
  107 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    0.2980
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.236131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.199922 restraints weight = 5547.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.203238 restraints weight = 4233.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.205707 restraints weight = 3102.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6076  Z= 0.191
  Angle     :  0.567  16.787   8200  Z= 0.291
  Chirality :  0.047   0.140    906
  Planarity :  0.004   0.056   1056
  Dihedral  :  7.503  86.204    860
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.78 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.31), residues: 742
  helix:  0.92 (0.32), residues: 258
  sheet:  0.56 (0.46), residues: 128
  loop : -0.98 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  39 
 HIS   0.004   0.001   HIS D  31 
 PHE   0.015   0.001   PHE D 221 
 TYR   0.005   0.001   TYR D 267 
 ARG   0.003   0.000   ARG C 333 

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.628 
Fit side-chains
REVERT: C    1 MET cc_start: 0.7205 (mmm) cc_final: 0.6639 (ttt)
REVERT: C   92 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.5920 (mm)
REVERT: C  356 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7417 (tp)
REVERT: D    1 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6589 (ttt)
REVERT: D   34 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.4592 (m-10)
REVERT: D  313 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.6124 (t)
REVERT: D  324 MET cc_start: 0.6193 (ptt) cc_final: 0.5922 (ptt)
  outliers start: 19
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1600
  time to fit residues: 23.3092
Evaluate side-chains
  109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   28 ASN
Chi-restraints excluded: chain D residue   34 PHE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  268 VAL
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain D residue  313 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.232111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.195103 restraints weight = 5649.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.195964 restraints weight = 4561.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.199316 restraints weight = 3658.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6076  Z= 0.250
  Angle     :  0.592  17.025   8200  Z= 0.305
  Chirality :  0.048   0.145    906
  Planarity :  0.005   0.056   1056
  Dihedral  :  7.785  83.415    860
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 22.48 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.30), residues: 742
  helix:  0.73 (0.31), residues: 258
  sheet:  0.45 (0.46), residues: 128
  loop : -1.09 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  39 
 HIS   0.005   0.001   HIS D  31 
 PHE   0.014   0.002   PHE C 147 
 TYR   0.008   0.001   TYR C 267 
 ARG   0.003   0.000   ARG C 333 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1831.97 seconds
wall clock time: 34 minutes 3.84 seconds (2043.84 seconds total)