Starting phenix.real_space_refine
on Sat Apr 26 23:25:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w22_43737/04_2025/8w22_43737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w22_43737/04_2025/8w22_43737.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w22_43737/04_2025/8w22_43737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w22_43737/04_2025/8w22_43737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w22_43737/04_2025/8w22_43737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w22_43737/04_2025/8w22_43737.cif"
  }
  resolution = 4.0
  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=   0.072
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    2333      2.51       5
     N     723      2.21       5
     O     681      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3750
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 685
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 3, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 53
    Chain: "B"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 805
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 65
    Chain: "C"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 2260
          Classifications: {'peptide': 405}
          Incomplete info: {'truncation_to_alanine': 242}
          Link IDs: {'PTRANS': 17, 'TRANS': 387}
          Chain breaks: 12
          Unresolved non-hydrogen bonds: 798
          Unresolved non-hydrogen angles: 1047
          Unresolved non-hydrogen dihedrals: 629
          Unresolved non-hydrogen chiralities: 100
          Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 37, 'TYR:plan': 7, 'ASN:plan1': 18, 'TRP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 428
  Time building chain proxies: 3.59, per 1000 atoms: 0.96
  Number of scatterers: 3750
  At special positions: 0
  Unit cell: (69.126, 131.508, 116.334, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O     681      8.00
     N     723      7.00
     C    2333      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  78 " - pdb=" SG  CYS B  96 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C  71 " distance=2.08
    Simple disulfide: pdb=" SG  CYS C 192 " - pdb=" SG  CYS C 222 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 603.0 milliseconds
  

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1122

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 9 sheets defined
      19.4% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 111
      removed outlier: 3.577A  pdb=" N   MET A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 123
      removed outlier: 3.959A  pdb=" N   ASP A 121 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 134
    Processing helix  chain 'A' and resid 136 through 139
    Processing helix  chain 'A' and resid 140 through 145
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 158 through 170
    Processing helix  chain 'A' and resid 172 through 180
    Processing helix  chain 'A' and resid 182 through 197
    Processing helix  chain 'B' and resid 54 through 62
      removed outlier: 3.504A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 151
    Processing helix  chain 'C' and resid 69 through 73
    Processing helix  chain 'C' and resid 238 through 247
    Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76
      removed outlier: 3.711A  pdb=" N   CYS B  96 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106
      removed outlier: 3.525A  pdb=" N   ALA B 104 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   THR B 126 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   LEU B 162 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LYS B 124 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48
      removed outlier: 3.536A  pdb=" N   GLU C 112 " --> pdb=" O   ARG C 125 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   THR C  91 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138
      removed outlier: 7.338A  pdb=" N   ARG C 137 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   GLY C 212 " --> pdb=" O   ARG C 137 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE C 233 " --> pdb=" O   ASN C 215 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   SER C 217 " --> pdb=" O   ASP C 231 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP C 231 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   THR C 184 " --> pdb=" O   VAL C 173 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   VAL C 173 " --> pdb=" O   THR C 184 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   ASP C 203 " --> pdb=" O   PRO C 148 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL C 152 " --> pdb=" O   PRO C 199 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY C 212 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLN C 202 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   LEU C 210 " --> pdb=" O   GLN C 202 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   LYS C 204 " --> pdb=" O   LEU C 208 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   LEU C 208 " --> pdb=" O   LYS C 204 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262
    Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334
    Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369
    Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413
      removed outlier: 3.529A  pdb=" N   THR C 411 " --> pdb=" O   THR C 425 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   THR C 425 " --> pdb=" O   THR C 411 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486

    173 hydrogen bonds defined for protein.
    453 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: 1.19

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1142
        1.33 -     1.45: 504
        1.45 -     1.58: 2130
        1.58 -     1.70: 0
        1.70 -     1.82: 20
  Bond restraints: 3796
  Sorted by residual:
  bond pdb=" NE  ARG A 106 "
       pdb=" CZ  ARG A 106 "
    ideal  model  delta    sigma   weight residual
    1.326  1.355 -0.029 1.10e-02 8.26e+03 6.76e+00
  bond pdb=" NE  ARG C 119 "
       pdb=" CZ  ARG C 119 "
    ideal  model  delta    sigma   weight residual
    1.326  1.353 -0.027 1.10e-02 8.26e+03 6.04e+00
  bond pdb=" NE  ARG A 162 "
       pdb=" CZ  ARG A 162 "
    ideal  model  delta    sigma   weight residual
    1.326  1.351 -0.025 1.10e-02 8.26e+03 5.31e+00
  bond pdb=" NE  ARG C  97 "
       pdb=" CZ  ARG C  97 "
    ideal  model  delta    sigma   weight residual
    1.326  1.351 -0.025 1.10e-02 8.26e+03 5.20e+00
  bond pdb=" NE  ARG A 124 "
       pdb=" CZ  ARG A 124 "
    ideal  model  delta    sigma   weight residual
    1.326  1.351 -0.025 1.10e-02 8.26e+03 5.05e+00
  ... (remaining 3791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 4429
        1.58 -     3.16: 651
        3.16 -     4.75: 60
        4.75 -     6.33: 27
        6.33 -     7.91: 28
  Bond angle restraints: 5195
  Sorted by residual:
  angle pdb=" C   VAL C 114 "
        pdb=" N   PRO C 115 "
        pdb=" CA  PRO C 115 "
      ideal   model   delta    sigma   weight residual
     119.85  127.71   -7.86 1.01e+00 9.80e-01 6.05e+01
  angle pdb=" C   ASP B 121 "
        pdb=" N   PRO B 122 "
        pdb=" CA  PRO B 122 "
      ideal   model   delta    sigma   weight residual
     119.76  126.92   -7.16 1.03e+00 9.43e-01 4.84e+01
  angle pdb=" C   ARG C 502 "
        pdb=" N   PRO C 503 "
        pdb=" CA  PRO C 503 "
      ideal   model   delta    sigma   weight residual
     120.03  126.91   -6.88 9.90e-01 1.02e+00 4.83e+01
  angle pdb=" C   GLY A 158 "
        pdb=" N   PRO A 159 "
        pdb=" CA  PRO A 159 "
      ideal   model   delta    sigma   weight residual
     119.32  127.23   -7.91 1.14e+00 7.69e-01 4.81e+01
  angle pdb=" C   MET B  43 "
        pdb=" N   PRO B  44 "
        pdb=" CA  PRO B  44 "
      ideal   model   delta    sigma   weight residual
     120.31  127.11   -6.80 9.80e-01 1.04e+00 4.81e+01
  ... (remaining 5190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.31: 2128
       12.31 -    24.61: 57
       24.61 -    36.92: 16
       36.92 -    49.23: 6
       49.23 -    61.53: 6
  Dihedral angle restraints: 2213
    sinusoidal: 467
      harmonic: 1746
  Sorted by residual:
  dihedral pdb=" CB  CYS C 192 "
           pdb=" SG  CYS C 192 "
           pdb=" SG  CYS C 222 "
           pdb=" CB  CYS C 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.53  -61.53     1      1.00e+01 1.00e-02 5.02e+01
  dihedral pdb=" CB  CYS C  55 "
           pdb=" SG  CYS C  55 "
           pdb=" SG  CYS C  71 "
           pdb=" CB  CYS C  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.06  -44.06     1      1.00e+01 1.00e-02 2.70e+01
  dihedral pdb=" CB  CYS B  78 "
           pdb=" SG  CYS B  78 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  120.80  -27.80     1      1.00e+01 1.00e-02 1.11e+01
  ... (remaining 2210 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 349
       0.039 -    0.079: 170
       0.079 -    0.118: 73
       0.118 -    0.157: 24
       0.157 -    0.197: 3
  Chirality restraints: 619
  Sorted by residual:
  chirality pdb=" CA  ILE C 191 "
            pdb=" N   ILE C 191 "
            pdb=" C   ILE C 191 "
            pdb=" CB  ILE C 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CA  ILE C 130 "
            pdb=" N   ILE C 130 "
            pdb=" C   ILE C 130 "
            pdb=" CB  ILE C 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CG  LEU C  46 "
            pdb=" CB  LEU C  46 "
            pdb=" CD1 LEU C  46 "
            pdb=" CD2 LEU C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.70e-01
  ... (remaining 616 not shown)

  Planarity restraints: 718
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  52 "   -0.028 2.00e-02 2.50e+03   1.43e-02 4.08e+00
        pdb=" CG  TYR B  52 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  52 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  52 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  52 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  52 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  52 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  52 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C 199 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.34e+00
        pdb=" C   PRO C 199 "    0.032 2.00e-02 2.50e+03
        pdb=" O   PRO C 199 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU C 200 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  52 "    0.021 2.00e-02 2.50e+03   1.11e-02 2.48e+00
        pdb=" CG  TYR C  52 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  52 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  52 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  52 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  52 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  52 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C  52 "    0.015 2.00e-02 2.50e+03
  ... (remaining 715 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1763
        2.98 -     3.46: 3227
        3.46 -     3.94: 5318
        3.94 -     4.42: 5604
        4.42 -     4.90: 9568
  Nonbonded interactions: 25480
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 147 "
            pdb=" C   GLY B 148 "
     model   vdw
     2.497 3.270
  nonbonded pdb=" O   TYR B 147 "
            pdb=" N   ALA B 150 "
     model   vdw
     2.511 3.120
  nonbonded pdb=" N   GLY C 194 "
            pdb=" N   ASP C 195 "
     model   vdw
     2.565 2.560
  nonbonded pdb=" N   LYS C  39 "
            pdb=" N   LEU C  40 "
     model   vdw
     2.578 2.560
  nonbonded pdb=" N   GLY C 268 "
            pdb=" N   ARG C 269 "
     model   vdw
     2.602 2.560
  ... (remaining 25475 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:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.970
  Find NCS groups from input model:        0.040
  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:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
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      :  0.008   0.051   3799  Z= 0.495
  Angle     :  1.269   7.910   5201  Z= 0.883
  Chirality :  0.055   0.197    619
  Planarity :  0.005   0.018    718
  Dihedral  :  7.997  59.354   1082
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  2.84 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.30 (0.35), residues: 599
  helix: -0.58 (0.43), residues: 110
  sheet:  1.43 (0.46), residues: 140
  loop :  0.03 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.004   TRP C  64 
 HIS   0.004   0.001   HIS C 116 
 PHE   0.018   0.003   PHE C 171 
 TYR   0.028   0.004   TYR B  52 
 ARG   0.004   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20361 (  173)
  hydrogen bonds       : angle       8.01423 (  453)
  SS BOND              : bond        0.03142 (    3)
  SS BOND              : angle       2.84746 (    6)
  covalent geometry    : bond        0.00810 ( 3796)
  covalent geometry    : angle       1.26640 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  106 ARG cc_start: 0.6014 (ttm110) cc_final: 0.5118 (tpp-160)
REVERT: A  170 GLN cc_start: 0.8282 (mt0) cc_final: 0.8030 (mt0)
REVERT: B  100 MET cc_start: 0.8401 (mmm) cc_final: 0.7447 (mpp)
REVERT: C  125 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7217 (tmt-80)
REVERT: C  137 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7137 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2058
  time to fit residues: 17.5697
Evaluate side-chains
  41 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 47 optimal weight:    0.3980
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.151266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.121212 restraints weight = 7309.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.118819 restraints weight = 6787.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120216 restraints weight = 5303.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3799  Z= 0.196
  Angle     :  0.620   5.445   5201  Z= 0.339
  Chirality :  0.047   0.163    619
  Planarity :  0.005   0.028    718
  Dihedral  :  4.303  18.740    644
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.44 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.83 (0.36), residues: 599
  helix:  0.85 (0.49), residues: 115
  sheet:  0.98 (0.42), residues: 169
  loop :  0.31 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 117 
 HIS   0.002   0.001   HIS C 116 
 PHE   0.016   0.002   PHE C 171 
 TYR   0.017   0.002   TYR C  52 
 ARG   0.005   0.001   ARG A 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04746 (  173)
  hydrogen bonds       : angle       5.35096 (  453)
  SS BOND              : bond        0.00162 (    3)
  SS BOND              : angle       1.23103 (    6)
  covalent geometry    : bond        0.00428 ( 3796)
  covalent geometry    : angle       0.61880 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A  106 ARG cc_start: 0.5715 (ttm110) cc_final: 0.4888 (tpp-160)
REVERT: A  156 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8457 (tt)
REVERT: B  100 MET cc_start: 0.9006 (mmm) cc_final: 0.8648 (mmt)
REVERT: C  125 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7569 (tmt-80)
REVERT: C  137 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7047 (mtp85)
  outliers start: 6
  outliers final: 4
  residues processed: 48
  average time/residue: 0.1344
  time to fit residues: 8.5442
Evaluate side-chains
  44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue  137 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 58 optimal weight:    0.4980
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.147630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.118230 restraints weight = 7133.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.115915 restraints weight = 6828.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.116946 restraints weight = 5603.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3799  Z= 0.201
  Angle     :  0.596   5.471   5201  Z= 0.322
  Chirality :  0.046   0.145    619
  Planarity :  0.004   0.029    718
  Dihedral  :  4.329  17.734    644
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 16.67 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.51 (0.36), residues: 599
  helix:  1.04 (0.52), residues: 110
  sheet:  0.72 (0.43), residues: 161
  loop : -0.02 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 117 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.014   0.002   PHE C 171 
 TYR   0.013   0.002   TYR A 185 
 ARG   0.002   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04887 (  173)
  hydrogen bonds       : angle       5.25345 (  453)
  SS BOND              : bond        0.00685 (    3)
  SS BOND              : angle       1.56443 (    6)
  covalent geometry    : bond        0.00446 ( 3796)
  covalent geometry    : angle       0.59352 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.426 
Fit side-chains
REVERT: C  121 MET cc_start: 0.7222 (mmm) cc_final: 0.6821 (tpp)
REVERT: C  125 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7589 (ttt90)
REVERT: C  137 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7257 (mtp85)
  outliers start: 9
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1172
  time to fit residues: 7.8086
Evaluate side-chains
  46 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0670
   chunk 56 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
C 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.149252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.121742 restraints weight = 7056.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120899 restraints weight = 6023.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122235 restraints weight = 5460.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3799  Z= 0.161
  Angle     :  0.533   5.222   5201  Z= 0.285
  Chirality :  0.045   0.140    619
  Planarity :  0.004   0.036    718
  Dihedral  :  3.947  14.968    644
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 15.56 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.41 (0.37), residues: 599
  helix:  1.09 (0.54), residues: 109
  sheet:  0.51 (0.43), residues: 162
  loop : -0.04 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 117 
 HIS   0.005   0.001   HIS B  72 
 PHE   0.016   0.002   PHE C 171 
 TYR   0.009   0.001   TYR A 185 
 ARG   0.002   0.000   ARG A 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03936 (  173)
  hydrogen bonds       : angle       5.01940 (  453)
  SS BOND              : bond        0.00352 (    3)
  SS BOND              : angle       1.34782 (    6)
  covalent geometry    : bond        0.00361 ( 3796)
  covalent geometry    : angle       0.53128 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  125 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7724 (tt)
REVERT: C  121 MET cc_start: 0.7311 (mmm) cc_final: 0.6888 (tpp)
REVERT: C  125 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7834 (ttt90)
REVERT: C  137 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7358 (mtp85)
  outliers start: 9
  outliers final: 6
  residues processed: 48
  average time/residue: 0.1197
  time to fit residues: 7.8488
Evaluate side-chains
  47 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0270
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.146886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.119518 restraints weight = 7476.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.118878 restraints weight = 6003.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.119960 restraints weight = 5969.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3799  Z= 0.145
  Angle     :  0.510   5.167   5201  Z= 0.272
  Chirality :  0.045   0.139    619
  Planarity :  0.004   0.039    718
  Dihedral  :  3.764  16.601    644
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 17.78 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.49 (0.37), residues: 599
  helix:  1.18 (0.55), residues: 109
  sheet:  0.52 (0.43), residues: 155
  loop :  0.04 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 117 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.015   0.002   PHE C 171 
 TYR   0.009   0.001   TYR A 185 
 ARG   0.001   0.000   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  173)
  hydrogen bonds       : angle       4.95402 (  453)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       0.83235 (    6)
  covalent geometry    : bond        0.00323 ( 3796)
  covalent geometry    : angle       0.50907 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.385 
Fit side-chains
REVERT: C  121 MET cc_start: 0.7335 (mmm) cc_final: 0.6978 (tpp)
REVERT: C  125 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7797 (ttt90)
REVERT: C  137 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7379 (mtp85)
  outliers start: 11
  outliers final: 8
  residues processed: 49
  average time/residue: 0.1308
  time to fit residues: 8.6780
Evaluate side-chains
  44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0980
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118894 restraints weight = 7411.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.118058 restraints weight = 6035.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.119235 restraints weight = 6042.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3799  Z= 0.144
  Angle     :  0.508   5.573   5201  Z= 0.268
  Chirality :  0.045   0.142    619
  Planarity :  0.004   0.040    718
  Dihedral  :  3.712  15.088    644
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 18.33 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.46 (0.37), residues: 599
  helix:  1.18 (0.55), residues: 109
  sheet:  0.54 (0.44), residues: 145
  loop : -0.00 (0.37), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 117 
 HIS   0.004   0.001   HIS B  72 
 PHE   0.014   0.002   PHE C 171 
 TYR   0.006   0.001   TYR A 185 
 ARG   0.001   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  173)
  hydrogen bonds       : angle       4.96355 (  453)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       0.84864 (    6)
  covalent geometry    : bond        0.00323 ( 3796)
  covalent geometry    : angle       0.50718 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.455 
Fit side-chains
REVERT: C  121 MET cc_start: 0.7348 (mmm) cc_final: 0.6969 (tpp)
REVERT: C  125 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7802 (ttt90)
REVERT: C  137 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7401 (mtp85)
  outliers start: 10
  outliers final: 8
  residues processed: 45
  average time/residue: 0.1601
  time to fit residues: 9.4274
Evaluate side-chains
  43 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  112 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0670
   chunk 45 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0370
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.148210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.119903 restraints weight = 7311.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118201 restraints weight = 6341.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.119247 restraints weight = 5205.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3799  Z= 0.109
  Angle     :  0.477   6.897   5201  Z= 0.246
  Chirality :  0.044   0.132    619
  Planarity :  0.003   0.043    718
  Dihedral  :  3.414  14.492    644
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 18.89 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.48 (0.37), residues: 599
  helix:  1.28 (0.55), residues: 109
  sheet:  0.43 (0.45), residues: 137
  loop :  0.05 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 117 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.012   0.001   PHE C 171 
 TYR   0.005   0.001   TYR A 138 
 ARG   0.001   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (  173)
  hydrogen bonds       : angle       4.67193 (  453)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.67398 (    6)
  covalent geometry    : bond        0.00245 ( 3796)
  covalent geometry    : angle       0.47707 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.423 
Fit side-chains
REVERT: B  112 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8482 (mp10)
REVERT: C  121 MET cc_start: 0.7367 (mmm) cc_final: 0.6995 (tpp)
REVERT: C  125 ARG cc_start: 0.8148 (ttt180) cc_final: 0.7842 (ttt90)
REVERT: C  137 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7314 (mtp85)
  outliers start: 10
  outliers final: 7
  residues processed: 47
  average time/residue: 0.1184
  time to fit residues: 7.5522
Evaluate side-chains
  45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  112 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0050
   chunk 47 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0060
   overall best weight:    0.1906

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.150342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.122835 restraints weight = 7376.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.121989 restraints weight = 5639.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123206 restraints weight = 4930.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.5266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3799  Z= 0.076
  Angle     :  0.452   7.688   5201  Z= 0.229
  Chirality :  0.043   0.131    619
  Planarity :  0.003   0.045    718
  Dihedral  :  3.079  13.804    644
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 20.00 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.86 (0.37), residues: 599
  helix:  1.38 (0.54), residues: 110
  sheet:  0.62 (0.43), residues: 157
  loop :  0.40 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 117 
 HIS   0.002   0.001   HIS B  72 
 PHE   0.012   0.001   PHE C 171 
 TYR   0.006   0.001   TYR A 138 
 ARG   0.002   0.000   ARG A 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02591 (  173)
  hydrogen bonds       : angle       4.32636 (  453)
  SS BOND              : bond        0.00134 (    3)
  SS BOND              : angle       0.54501 (    6)
  covalent geometry    : bond        0.00168 ( 3796)
  covalent geometry    : angle       0.45217 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.399 
Fit side-chains
REVERT: C  121 MET cc_start: 0.7297 (mmm) cc_final: 0.6976 (tpp)
REVERT: C  125 ARG cc_start: 0.8146 (ttt180) cc_final: 0.7882 (ttt90)
REVERT: C  137 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7372 (mtp85)
  outliers start: 7
  outliers final: 7
  residues processed: 45
  average time/residue: 0.1165
  time to fit residues: 7.1542
Evaluate side-chains
  44 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 38 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.145467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116855 restraints weight = 7281.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114948 restraints weight = 6178.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116264 restraints weight = 4775.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.5441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3799  Z= 0.138
  Angle     :  0.496   5.870   5201  Z= 0.260
  Chirality :  0.044   0.136    619
  Planarity :  0.004   0.042    718
  Dihedral  :  3.433  15.239    644
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 21.67 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.59 (0.37), residues: 599
  helix:  1.32 (0.55), residues: 109
  sheet:  0.78 (0.47), residues: 128
  loop :  0.02 (0.36), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B  72 
 PHE   0.014   0.002   PHE C 171 
 TYR   0.006   0.001   TYR A 185 
 ARG   0.002   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  173)
  hydrogen bonds       : angle       4.73102 (  453)
  SS BOND              : bond        0.00272 (    3)
  SS BOND              : angle       0.91673 (    6)
  covalent geometry    : bond        0.00311 ( 3796)
  covalent geometry    : angle       0.49533 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.421 
Fit side-chains
REVERT: B  112 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8473 (mp10)
REVERT: C  121 MET cc_start: 0.7406 (mmm) cc_final: 0.7044 (tpp)
REVERT: C  125 ARG cc_start: 0.8139 (ttt180) cc_final: 0.7832 (ttt90)
REVERT: C  137 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7341 (mtp85)
  outliers start: 8
  outliers final: 6
  residues processed: 44
  average time/residue: 0.1188
  time to fit residues: 7.1695
Evaluate side-chains
  41 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  112 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 1 optimal weight:    0.1980
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.142820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.115728 restraints weight = 7526.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.113366 restraints weight = 7299.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.115026 restraints weight = 7565.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.5735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3799  Z= 0.217
  Angle     :  0.582   6.991   5201  Z= 0.313
  Chirality :  0.047   0.156    619
  Planarity :  0.004   0.040    718
  Dihedral  :  4.167  17.475    644
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.78 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.17 (0.37), residues: 599
  helix:  1.01 (0.55), residues: 107
  sheet:  0.15 (0.43), residues: 147
  loop : -0.10 (0.37), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 117 
 HIS   0.005   0.002   HIS B  72 
 PHE   0.015   0.002   PHE B  97 
 TYR   0.012   0.001   TYR B  52 
 ARG   0.002   0.000   ARG A 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  173)
  hydrogen bonds       : angle       5.53942 (  453)
  SS BOND              : bond        0.00340 (    3)
  SS BOND              : angle       1.15244 (    6)
  covalent geometry    : bond        0.00490 ( 3796)
  covalent geometry    : angle       0.58115 ( 5195)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  196 VAL cc_start: 0.7124 (p) cc_final: 0.6755 (p)
REVERT: B  112 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8464 (mp10)
REVERT: C  121 MET cc_start: 0.7276 (mmm) cc_final: 0.6891 (tpp)
REVERT: C  125 ARG cc_start: 0.8177 (ttt180) cc_final: 0.7883 (ttt90)
REVERT: C  137 ARG cc_start: 0.8392 (mtp180) cc_final: 0.7520 (mtp85)
  outliers start: 6
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1393
  time to fit residues: 7.7119
Evaluate side-chains
  39 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  112 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  164 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.143972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117181 restraints weight = 7437.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.115469 restraints weight = 6723.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116574 restraints weight = 7681.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.5871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3799  Z= 0.187
  Angle     :  0.554   7.570   5201  Z= 0.294
  Chirality :  0.046   0.150    619
  Planarity :  0.004   0.045    718
  Dihedral  :  4.005  17.292    644
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 21.11 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.07 (0.37), residues: 599
  helix:  0.99 (0.55), residues: 107
  sheet:  0.04 (0.43), residues: 147
  loop : -0.17 (0.37), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 117 
 HIS   0.006   0.002   HIS B  72 
 PHE   0.013   0.002   PHE B  97 
 TYR   0.007   0.001   TYR B  52 
 ARG   0.002   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  173)
  hydrogen bonds       : angle       5.38271 (  453)
  SS BOND              : bond        0.00325 (    3)
  SS BOND              : angle       1.17902 (    6)
  covalent geometry    : bond        0.00425 ( 3796)
  covalent geometry    : angle       0.55254 ( 5195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1681.64 seconds
wall clock time: 29 minutes 50.69 seconds (1790.69 seconds total)