Starting phenix.real_space_refine
on Thu Jul  2 05:14:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wpl_66144/07_2026/9wpl_66144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wpl_66144/07_2026/9wpl_66144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wpl_66144/07_2026/9wpl_66144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wpl_66144/07_2026/9wpl_66144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wpl_66144/07_2026/9wpl_66144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wpl_66144/07_2026/9wpl_66144.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.080
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      54      5.16       5
     C    4592      2.51       5
     N     978      2.21       5
     O    1100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6730
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2542
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 19, 'TRANS': 307}
    Chain: "B"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 426
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 2, 'TRANS': 50}
    Chain: "C"
      Number of atoms: 2542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2542
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 19, 'TRANS': 307}
    Chain: "D"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 426
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 2, 'TRANS': 50}
    Chain: "A"
      Number of atoms: 369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 369
          Unusual residues: {'CLR': 4, 'PLM': 7, 'POV': 3}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'PLM:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 369
          Unusual residues: {'CLR': 4, 'PLM': 7, 'POV': 3}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'PLM:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.58, per 1000 atoms: 0.23
  Number of scatterers: 6730
  At special positions: 0
  Unit cell: (91.3, 91.3, 92.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P       6     15.00
     O    1100      8.00
     N     978      7.00
     C    4592      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  32 " - pdb=" SG  CYS A 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  32 " - pdb=" SG  CYS C 284 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=14, symmetry=0
  Number of additional bonds: simple=14, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 285.7 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1436

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      76.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 25
    Processing helix  chain 'A' and resid 29 through 33
    Processing helix  chain 'A' and resid 38 through 44
      removed outlier: 3.600A  pdb=" N   ARG A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 78
    Processing helix  chain 'A' and resid 81 through 93
      removed outlier: 3.593A  pdb=" N   ARG A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 108
    Processing helix  chain 'A' and resid 111 through 139
      removed outlier: 4.163A  pdb=" N   TYR A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 173 through 202
      Proline residue:  A 184  - end of helix
      removed outlier: 4.017A  pdb=" N   TYR A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 247
      removed outlier: 3.560A  pdb=" N   TRP A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLN A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 280
      removed outlier: 4.102A  pdb=" N   GLN A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 289 through 318
      removed outlier: 3.943A  pdb=" N   LEU A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 28
    Processing helix  chain 'B' and resid 33 through 68
    Processing helix  chain 'C' and resid 15 through 25
    Processing helix  chain 'C' and resid 29 through 33
    Processing helix  chain 'C' and resid 38 through 44
      removed outlier: 3.600A  pdb=" N   ARG C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 78
    Processing helix  chain 'C' and resid 81 through 93
      removed outlier: 3.592A  pdb=" N   ARG C  86 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR C  87 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER C  93 " --> pdb=" O   LEU C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 108
    Processing helix  chain 'C' and resid 111 through 139
      removed outlier: 4.163A  pdb=" N   TYR C 128 " --> pdb=" O   ALA C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 148
    Processing helix  chain 'C' and resid 173 through 202
      Proline residue:  C 184  - end of helix
      removed outlier: 4.017A  pdb=" N   TYR C 187 " --> pdb=" O   GLY C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 247
      removed outlier: 3.560A  pdb=" N   TRP C 220 " --> pdb=" O   SER C 216 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLN C 242 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 280
      removed outlier: 4.102A  pdb=" N   GLN C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      Proline residue:  C 270  - end of helix
    Processing helix  chain 'C' and resid 289 through 318
      removed outlier: 3.942A  pdb=" N   LEU C 308 " --> pdb=" O   LEU C 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 28
    Processing helix  chain 'D' and resid 33 through 68

    442 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1010
        1.33 -     1.45: 1530
        1.45 -     1.57: 4236
        1.57 -     1.69: 12
        1.69 -     1.82: 80
  Bond restraints: 6868
  Sorted by residual:
  bond pdb=" N   ASP C 204 "
       pdb=" CA  ASP C 204 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 1.33e-02 5.65e+03 6.35e+00
  bond pdb=" N   ASP A 204 "
       pdb=" CA  ASP A 204 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.33e-02 5.65e+03 6.28e+00
  bond pdb=" N   LYS C  77 "
       pdb=" CA  LYS C  77 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.31e-02 5.83e+03 5.79e+00
  bond pdb=" N   LYS A  77 "
       pdb=" CA  LYS A  77 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.31e-02 5.83e+03 5.78e+00
  bond pdb=" N   LEU C  19 "
       pdb=" CA  LEU C  19 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.47e+00
  ... (remaining 6863 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 9007
        2.00 -     4.01: 197
        4.01 -     6.01: 22
        6.01 -     8.02: 8
        8.02 -    10.02: 2
  Bond angle restraints: 9236
  Sorted by residual:
  angle pdb=" CA  ASP C 204 "
        pdb=" CB  ASP C 204 "
        pdb=" CG  ASP C 204 "
      ideal   model   delta    sigma   weight residual
     112.60  116.52   -3.92 1.00e+00 1.00e+00 1.53e+01
  angle pdb=" CA  ASP A 204 "
        pdb=" CB  ASP A 204 "
        pdb=" CG  ASP A 204 "
      ideal   model   delta    sigma   weight residual
     112.60  116.50   -3.90 1.00e+00 1.00e+00 1.52e+01
  angle pdb=" CA  THR A 173 "
        pdb=" C   THR A 173 "
        pdb=" O   THR A 173 "
      ideal   model   delta    sigma   weight residual
     121.51  117.75    3.76 1.12e+00 7.97e-01 1.13e+01
  angle pdb=" CA  THR C 173 "
        pdb=" C   THR C 173 "
        pdb=" O   THR C 173 "
      ideal   model   delta    sigma   weight residual
     121.51  117.76    3.75 1.12e+00 7.97e-01 1.12e+01
  angle pdb=" CB  GLU A 142 "
        pdb=" CG  GLU A 142 "
        pdb=" CD  GLU A 142 "
      ideal   model   delta    sigma   weight residual
     112.60  118.12   -5.52 1.70e+00 3.46e-01 1.05e+01
  ... (remaining 9231 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.24: 3890
       12.24 -    24.47: 487
       24.47 -    36.71: 233
       36.71 -    48.94: 86
       48.94 -    61.18: 38
  Dihedral angle restraints: 4734
    sinusoidal: 2518
      harmonic: 2216
  Sorted by residual:
  dihedral pdb=" CG  ARG A  85 "
           pdb=" CD  ARG A  85 "
           pdb=" NE  ARG A  85 "
           pdb=" CZ  ARG A  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.70   42.30     2      1.50e+01 4.44e-03 9.66e+00
  dihedral pdb=" CG  ARG C  85 "
           pdb=" CD  ARG C  85 "
           pdb=" NE  ARG C  85 "
           pdb=" CZ  ARG C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.71   42.29     2      1.50e+01 4.44e-03 9.66e+00
  dihedral pdb=" CB  MET A 153 "
           pdb=" CG  MET A 153 "
           pdb=" SD  MET A 153 "
           pdb=" CE  MET A 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    5.67   54.33     3      1.50e+01 4.44e-03 9.27e+00
  ... (remaining 4731 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 768
       0.032 -    0.065: 220
       0.065 -    0.097: 64
       0.097 -    0.130: 26
       0.130 -    0.162: 8
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  MET A 181 "
            pdb=" N   MET A 181 "
            pdb=" C   MET A 181 "
            pdb=" CB  MET A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.57e-01
  chirality pdb=" CA  ILE A  28 "
            pdb=" N   ILE A  28 "
            pdb=" C   ILE A  28 "
            pdb=" CB  ILE A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  MET C 181 "
            pdb=" N   MET C 181 "
            pdb=" C   MET C 181 "
            pdb=" CB  MET C 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.26e-01
  ... (remaining 1083 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 117 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.60e+00
        pdb=" C   MET A 117 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET A 117 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   THR A 118 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 117 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   MET C 117 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   MET C 117 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR C 118 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 119 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" C   ILE C 119 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ILE C 119 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   THR C 120 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1773
        2.82 -     3.34: 5989
        3.34 -     3.86: 10160
        3.86 -     4.38: 12121
        4.38 -     4.90: 20871
  Nonbonded interactions: 50914
  Sorted by model distance:
  nonbonded pdb=" O   PRO B  35 "
            pdb=" OG  SER B  39 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   PRO D  35 "
            pdb=" OG  SER D  39 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   LEU C  75 "
            pdb=" OG1 THR C  79 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   LEU A  75 "
            pdb=" OG1 THR A  79 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   LEU C 225 "
            pdb=" OG1 THR C 229 "
     model   vdw
     2.368 3.040
  ... (remaining 50909 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 403 or resid 405 through 410 or resid 412 throug \ 
h 413))
  selection = (chain 'C' and (resid 2 through 403 or resid 405 through 410 or resid 412 throug \ 
h 413))
}
ncs_group {
  reference = chain 'B'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.740
  Find NCS groups from input model:        0.130
  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:9.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6884  Z= 0.267
  Angle     :  0.714  10.024   9240  Z= 0.404
  Chirality :  0.038   0.162   1086
  Planarity :  0.006   0.052   1024
  Dihedral  : 14.391  61.179   3292
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.58 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.29), residues: 752
  helix:  2.13 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop : -2.03 (0.41), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 169 
 TYR   0.020   0.002   TYR C  76 
 PHE   0.016   0.002   PHE A 127 
 TRP   0.007   0.001   TRP C 220 
 HIS   0.004   0.001   HIS D  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.27 ( 6868)
  covalent geometry    : angle       0.71450 /  0.40 ( 9236)
  SS BOND              : bond        0.00434 /  0.22 (    2)
  SS BOND              : angle       0.69640 /  0.36 (    4)
  hydrogen bonds       : bond        0.12673 /  8.02 (  442)
  hydrogen bonds       : angle       4.87807 /  3.49 ( 1314)
  Misc. bond           : bond        0.00051 /  0.03 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7499 (mtm-85)
REVERT: A  320 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7945 (mttp)
REVERT: B   67 MET cc_start: 0.4587 (mtp) cc_final: 0.4268 (mtp)
REVERT: C   44 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7506 (mtm-85)
REVERT: C  320 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7944 (mttp)
REVERT: D   67 MET cc_start: 0.4400 (mtp) cc_final: 0.4146 (mtp)
  outliers start: 0
  outliers final: 2
  residues processed: 137
  average time/residue: 0.5745
  time to fit residues: 82.3667
Evaluate side-chains
  132 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain C residue   20 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.183572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.134393 restraints weight = 7053.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.76
r_work: 0.3408 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.0766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6884  Z= 0.145
  Angle     :  0.518   6.426   9240  Z= 0.261
  Chirality :  0.036   0.156   1086
  Planarity :  0.005   0.049   1024
  Dihedral  : 10.380  57.775   1890
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.73 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.30), residues: 752
  helix:  2.66 (0.20), residues: 576
  sheet:  None (None), residues: 0
  loop : -1.88 (0.42), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 169 
 TYR   0.013   0.002   TYR A 123 
 PHE   0.016   0.002   PHE A 127 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.004   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 6868)
  covalent geometry    : angle       0.51747 /  0.26 ( 9236)
  SS BOND              : bond        0.00487 /  0.24 (    2)
  SS BOND              : angle       0.83333 /  0.43 (    4)
  hydrogen bonds       : bond        0.06094 /  4.08 (  442)
  hydrogen bonds       : angle       3.75585 /  2.73 ( 1314)
  Misc. bond           : bond        0.00039 /  0.03 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7153 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6609 (tm-30)
REVERT: A  136 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6597 (mt-10)
REVERT: A  320 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7635 (mttp)
REVERT: B   67 MET cc_start: 0.4266 (mtp) cc_final: 0.4015 (mtp)
REVERT: C   35 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8098 (mm-40)
REVERT: C   44 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7172 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6545 (tm-30)
REVERT: C  147 THR cc_start: 0.8606 (m) cc_final: 0.7956 (p)
REVERT: C  320 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7630 (mttp)
REVERT: D   67 MET cc_start: 0.4318 (mtp) cc_final: 0.4088 (mtp)
  outliers start: 17
  outliers final: 7
  residues processed: 144
  average time/residue: 0.5021
  time to fit residues: 75.9508
Evaluate side-chains
  147 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain C residue   77 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain D residue   30 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0770
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    1.1344

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.182143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.133288 restraints weight = 6975.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.74
r_work: 0.3393 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.0953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6884  Z= 0.146
  Angle     :  0.513   6.296   9240  Z= 0.257
  Chirality :  0.036   0.135   1086
  Planarity :  0.004   0.049   1024
  Dihedral  : 10.459  58.219   1884
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 18.37 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.30), residues: 752
  helix:  2.70 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.86 (0.42), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 169 
 TYR   0.016   0.002   TYR C 123 
 PHE   0.015   0.002   PHE C 127 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 6868)
  covalent geometry    : angle       0.51232 /  0.26 ( 9236)
  SS BOND              : bond        0.00555 /  0.28 (    2)
  SS BOND              : angle       0.97294 /  0.51 (    4)
  hydrogen bonds       : bond        0.05922 /  3.97 (  442)
  hydrogen bonds       : angle       3.67588 /  2.66 ( 1314)
  Misc. bond           : bond        0.00037 /  0.02 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8179 (mm-40)
REVERT: A   44 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7133 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6658 (tm-30)
REVERT: A  320 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7559 (mttp)
REVERT: B   67 MET cc_start: 0.4356 (mtp) cc_final: 0.4101 (mtp)
REVERT: C   35 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8170 (mm-40)
REVERT: C   44 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7141 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6645 (tm-30)
REVERT: C  320 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7575 (mttp)
REVERT: D   67 MET cc_start: 0.4280 (mtp) cc_final: 0.4061 (mtp)
  outliers start: 31
  outliers final: 13
  residues processed: 152
  average time/residue: 0.4903
  time to fit residues: 78.4584
Evaluate side-chains
  148 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain C residue    8 ILE
Chi-restraints excluded: chain C residue   50 GLU
Chi-restraints excluded: chain C residue   77 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain D residue   30 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.181150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.132064 restraints weight = 7076.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.78
r_work: 0.3374 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6884  Z= 0.162
  Angle     :  0.533   5.928   9240  Z= 0.268
  Chirality :  0.037   0.137   1086
  Planarity :  0.005   0.049   1024
  Dihedral  : 10.674  58.263   1884
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.03 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.30), residues: 752
  helix:  2.63 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.92 (0.40), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 169 
 TYR   0.015   0.002   TYR C 123 
 PHE   0.015   0.002   PHE A 127 
 TRP   0.009   0.001   TRP C 220 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 6868)
  covalent geometry    : angle       0.53299 /  0.27 ( 9236)
  SS BOND              : bond        0.00540 /  0.27 (    2)
  SS BOND              : angle       1.14716 /  0.60 (    4)
  hydrogen bonds       : bond        0.06112 /  4.11 (  442)
  hydrogen bonds       : angle       3.69878 /  2.68 ( 1314)
  Misc. bond           : bond        0.00036 /  0.03 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7069 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6662 (tm-30)
REVERT: A  214 GLU cc_start: 0.7863 (pp20) cc_final: 0.6900 (pp20)
REVERT: A  320 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7562 (mttp)
REVERT: B   24 MET cc_start: 0.7252 (mmt) cc_final: 0.7048 (mmt)
REVERT: B   67 MET cc_start: 0.4349 (mtp) cc_final: 0.4089 (mtp)
REVERT: C   44 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7098 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6657 (tm-30)
REVERT: C  320 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7569 (mttp)
REVERT: D   67 MET cc_start: 0.4257 (mtp) cc_final: 0.4050 (mtp)
  outliers start: 22
  outliers final: 14
  residues processed: 144
  average time/residue: 0.5117
  time to fit residues: 77.2923
Evaluate side-chains
  146 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   77 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain C residue  274 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.178545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.126716 restraints weight = 6975.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.86
r_work: 0.3353 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6884  Z= 0.170
  Angle     :  0.543   5.733   9240  Z= 0.274
  Chirality :  0.037   0.137   1086
  Planarity :  0.005   0.050   1024
  Dihedral  : 10.998  59.455   1884
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.43 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.30), residues: 752
  helix:  2.51 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -2.02 (0.41), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 169 
 TYR   0.015   0.002   TYR C 123 
 PHE   0.014   0.002   PHE C 127 
 TRP   0.010   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.17 ( 6868)
  covalent geometry    : angle       0.54245 /  0.27 ( 9236)
  SS BOND              : bond        0.00598 /  0.30 (    2)
  SS BOND              : angle       1.25805 /  0.66 (    4)
  hydrogen bonds       : bond        0.06290 /  4.24 (  442)
  hydrogen bonds       : angle       3.72009 /  2.69 ( 1314)
  Misc. bond           : bond        0.00036 /  0.03 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7106 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6719 (tm-30)
REVERT: A  214 GLU cc_start: 0.7822 (pp20) cc_final: 0.6882 (pp20)
REVERT: A  320 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7594 (mttt)
REVERT: B   67 MET cc_start: 0.4336 (mtp) cc_final: 0.4081 (mtp)
REVERT: C   44 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7073 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6713 (tm-30)
REVERT: C  252 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6914 (mmt)
REVERT: C  320 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7567 (mttt)
REVERT: D   67 MET cc_start: 0.4254 (mtp) cc_final: 0.4048 (mtp)
  outliers start: 30
  outliers final: 20
  residues processed: 151
  average time/residue: 0.5125
  time to fit residues: 81.5043
Evaluate side-chains
  155 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain C residue    8 ILE
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   77 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  289 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0170
   chunk 39 optimal weight:    0.0670
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.182360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.131147 restraints weight = 7001.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.86
r_work: 0.3296 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6884  Z= 0.124
  Angle     :  0.485   5.478   9240  Z= 0.245
  Chirality :  0.035   0.134   1086
  Planarity :  0.004   0.048   1024
  Dihedral  : 10.431  59.702   1884
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.84 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.84 (0.30), residues: 752
  helix:  2.87 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.81 (0.40), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 169 
 TYR   0.017   0.002   TYR A  76 
 PHE   0.012   0.001   PHE C 127 
 TRP   0.008   0.001   TRP D  26 
 HIS   0.002   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 6868)
  covalent geometry    : angle       0.48512 /  0.25 ( 9236)
  SS BOND              : bond        0.00422 /  0.21 (    2)
  SS BOND              : angle       0.77000 /  0.40 (    4)
  hydrogen bonds       : bond        0.05169 /  3.47 (  442)
  hydrogen bonds       : angle       3.48301 /  2.53 ( 1314)
  Misc. bond           : bond        0.00020 /  0.01 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7078 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6667 (tm-30)
REVERT: A  320 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7408 (mttt)
REVERT: B   24 MET cc_start: 0.7196 (mmt) cc_final: 0.6928 (mmt)
REVERT: B   67 MET cc_start: 0.4285 (mtp) cc_final: 0.4056 (mtp)
REVERT: C   44 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7061 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6680 (tm-30)
REVERT: C  320 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7441 (mttt)
REVERT: D   67 MET cc_start: 0.4379 (mtp) cc_final: 0.4166 (mtp)
  outliers start: 18
  outliers final: 7
  residues processed: 126
  average time/residue: 0.4662
  time to fit residues: 62.1718
Evaluate side-chains
  122 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain C residue   77 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  204 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0270
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.9040

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.180941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129536 restraints weight = 6919.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.86
r_work: 0.3417 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6884  Z= 0.134
  Angle     :  0.495   5.339   9240  Z= 0.250
  Chirality :  0.036   0.134   1086
  Planarity :  0.004   0.048   1024
  Dihedral  : 10.454  59.629   1884
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.89 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.30), residues: 752
  helix:  2.82 (0.20), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.83 (0.41), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 169 
 TYR   0.014   0.001   TYR C 123 
 PHE   0.015   0.001   PHE C 127 
 TRP   0.008   0.001   TRP D  26 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 6868)
  covalent geometry    : angle       0.49445 /  0.25 ( 9236)
  SS BOND              : bond        0.00447 /  0.22 (    2)
  SS BOND              : angle       0.91204 /  0.48 (    4)
  hydrogen bonds       : bond        0.05376 /  3.62 (  442)
  hydrogen bonds       : angle       3.51006 /  2.55 ( 1314)
  Misc. bond           : bond        0.00024 /  0.02 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   38 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7565 (p)
REVERT: A   44 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7042 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6620 (tm-30)
REVERT: A  320 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7403 (mttt)
REVERT: B   67 MET cc_start: 0.4339 (mtp) cc_final: 0.4120 (mtp)
REVERT: C   38 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7551 (p)
REVERT: C   44 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7025 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6628 (tm-30)
REVERT: C  320 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7409 (mttp)
REVERT: D   67 MET cc_start: 0.4381 (mtp) cc_final: 0.4171 (mtp)
  outliers start: 12
  outliers final: 6
  residues processed: 122
  average time/residue: 0.4721
  time to fit residues: 60.8727
Evaluate side-chains
  123 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  204 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.181187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.129729 restraints weight = 7010.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.86
r_work: 0.3423 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6884  Z= 0.132
  Angle     :  0.491   5.274   9240  Z= 0.248
  Chirality :  0.035   0.134   1086
  Planarity :  0.004   0.046   1024
  Dihedral  : 10.412  59.960   1884
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 22.29 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.30), residues: 752
  helix:  2.83 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.77 (0.41), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 169 
 TYR   0.016   0.002   TYR A  76 
 PHE   0.014   0.001   PHE C 127 
 TRP   0.007   0.001   TRP B  26 
 HIS   0.002   0.001   HIS D  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 6868)
  covalent geometry    : angle       0.49060 /  0.25 ( 9236)
  SS BOND              : bond        0.00432 /  0.22 (    2)
  SS BOND              : angle       0.85531 /  0.45 (    4)
  hydrogen bonds       : bond        0.05314 /  3.58 (  442)
  hydrogen bonds       : angle       3.48518 /  2.53 ( 1314)
  Misc. bond           : bond        0.00025 /  0.02 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   38 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7579 (p)
REVERT: A   44 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7025 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6625 (tm-30)
REVERT: A  320 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7401 (mttt)
REVERT: B   67 MET cc_start: 0.4273 (mtp) cc_final: 0.4054 (mtp)
REVERT: C   38 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7554 (p)
REVERT: C   44 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7001 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6626 (tm-30)
REVERT: C  320 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7388 (mttt)
REVERT: D   67 MET cc_start: 0.4374 (mtp) cc_final: 0.4159 (mtp)
  outliers start: 17
  outliers final: 8
  residues processed: 125
  average time/residue: 0.4767
  time to fit residues: 63.0479
Evaluate side-chains
  124 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  299 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    0.3980
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.177991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125849 restraints weight = 6916.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.83
r_work: 0.3355 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6884  Z= 0.177
  Angle     :  0.547   5.324   9240  Z= 0.275
  Chirality :  0.038   0.136   1086
  Planarity :  0.005   0.047   1024
  Dihedral  : 11.016  59.729   1884
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.19 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.30), residues: 752
  helix:  2.56 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.90 (0.41), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 169 
 TYR   0.015   0.002   TYR A 123 
 PHE   0.017   0.002   PHE C  33 
 TRP   0.011   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.18 ( 6868)
  covalent geometry    : angle       0.54606 /  0.27 ( 9236)
  SS BOND              : bond        0.00586 /  0.29 (    2)
  SS BOND              : angle       1.22410 /  0.64 (    4)
  hydrogen bonds       : bond        0.06271 /  4.23 (  442)
  hydrogen bonds       : angle       3.67304 /  2.66 ( 1314)
  Misc. bond           : bond        0.00036 /  0.03 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7071 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6718 (tm-30)
REVERT: A  289 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8342 (p)
REVERT: A  320 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7482 (mttt)
REVERT: C   44 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7025 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6701 (tm-30)
REVERT: C  289 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8352 (p)
REVERT: C  320 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7476 (mttt)
  outliers start: 13
  outliers final: 10
  residues processed: 139
  average time/residue: 0.4847
  time to fit residues: 70.8911
Evaluate side-chains
  139 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  299 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0670
   chunk 24 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 40 optimal weight:    0.3980
   chunk 64 optimal weight:    0.5980
   overall best weight:    1.4122

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.178901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127241 restraints weight = 6981.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.86
r_work: 0.3255 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6884  Z= 0.165
  Angle     :  0.562   6.749   9240  Z= 0.288
  Chirality :  0.038   0.134   1086
  Planarity :  0.005   0.047   1024
  Dihedral  : 11.128  59.849   1884
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.55 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.30), residues: 752
  helix:  2.49 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.89 (0.41), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 169 
 TYR   0.016   0.002   TYR C  76 
 PHE   0.014   0.002   PHE C  33 
 TRP   0.009   0.001   TRP A 220 
 HIS   0.003   0.001   HIS C 300 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.16 ( 6868)
  covalent geometry    : angle       0.56197 /  0.29 ( 9236)
  SS BOND              : bond        0.00569 /  0.29 (    2)
  SS BOND              : angle       1.13891 /  0.60 (    4)
  hydrogen bonds       : bond        0.06109 /  4.11 (  442)
  hydrogen bonds       : angle       3.74099 /  2.71 ( 1314)
  Misc. bond           : bond        0.00034 /  0.02 (   14)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7073 (mtm-85)
REVERT: A   70 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6732 (tm-30)
REVERT: A  214 GLU cc_start: 0.7829 (pp20) cc_final: 0.7157 (pp20)
REVERT: A  289 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8358 (p)
REVERT: A  320 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7457 (mttt)
REVERT: C   44 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7054 (mtm-85)
REVERT: C   70 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6733 (tm-30)
REVERT: C  289 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8379 (p)
REVERT: C  320 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7453 (mttt)
  outliers start: 15
  outliers final: 14
  residues processed: 137
  average time/residue: 0.4856
  time to fit residues: 70.0208
Evaluate side-chains
  140 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  204 ASP
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  315 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0050
   chunk 14 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 ASN
A 178 GLN
C  78 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.181284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.129822 restraints weight = 6864.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.84
r_work: 0.3421 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6884  Z= 0.146
  Angle     :  0.559  14.507   9240  Z= 0.286
  Chirality :  0.037   0.186   1086
  Planarity :  0.005   0.045   1024
  Dihedral  : 10.754  59.762   1884
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 25.15 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.73 (0.30), residues: 752
  helix:  2.81 (0.21), residues: 574
  sheet:  None (None), residues: 0
  loop : -1.81 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 169 
 TYR   0.013   0.001   TYR A 123 
 PHE   0.014   0.001   PHE A  33 
 TRP   0.008   0.001   TRP B  26 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 6868)
  covalent geometry    : angle       0.55922 /  0.29 ( 9236)
  SS BOND              : bond        0.00415 /  0.21 (    2)
  SS BOND              : angle       0.81850 /  0.43 (    4)
  hydrogen bonds       : bond        0.05394 /  3.62 (  442)
  hydrogen bonds       : angle       3.59307 /  2.62 ( 1314)
  Misc. bond           : bond        0.00021 /  0.01 (   14)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2525.76 seconds
wall clock time: 43 minutes 47.99 seconds (2627.99 seconds total)