Starting phenix.real_space_refine
on Thu Mar  6 01:23:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5msh_3565/03_2025/5msh_3565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5msh_3565/03_2025/5msh_3565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5msh_3565/03_2025/5msh_3565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5msh_3565/03_2025/5msh_3565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5msh_3565/03_2025/5msh_3565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5msh_3565/03_2025/5msh_3565.cif"
  }
  resolution = 4.25
  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=   0.003 sd=   0.022
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      31      5.16       5
     C    2732      2.51       5
     N     719      2.21       5
     O     805      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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4287
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1422
          Classifications: {'peptide': 182}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 163}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2865
          Classifications: {'peptide': 369}
          Link IDs: {'PTRANS': 14, 'TRANS': 354}
  Time building chain proxies: 4.67, per 1000 atoms: 1.09
  Number of scatterers: 4287
  At special positions: 0
  Unit cell: (92.4, 74.8, 99, 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      31     16.00
     O     805      8.00
     N     719      7.00
     C    2732      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 545.5 milliseconds
  

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1022

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      12.9% alpha, 46.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 61
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 20 through 22
      No H-bonds generated for 'chain 'B' and resid 20 through 22'
    Processing helix  chain 'B' and resid 48 through 52
    Processing helix  chain 'B' and resid 58 through 65
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 137 through 144
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 277 through 281
    Processing helix  chain 'B' and resid 300 through 304
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51
      removed outlier: 5.732A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
      removed outlier: 5.732A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA A  63 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ASN A 174 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41
      removed outlier: 3.654A  pdb=" N   ARG A 106 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32
      removed outlier: 5.989A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE B 172 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46
      removed outlier: 6.330A  pdb=" N   VAL B 150 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ASP B  44 " --> pdb=" O   MET B 148 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   MET B 148 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   CYS B  87 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP B 111 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202
      removed outlier: 8.083A  pdb=" N   GLN B 188 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   GLY B 356 " --> pdb=" O   GLN B 188 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TRP B 190 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   PHE B 354 " --> pdb=" O   TRP B 190 " (cutoff:3.500A)
      removed outlier: 9.516A  pdb=" N   LYS B 352 " --> pdb=" O   PRO B 192 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   ASN B 194 " --> pdb=" O   GLY B 350 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   GLY B 350 " --> pdb=" O   ASN B 194 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   TRP B 196 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU B 348 " --> pdb=" O   TRP B 196 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   LYS B 347 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   THR B 251 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL B 349 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   GLU B 249 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ILE B 351 " --> pdb=" O   HIS B 247 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   HIS B 247 " --> pdb=" O   ILE B 351 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ASP B 353 " --> pdb=" O   GLU B 245 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   GLU B 245 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202
      removed outlier: 8.083A  pdb=" N   GLN B 188 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   GLY B 356 " --> pdb=" O   GLN B 188 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TRP B 190 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   PHE B 354 " --> pdb=" O   TRP B 190 " (cutoff:3.500A)
      removed outlier: 9.516A  pdb=" N   LYS B 352 " --> pdb=" O   PRO B 192 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   ASN B 194 " --> pdb=" O   GLY B 350 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   GLY B 350 " --> pdb=" O   ASN B 194 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   TRP B 196 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU B 348 " --> pdb=" O   TRP B 196 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   LYS B 347 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   THR B 251 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL B 349 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   GLU B 249 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ILE B 351 " --> pdb=" O   HIS B 247 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   HIS B 247 " --> pdb=" O   ILE B 351 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ASP B 353 " --> pdb=" O   GLU B 245 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   GLU B 245 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214

    174 hydrogen bonds defined for protein.
    417 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: 1.28

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1083
        1.32 -     1.45: 1049
        1.45 -     1.57: 2218
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 4398
  Sorted by residual:
  bond pdb=" N   PRO A  13 "
       pdb=" CA  PRO A  13 "
    ideal  model  delta    sigma   weight residual
    1.466  1.406  0.059 1.19e-02 7.06e+03 2.48e+01
  bond pdb=" N   PRO B 282 "
       pdb=" CA  PRO B 282 "
    ideal  model  delta    sigma   weight residual
    1.467  1.418  0.048 1.17e-02 7.31e+03 1.72e+01
  bond pdb=" N   PRO B 214 "
       pdb=" CA  PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.466  1.420  0.046 1.19e-02 7.06e+03 1.48e+01
  bond pdb=" N   PRO A 181 "
       pdb=" CA  PRO A 181 "
    ideal  model  delta    sigma   weight residual
    1.467  1.421  0.046 1.21e-02 6.83e+03 1.47e+01
  bond pdb=" N   PRO B 324 "
       pdb=" CA  PRO B 324 "
    ideal  model  delta    sigma   weight residual
    1.466  1.424  0.042 1.19e-02 7.06e+03 1.22e+01
  ... (remaining 4393 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 4957
        1.80 -     3.61: 783
        3.61 -     5.41: 178
        5.41 -     7.22: 53
        7.22 -     9.02: 19
  Bond angle restraints: 5990
  Sorted by residual:
  angle pdb=" CA  ARG A  77 "
        pdb=" C   ARG A  77 "
        pdb=" O   ARG A  77 "
      ideal   model   delta    sigma   weight residual
     120.80  113.22    7.58 1.11e+00 8.12e-01 4.67e+01
  angle pdb=" C   GLY A 126 "
        pdb=" N   PRO A 127 "
        pdb=" CA  PRO A 127 "
      ideal   model   delta    sigma   weight residual
     119.64  125.81   -6.17 1.01e+00 9.80e-01 3.73e+01
  angle pdb=" C   GLY A   1 "
        pdb=" N   PRO A   2 "
        pdb=" CA  PRO A   2 "
      ideal   model   delta    sigma   weight residual
     119.56  125.71   -6.15 1.01e+00 9.80e-01 3.71e+01
  angle pdb=" C   GLU B 178 "
        pdb=" N   PRO B 179 "
        pdb=" CA  PRO B 179 "
      ideal   model   delta    sigma   weight residual
     120.31  126.08   -5.77 9.80e-01 1.04e+00 3.46e+01
  angle pdb=" C   ASN A 152 "
        pdb=" N   PRO A 153 "
        pdb=" CA  PRO A 153 "
      ideal   model   delta    sigma   weight residual
     119.84  127.08   -7.24 1.25e+00 6.40e-01 3.35e+01
  ... (remaining 5985 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 2515
       17.09 -    34.18: 44
       34.18 -    51.27: 11
       51.27 -    68.36: 7
       68.36 -    85.44: 6
  Dihedral angle restraints: 2583
    sinusoidal: 998
      harmonic: 1585
  Sorted by residual:
  dihedral pdb=" CA  ARG A  77 "
           pdb=" C   ARG A  77 "
           pdb=" N   GLY A  78 "
           pdb=" CA  GLY A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   36.50  -36.50     0      5.00e+00 4.00e-02 5.33e+01
  dihedral pdb=" C   HIS B  66 "
           pdb=" N   HIS B  66 "
           pdb=" CA  HIS B  66 "
           pdb=" CB  HIS B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.97    9.37     0      2.50e+00 1.60e-01 1.40e+01
  dihedral pdb=" N   HIS B  66 "
           pdb=" C   HIS B  66 "
           pdb=" CA  HIS B  66 "
           pdb=" CB  HIS B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.11   -8.31     0      2.50e+00 1.60e-01 1.11e+01
  ... (remaining 2580 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 505
       0.083 -    0.166: 141
       0.166 -    0.249: 17
       0.249 -    0.333: 2
       0.333 -    0.416: 1
  Chirality restraints: 666
  Sorted by residual:
  chirality pdb=" CA  HIS B  66 "
            pdb=" N   HIS B  66 "
            pdb=" C   HIS B  66 "
            pdb=" CB  HIS B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.32e+00
  chirality pdb=" CA  MET B 231 "
            pdb=" N   MET B 231 "
            pdb=" C   MET B 231 "
            pdb=" CB  MET B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CA  ASN B 233 "
            pdb=" N   ASN B 233 "
            pdb=" C   ASN B 233 "
            pdb=" CB  ASN B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 663 not shown)

  Planarity restraints: 772
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  77 "   -0.061 2.00e-02 2.50e+03   1.25e-01 1.56e+02
        pdb=" C   ARG A  77 "    0.216 2.00e-02 2.50e+03
        pdb=" O   ARG A  77 "   -0.080 2.00e-02 2.50e+03
        pdb=" N   GLY A  78 "   -0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 128 "    0.052 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO B 129 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "    0.036 2.00e-02 2.50e+03   1.75e-02 7.62e+00
        pdb=" CG  TRP A  47 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "    0.017 2.00e-02 2.50e+03
  ... (remaining 769 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1481
        2.84 -     3.35: 3794
        3.35 -     3.87: 7265
        3.87 -     4.38: 8569
        4.38 -     4.90: 14240
  Nonbonded interactions: 35349
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 128 "
            pdb=" OD1 ASN B 128 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" N   GLU B 279 "
            pdb=" OE1 GLU B 279 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" OG  SER B 366 "
            pdb=" N   ARG B 367 "
     model   vdw
     2.420 3.120
  nonbonded pdb=" O   PHE A 133 "
            pdb=" CD1 PHE A 133 "
     model   vdw
     2.429 3.340
  nonbonded pdb=" N   GLU A 101 "
            pdb=" OE1 GLU A 101 "
     model   vdw
     2.467 3.120
  ... (remaining 35344 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:             5.920
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.290
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0197
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      :  0.014   0.059   4398  Z= 0.942
  Angle     :  1.562   9.020   5990  Z= 1.032
  Chirality :  0.074   0.416    666
  Planarity :  0.009   0.125    772
  Dihedral  :  9.556  85.444   1561
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  1.47 %
    Allowed  :  6.06 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -0.93 (0.34), residues: 545
  helix: -2.30 (0.58), residues: 57
  sheet:  0.82 (0.38), residues: 181
  loop : -1.20 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.005   TRP A  47 
 HIS   0.003   0.001   HIS B 247 
 PHE   0.026   0.004   PHE B 202 
 TYR   0.031   0.005   TYR B 100 
 ARG   0.004   0.001   ARG B 367 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.6148 (tttt) cc_final: 0.4973 (mtmm)
REVERT: A   89 GLN cc_start: 0.3743 (mt0) cc_final: 0.3304 (pt0)
REVERT: B   24 LYS cc_start: -0.1135 (mttm) cc_final: -0.1570 (mttt)
REVERT: B  200 LEU cc_start: 0.3159 (mt) cc_final: 0.2814 (mp)
REVERT: B  347 LYS cc_start: 0.5153 (ttpt) cc_final: 0.4869 (pttt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.2408
  time to fit residues: 18.7271
Evaluate side-chains
  42 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:   20.0000
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0470
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 31 optimal weight:   30.0000
   chunk 49 optimal weight:    6.9990
   overall best weight:    3.9884

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

Flipped N/Q/H residues before XYZ refinement:
B 110 GLN
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5335 r_free = 0.5335 target = 0.307616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.302637 restraints weight = 8549.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.304218 restraints weight = 5559.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.5316 r_free = 0.5316 target = 0.305395 restraints weight = 3749.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.5317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0487
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4398  Z= 0.196
  Angle     :  0.684   7.865   5990  Z= 0.368
  Chirality :  0.049   0.157    666
  Planarity :  0.005   0.045    772
  Dihedral  :  5.341  28.245    587
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.85 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.50 (0.34), residues: 545
  helix: -1.43 (0.69), residues: 52
  sheet:  0.73 (0.40), residues: 176
  loop : -0.75 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  47 
 HIS   0.006   0.002   HIS A  50 
 PHE   0.013   0.002   PHE A 133 
 TYR   0.012   0.002   TYR B 278 
 ARG   0.004   0.001   ARG B 143 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.496 
Fit side-chains
REVERT: B    2 GLU cc_start: -0.0103 (mt-10) cc_final: -0.0572 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1909
  time to fit residues: 12.1810
Evaluate side-chains
  31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 28 optimal weight:   50.0000
   chunk 19 optimal weight:   30.0000
   chunk 46 optimal weight:   20.0000
   chunk 31 optimal weight:   50.0000
   chunk 25 optimal weight:   50.0000
   chunk 36 optimal weight:   50.0000
   chunk 53 optimal weight:   40.0000
   chunk 34 optimal weight:   50.0000
   chunk 43 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:   14.9994

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5271 r_free = 0.5271 target = 0.301109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.5249 r_free = 0.5249 target = 0.298970 restraints weight = 8673.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.5254 r_free = 0.5254 target = 0.299429 restraints weight = 6582.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5255 r_free = 0.5255 target = 0.299603 restraints weight = 5119.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.5255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1343
moved from start:          0.5182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.095   4398  Z= 0.449
  Angle     :  0.999  22.549   5990  Z= 0.538
  Chirality :  0.061   0.541    666
  Planarity :  0.009   0.106    772
  Dihedral  :  6.695  29.899    587
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  5.50 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  2.95 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.89 (0.34), residues: 545
  helix: -1.42 (0.73), residues: 51
  sheet:  0.37 (0.41), residues: 170
  loop : -0.99 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A  86 
 HIS   0.019   0.004   HIS A  50 
 PHE   0.041   0.003   PHE A  32 
 TYR   0.024   0.003   TYR A  52 
 ARG   0.020   0.002   ARG B  97 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A   44 ASP cc_start: 0.2942 (OUTLIER) cc_final: 0.1178 (t0)
REVERT: A   87 ASP cc_start: 0.5908 (p0) cc_final: 0.5701 (p0)
REVERT: A  164 ARG cc_start: 0.0066 (tpm170) cc_final: -0.2417 (tpt-90)
REVERT: B    2 GLU cc_start: -0.0199 (mt-10) cc_final: -0.0554 (tm-30)
REVERT: B  343 ASN cc_start: -0.1315 (m-40) cc_final: -0.1566 (m-40)
  outliers start: 3
  outliers final: 2
  residues processed: 52
  average time/residue: 0.1554
  time to fit residues: 10.8081
Evaluate side-chains
  42 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:   50.0000
   chunk 22 optimal weight:   40.0000
   chunk 38 optimal weight:   50.0000
   chunk 12 optimal weight:    9.9990
   chunk 51 optimal weight:   50.0000
   chunk 40 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 48 optimal weight:   40.0000
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 52 optimal weight:    0.5980
   overall best weight:    7.1190

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.300692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.300406 restraints weight = 8709.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.300459 restraints weight = 6731.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.300504 restraints weight = 4530.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.5259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1240
moved from start:          0.5621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4398  Z= 0.222
  Angle     :  0.681   9.092   5990  Z= 0.367
  Chirality :  0.048   0.229    666
  Planarity :  0.006   0.050    772
  Dihedral  :  5.739  28.060    587
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.59 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.98 (0.34), residues: 545
  helix: -1.43 (0.70), residues: 51
  sheet:  0.06 (0.38), residues: 188
  loop : -0.94 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  86 
 HIS   0.003   0.001   HIS A  50 
 PHE   0.019   0.002   PHE A  24 
 TYR   0.021   0.002   TYR A  93 
 ARG   0.003   0.001   ARG A 154 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.6762 (tppt) cc_final: 0.6137 (ptpp)
REVERT: A  163 MET cc_start: -0.0835 (mmm) cc_final: -0.2886 (tmm)
REVERT: B   24 LYS cc_start: -0.0974 (mttm) cc_final: -0.2371 (pttt)
REVERT: B  113 MET cc_start: 0.2354 (ttp) cc_final: 0.1933 (tmm)
REVERT: B  199 LYS cc_start: -0.1762 (tttt) cc_final: -0.2120 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1926
  time to fit residues: 12.1925
Evaluate side-chains
  38 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 33 optimal weight:   50.0000
   chunk 9 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:   50.0000
   chunk 46 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.5258 r_free = 0.5258 target = 0.299908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5257 r_free = 0.5257 target = 0.299819 restraints weight = 8799.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5257 r_free = 0.5257 target = 0.299842 restraints weight = 6086.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5257 r_free = 0.5257 target = 0.299842 restraints weight = 4144.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.5257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1337
moved from start:          0.6239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4398  Z= 0.220
  Angle     :  0.669   9.398   5990  Z= 0.358
  Chirality :  0.048   0.210    666
  Planarity :  0.006   0.052    772
  Dihedral  :  5.448  28.752    587
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.24 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.05 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.94 (0.35), residues: 545
  helix: -1.05 (0.73), residues: 51
  sheet: -0.00 (0.38), residues: 189
  loop : -0.91 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  86 
 HIS   0.008   0.001   HIS A  50 
 PHE   0.017   0.002   PHE A  24 
 TYR   0.016   0.002   TYR A  93 
 ARG   0.006   0.001   ARG B 195 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A   44 ASP cc_start: 0.2725 (OUTLIER) cc_final: 0.0503 (t0)
REVERT: A  163 MET cc_start: -0.0502 (mmm) cc_final: -0.2680 (tmm)
REVERT: B  140 MET cc_start: 0.3049 (tpt) cc_final: 0.2709 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1462
  time to fit residues: 8.6758
Evaluate side-chains
  39 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.0070
   chunk 38 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 6 optimal weight:   50.0000
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    3.0006

-------------------------------------------------------------------------------
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 = 0.5270 r_free = 0.5270 target = 0.301509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.5215 r_free = 0.5215 target = 0.295987 restraints weight = 8430.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.5227 r_free = 0.5227 target = 0.297143 restraints weight = 6111.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.5235 r_free = 0.5235 target = 0.297965 restraints weight = 4538.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.5235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1336
moved from start:          0.6400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4398  Z= 0.154
  Angle     :  0.568   5.862   5990  Z= 0.302
  Chirality :  0.045   0.170    666
  Planarity :  0.005   0.051    772
  Dihedral  :  4.881  23.775    587
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.14 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.65 (0.35), residues: 545
  helix: -0.75 (0.83), residues: 45
  sheet:  0.06 (0.39), residues: 192
  loop : -0.65 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  47 
 HIS   0.001   0.000   HIS B  66 
 PHE   0.016   0.002   PHE B  62 
 TYR   0.014   0.001   TYR A 145 
 ARG   0.008   0.000   ARG A 164 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   46 ASN cc_start: 0.4510 (m110) cc_final: 0.2795 (t0)
REVERT: B   59 THR cc_start: 0.4008 (t) cc_final: 0.3748 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1456
  time to fit residues: 8.7065
Evaluate side-chains
  36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 16 optimal weight:    8.9990
   chunk 48 optimal weight:   40.0000
   chunk 33 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 46 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 45 optimal weight:   10.0000
   chunk 35 optimal weight:   30.0000
   chunk 17 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    7.2388

-------------------------------------------------------------------------------
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 = 0.5268 r_free = 0.5268 target = 0.300415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.5240 r_free = 0.5240 target = 0.297843 restraints weight = 8533.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.298286 restraints weight = 6532.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5246 r_free = 0.5246 target = 0.298480 restraints weight = 5354.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.5246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1518
moved from start:          0.6987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4398  Z= 0.241
  Angle     :  0.684  10.053   5990  Z= 0.363
  Chirality :  0.049   0.183    666
  Planarity :  0.006   0.050    772
  Dihedral  :  5.429  27.871    587
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.79 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.91 (0.35), residues: 545
  helix: -0.75 (0.89), residues: 39
  sheet: -0.15 (0.38), residues: 196
  loop : -0.85 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  86 
 HIS   0.011   0.002   HIS A  50 
 PHE   0.018   0.002   PHE A  91 
 TYR   0.019   0.002   TYR A  93 
 ARG   0.004   0.001   ARG B  17 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.436 
Fit side-chains
REVERT: B   59 THR cc_start: 0.4073 (t) cc_final: 0.3819 (t)
REVERT: B  136 TRP cc_start: -0.0043 (p-90) cc_final: -0.0574 (p-90)
REVERT: B  199 LYS cc_start: -0.1788 (tttt) cc_final: -0.2061 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1810
  time to fit residues: 10.1240
Evaluate side-chains
  38 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 37 optimal weight:   30.0000
   chunk 44 optimal weight:   30.0000
   chunk 6 optimal weight:   40.0000
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.5272 r_free = 0.5272 target = 0.300530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.5243 r_free = 0.5243 target = 0.297907 restraints weight = 8408.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.5248 r_free = 0.5248 target = 0.298434 restraints weight = 6059.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5250 r_free = 0.5250 target = 0.298594 restraints weight = 4876.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.5250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1415
moved from start:          0.7146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4398  Z= 0.161
  Angle     :  0.576   6.213   5990  Z= 0.305
  Chirality :  0.045   0.157    666
  Planarity :  0.005   0.052    772
  Dihedral  :  4.937  23.077    587
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.50 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -0.78 (0.35), residues: 545
  helix: -1.08 (0.80), residues: 45
  sheet:  0.01 (0.38), residues: 196
  loop : -0.73 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 190 
 HIS   0.002   0.001   HIS A  50 
 PHE   0.013   0.002   PHE A 180 
 TYR   0.014   0.001   TYR A 145 
 ARG   0.003   0.001   ARG A  61 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   46 ASN cc_start: 0.3732 (m110) cc_final: 0.2850 (t0)
REVERT: B  136 TRP cc_start: -0.0204 (p-90) cc_final: -0.0681 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1512
  time to fit residues: 8.1462
Evaluate side-chains
  36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:   30.0000
   chunk 24 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 14 optimal weight:   20.0000
   chunk 18 optimal weight:   40.0000
   chunk 13 optimal weight:   30.0000
   chunk 39 optimal weight:   50.0000
   chunk 23 optimal weight:   20.0000
   chunk 45 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9990
   overall best weight:   10.2190

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
A 157 GLN
B  66 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.298088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.298064 restraints weight = 8694.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.298068 restraints weight = 6254.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.298069 restraints weight = 4501.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.5245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1672
moved from start:          0.8053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   4398  Z= 0.322
  Angle     :  0.821  13.752   5990  Z= 0.437
  Chirality :  0.053   0.192    666
  Planarity :  0.007   0.066    772
  Dihedral  :  6.135  35.195    587
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.52 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.24 (0.35), residues: 545
  helix: -1.51 (0.76), residues: 45
  sheet: -0.05 (0.41), residues: 171
  loop : -1.15 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  86 
 HIS   0.011   0.002   HIS A  50 
 PHE   0.030   0.003   PHE A  91 
 TYR   0.025   0.003   TYR A  93 
 ARG   0.007   0.001   ARG A  77 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.448 
Fit side-chains
REVERT: B  136 TRP cc_start: 0.0229 (p-90) cc_final: -0.0316 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1750
  time to fit residues: 9.4425
Evaluate side-chains
  35 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:   50.0000
   chunk 44 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:   40.0000
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 35 optimal weight:   30.0000
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.299950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5255 r_free = 0.5255 target = 0.299701 restraints weight = 8538.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.299744 restraints weight = 6150.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.299764 restraints weight = 4190.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.5256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1488
moved from start:          0.8018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4398  Z= 0.174
  Angle     :  0.617   7.359   5990  Z= 0.327
  Chirality :  0.047   0.162    666
  Planarity :  0.006   0.051    772
  Dihedral  :  5.219  26.178    587
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.69 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -1.30 (0.34), residues: 545
  helix: -1.70 (0.69), residues: 52
  sheet: -0.30 (0.38), residues: 194
  loop : -1.04 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  47 
 HIS   0.002   0.001   HIS A  50 
 PHE   0.018   0.002   PHE B  62 
 TYR   0.015   0.002   TYR A 145 
 ARG   0.003   0.000   ARG B  97 

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.477 
Fit side-chains
REVERT: B   89 MET cc_start: -0.2799 (tmm) cc_final: -0.4323 (tmm)
REVERT: B  136 TRP cc_start: 0.0305 (p-90) cc_final: -0.0217 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1596
  time to fit residues: 7.6032
Evaluate side-chains
  33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:   50.0000
   chunk 18 optimal weight:    0.0470
   chunk 31 optimal weight:   20.0000
   chunk 28 optimal weight:   50.0000
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0050
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:   40.0000
   chunk 12 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.4098

-------------------------------------------------------------------------------
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 = 0.5276 r_free = 0.5276 target = 0.301523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.301287 restraints weight = 8615.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.301287 restraints weight = 6873.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.301287 restraints weight = 6873.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.5274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1357
moved from start:          0.7995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4398  Z= 0.141
  Angle     :  0.571   5.984   5990  Z= 0.299
  Chirality :  0.046   0.172    666
  Planarity :  0.005   0.053    772
  Dihedral  :  4.520  19.381    587
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.24 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.19 %
    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: -1.12 (0.35), residues: 545
  helix: -1.50 (0.72), residues: 51
  sheet: -0.23 (0.39), residues: 196
  loop : -0.91 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  47 
 HIS   0.002   0.000   HIS A  50 
 PHE   0.015   0.001   PHE A 159 
 TYR   0.014   0.001   TYR A 145 
 ARG   0.004   0.000   ARG A  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1774.69 seconds
wall clock time: 31 minutes 54.36 seconds (1914.36 seconds total)