Starting phenix.real_space_refine
on Tue Aug  4 16:08:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rh2_53955/08_2026/9rh2_53955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rh2_53955/08_2026/9rh2_53955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rh2_53955/08_2026/9rh2_53955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rh2_53955/08_2026/9rh2_53955.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rh2_53955/08_2026/9rh2_53955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rh2_53955/08_2026/9rh2_53955.map"
  }
  resolution = 2.7
  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=   0.002
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      20      5.16       5
     C    3024      2.51       5
     N     758      2.21       5
     O     838      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4640
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 2917
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 15, 'TRANS': 372}
    Chain: "B"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 907
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "C"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 816
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101}
  Time building chain proxies: 0.80, per 1000 atoms: 0.17
  Number of scatterers: 4640
  At special positions: 0
  Unit cell: (68.634, 77.004, 102.114, 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      20     16.00
     O     838      8.00
     N     758      7.00
     C    3024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 121.9 milliseconds
  

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      54.9% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 7
      removed outlier: 3.704A  pdb=" N   ARG A   6 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 31
      removed outlier: 3.600A  pdb=" N   GLY A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 43
      removed outlier: 4.589A  pdb=" N   GLY A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   TRP A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 85
    Processing helix  chain 'A' and resid 86 through 89
      removed outlier: 3.739A  pdb=" N   ALA A  89 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 86 through 89'
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 4.935A  pdb=" N   PHE A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      Proline residue:  A 108  - end of helix
      removed outlier: 3.904A  pdb=" N   PHE A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.517A  pdb=" N   GLU A 124 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TRP A 126 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 131
      removed outlier: 3.530A  pdb=" N   ALA A 131 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 143
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 3.513A  pdb=" N   LYS A 153 " --> pdb=" O   PRO A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 200
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 3.643A  pdb=" N   TYR A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 237
      removed outlier: 3.750A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 262
      Proline residue:  A 257  - end of helix
    Processing helix  chain 'A' and resid 262 through 272
    Processing helix  chain 'A' and resid 282 through 285
    Processing helix  chain 'A' and resid 286 through 298
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 324 through 335
    Processing helix  chain 'A' and resid 338 through 351
    Processing helix  chain 'A' and resid 354 through 384
      removed outlier: 3.576A  pdb=" N   VAL A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.944A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.520A  pdb=" N   LYS B   3 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL B  18 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.911A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   LYS B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   TRP B  47 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   THR B  40 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   LEU B  45 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.786A  pdb=" N   CYS B  96 " --> pdb=" O   TRP B 108 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   TRP B 108 " --> pdb=" O   CYS B  96 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   LYS B  98 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.390A  pdb=" N   GLN C  37 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ARG C  46 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.677A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)

    301 hydrogen bonds defined for protein.
    831 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: 0.94

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1181
        1.33 -     1.45: 873
        1.45 -     1.57: 2657
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 4744
  Sorted by residual:
  bond pdb=" CA  SER A   9 "
       pdb=" CB  SER A   9 "
    ideal  model  delta    sigma   weight residual
    1.529  1.479  0.050 1.62e-02 3.81e+03 9.46e+00
  bond pdb=" N   SER A  10 "
       pdb=" CA  SER A  10 "
    ideal  model  delta    sigma   weight residual
    1.452  1.486 -0.034 1.25e-02 6.40e+03 7.39e+00
  bond pdb=" N   HIS A   5 "
       pdb=" CA  HIS A   5 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.31e-02 5.83e+03 7.37e+00
  bond pdb=" N   ASP A  11 "
       pdb=" CA  ASP A  11 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.28e-02 6.10e+03 6.31e+00
  bond pdb=" CA  ALA A  12 "
       pdb=" CB  ALA A  12 "
    ideal  model  delta    sigma   weight residual
    1.530  1.485  0.045 1.85e-02 2.92e+03 5.98e+00
  ... (remaining 4739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 6264
        1.64 -     3.27: 144
        3.27 -     4.91: 35
        4.91 -     6.55: 5
        6.55 -     8.19: 3
  Bond angle restraints: 6451
  Sorted by residual:
  angle pdb=" C   LYS A   2 "
        pdb=" N   HIS A   3 "
        pdb=" CA  HIS A   3 "
      ideal   model   delta    sigma   weight residual
     120.58  127.13   -6.55 1.71e+00 3.42e-01 1.47e+01
  angle pdb=" CA  ASP A  11 "
        pdb=" CB  ASP A  11 "
        pdb=" CG  ASP A  11 "
      ideal   model   delta    sigma   weight residual
     112.60  116.35   -3.75 1.00e+00 1.00e+00 1.41e+01
  angle pdb=" N   ALA A  12 "
        pdb=" CA  ALA A  12 "
        pdb=" C   ALA A  12 "
      ideal   model   delta    sigma   weight residual
     112.34  107.60    4.74 1.30e+00 5.92e-01 1.33e+01
  angle pdb=" CA  ARG C  66 "
        pdb=" C   ARG C  66 "
        pdb=" O   ARG C  66 "
      ideal   model   delta    sigma   weight residual
     121.33  117.49    3.84 1.08e+00 8.57e-01 1.26e+01
  angle pdb=" N   ILE C  29 "
        pdb=" CA  ILE C  29 "
        pdb=" C   ILE C  29 "
      ideal   model   delta    sigma   weight residual
     113.53  110.42    3.11 9.80e-01 1.04e+00 1.00e+01
  ... (remaining 6446 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.45: 2461
       14.45 -    28.91: 216
       28.91 -    43.36: 69
       43.36 -    57.81: 24
       57.81 -    72.27: 8
  Dihedral angle restraints: 2778
    sinusoidal: 1034
      harmonic: 1744
  Sorted by residual:
  dihedral pdb=" CA  ASN B 103 "
           pdb=" C   ASN B 103 "
           pdb=" N   ASP B 104 "
           pdb=" CA  ASP B 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  GLU B  99 "
           pdb=" C   GLU B  99 "
           pdb=" N   GLU B 100 "
           pdb=" CA  GLU B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.16   32.84     1      1.00e+01 1.00e-02 1.53e+01
  ... (remaining 2775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 650
       0.057 -    0.114: 100
       0.114 -    0.171: 9
       0.171 -    0.227: 1
       0.227 -    0.284: 2
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CA  ARG A   6 "
            pdb=" N   ARG A   6 "
            pdb=" C   ARG A   6 "
            pdb=" CB  ARG A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  ARG C  66 "
            pdb=" N   ARG C  66 "
            pdb=" C   ARG C  66 "
            pdb=" CB  ARG C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  LYS A   2 "
            pdb=" N   LYS A   2 "
            pdb=" C   LYS A   2 "
            pdb=" CB  LYS A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 759 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A   6 "    0.173 9.50e-02 1.11e+02   7.76e-02 3.74e+00
        pdb=" NE  ARG A   6 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A   6 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A   6 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  35 "    0.011 2.00e-02 2.50e+03   1.10e-02 3.00e+00
        pdb=" CG  TRP C  35 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  35 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  35 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  35 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  35 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 285 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.55e+00
        pdb=" C   THR A 285 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   THR A 285 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER A 286 "    0.009 2.00e-02 2.50e+03
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 506
        2.75 -     3.29: 4509
        3.29 -     3.82: 7846
        3.82 -     4.36: 9266
        4.36 -     4.90: 15932
  Nonbonded interactions: 38059
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 104 "
            pdb=" OG  SER C  34 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" CD1 ILE A 134 "
            pdb=" CB  ALA A 160 "
     model   vdw
     2.288 3.880
  nonbonded pdb=" O   ARG A   6 "
            pdb=" OG  SER A   9 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OH  TYR A  38 "
            pdb=" O   PHE A 269 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" O   PRO C   8 "
            pdb=" OG1 THR C 102 "
     model   vdw
     2.362 3.040
  ... (remaining 38054 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 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:             1.300
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.740
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
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      :  0.004   0.050   4746  Z= 0.210
  Angle     :  0.637   8.187   6455  Z= 0.372
  Chirality :  0.043   0.284    762
  Planarity :  0.004   0.078    794
  Dihedral  : 13.423  72.268   1660
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.15 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.08 (0.34), residues: 606
  helix:  1.44 (0.30), residues: 283
  sheet:  1.16 (0.47), residues: 119
  loop : -0.52 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 381 
 TYR   0.011   0.001   TYR C  49 
 PHE   0.016   0.002   PHE A 136 
 TRP   0.029   0.002   TRP C  35 
 HIS   0.004   0.001   HIS A   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.21 ( 4744)
  covalent geometry    : angle       0.63746 /  0.37 ( 6451)
  SS BOND              : bond        0.00221 /  0.12 (    2)
  SS BOND              : angle       0.24834 /  0.14 (    4)
  hydrogen bonds       : bond        0.20308 / 13.61 (  286)
  hydrogen bonds       : angle       7.33875 /  5.32 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7652 (tp) cc_final: 0.7165 (mt)
REVERT: A   84 MET cc_start: 0.8315 (mtm) cc_final: 0.8060 (ptm)
REVERT: A  176 THR cc_start: 0.8888 (p) cc_final: 0.8621 (t)
REVERT: A  177 ASN cc_start: 0.8373 (p0) cc_final: 0.8040 (p0)
REVERT: A  313 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6839 (mmm160)
REVERT: A  315 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8477 (mtmp)
REVERT: C   65 SER cc_start: 0.7688 (t) cc_final: 0.7396 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 84
  average time/residue: 0.4345
  time to fit residues: 37.9840
Evaluate side-chains
  71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN
A  93 GLN
A 177 ASN
A 326 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.170396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.096793 restraints weight = 5229.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.31
r_work: 0.2786 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4746  Z= 0.135
  Angle     :  0.560   6.821   6455  Z= 0.292
  Chirality :  0.040   0.154    762
  Planarity :  0.003   0.025    794
  Dihedral  :  4.447  20.096    653
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  :  9.96 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.80 (0.34), residues: 606
  helix:  2.15 (0.30), residues: 282
  sheet:  1.43 (0.49), residues: 113
  loop : -0.24 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 250 
 TYR   0.015   0.001   TYR C  49 
 PHE   0.013   0.001   PHE A 136 
 TRP   0.016   0.001   TRP C  35 
 HIS   0.004   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 4744)
  covalent geometry    : angle       0.56028 /  0.29 ( 6451)
  SS BOND              : bond        0.00364 /  0.17 (    2)
  SS BOND              : angle       0.59466 /  0.29 (    4)
  hydrogen bonds       : bond        0.04519 /  3.13 (  286)
  hydrogen bonds       : angle       5.16377 /  3.74 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7344 (tp) cc_final: 0.6864 (mt)
REVERT: A   54 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7986 (tt0)
REVERT: A  119 ASP cc_start: 0.8488 (t0) cc_final: 0.8265 (t0)
REVERT: A  177 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7992 (p0)
REVERT: A  313 ARG cc_start: 0.7777 (ttt180) cc_final: 0.7267 (mmm160)
REVERT: A  315 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8398 (mtmp)
REVERT: B  107 TYR cc_start: 0.7615 (m-10) cc_final: 0.7388 (m-10)
REVERT: C   65 SER cc_start: 0.7222 (t) cc_final: 0.6633 (p)
  outliers start: 16
  outliers final: 5
  residues processed: 80
  average time/residue: 0.3936
  time to fit residues: 32.9226
Evaluate side-chains
  74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   52 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 57 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 47 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.170898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.097005 restraints weight = 5245.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.33
r_work: 0.2793 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4746  Z= 0.121
  Angle     :  0.525   6.685   6455  Z= 0.271
  Chirality :  0.039   0.155    762
  Planarity :  0.003   0.026    794
  Dihedral  :  4.303  19.194    652
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 10.98 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.87 (0.34), residues: 606
  helix:  2.26 (0.30), residues: 282
  sheet:  1.42 (0.49), residues: 113
  loop : -0.26 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 250 
 TYR   0.012   0.001   TYR C  49 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.008   0.001   TRP C  35 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 4744)
  covalent geometry    : angle       0.52495 /  0.27 ( 6451)
  SS BOND              : bond        0.00233 /  0.11 (    2)
  SS BOND              : angle       0.33362 /  0.18 (    4)
  hydrogen bonds       : bond        0.04094 /  2.86 (  286)
  hydrogen bonds       : angle       4.94024 /  3.60 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7397 (tp) cc_final: 0.6849 (mt)
REVERT: A   54 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8008 (tt0)
REVERT: A  119 ASP cc_start: 0.8464 (t0) cc_final: 0.8211 (t0)
REVERT: A  313 ARG cc_start: 0.7728 (ttt180) cc_final: 0.7209 (mmm160)
REVERT: A  315 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8377 (mtmp)
REVERT: A  356 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7534 (pm20)
REVERT: A  383 ARG cc_start: 0.8079 (mmp80) cc_final: 0.7653 (mtp85)
REVERT: B   46 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6211 (mt-10)
REVERT: B   99 GLU cc_start: 0.6241 (pt0) cc_final: 0.5883 (pt0)
REVERT: B  107 TYR cc_start: 0.7550 (m-10) cc_final: 0.7275 (m-10)
REVERT: C   54 LEU cc_start: 0.8156 (mm) cc_final: 0.7767 (tp)
REVERT: C   65 SER cc_start: 0.7112 (t) cc_final: 0.6503 (p)
  outliers start: 13
  outliers final: 6
  residues processed: 76
  average time/residue: 0.4363
  time to fit residues: 34.5295
Evaluate side-chains
  74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   47 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 55 optimal weight:   30.0000
   chunk 51 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 ASN
A  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.171224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.097485 restraints weight = 5204.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.30
r_work: 0.2813 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4746  Z= 0.112
  Angle     :  0.510   6.381   6455  Z= 0.264
  Chirality :  0.039   0.155    762
  Planarity :  0.003   0.025    794
  Dihedral  :  4.175  19.530    652
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 10.57 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.94 (0.34), residues: 606
  helix:  2.21 (0.30), residues: 288
  sheet:  1.56 (0.48), residues: 109
  loop : -0.17 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.011   0.001   TYR C  49 
 PHE   0.009   0.001   PHE A  72 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 ( 4744)
  covalent geometry    : angle       0.51025 /  0.26 ( 6451)
  SS BOND              : bond        0.00232 /  0.11 (    2)
  SS BOND              : angle       0.26873 /  0.15 (    4)
  hydrogen bonds       : bond        0.03790 /  2.68 (  286)
  hydrogen bonds       : angle       4.80069 /  3.51 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7415 (tp) cc_final: 0.6853 (mt)
REVERT: A   54 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8016 (tt0)
REVERT: A   84 MET cc_start: 0.8303 (mtp) cc_final: 0.7990 (mmp)
REVERT: A  119 ASP cc_start: 0.8487 (t0) cc_final: 0.8225 (t0)
REVERT: A  313 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7218 (mmm160)
REVERT: A  315 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8466 (mmtm)
REVERT: A  356 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7447 (pm20)
REVERT: A  383 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7603 (mtp85)
REVERT: B   46 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6209 (mt-10)
REVERT: B  107 TYR cc_start: 0.7503 (m-10) cc_final: 0.7214 (m-10)
REVERT: C   54 LEU cc_start: 0.8161 (mm) cc_final: 0.7838 (tp)
REVERT: C   65 SER cc_start: 0.6939 (t) cc_final: 0.6358 (p)
REVERT: C   73 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7551 (mt)
  outliers start: 19
  outliers final: 10
  residues processed: 80
  average time/residue: 0.3930
  time to fit residues: 32.8357
Evaluate side-chains
  78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.171606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.097490 restraints weight = 5240.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.33
r_work: 0.2791 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2659 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4746  Z= 0.109
  Angle     :  0.496   5.608   6455  Z= 0.256
  Chirality :  0.038   0.127    762
  Planarity :  0.003   0.025    794
  Dihedral  :  4.126  21.542    652
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 11.38 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.05 (0.34), residues: 606
  helix:  2.26 (0.30), residues: 290
  sheet:  1.67 (0.48), residues: 109
  loop : -0.10 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.010   0.001   TYR C  49 
 PHE   0.009   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 4744)
  covalent geometry    : angle       0.49636 /  0.26 ( 6451)
  SS BOND              : bond        0.00209 /  0.10 (    2)
  SS BOND              : angle       0.27156 /  0.16 (    4)
  hydrogen bonds       : bond        0.03660 /  2.59 (  286)
  hydrogen bonds       : angle       4.70087 /  3.45 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7298 (tp) cc_final: 0.6774 (mt)
REVERT: A   82 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7588 (mp0)
REVERT: A   84 MET cc_start: 0.8327 (mtp) cc_final: 0.8057 (mmp)
REVERT: A  119 ASP cc_start: 0.8500 (t0) cc_final: 0.8223 (t0)
REVERT: A  313 ARG cc_start: 0.7796 (ttt180) cc_final: 0.7231 (mmm160)
REVERT: A  315 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8445 (mmtm)
REVERT: A  356 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7455 (pm20)
REVERT: A  383 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7611 (mtp85)
REVERT: B   46 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6270 (mt-10)
REVERT: B   81 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5227 (tpt)
REVERT: B  107 TYR cc_start: 0.7523 (m-10) cc_final: 0.7246 (m-10)
REVERT: C   54 LEU cc_start: 0.8176 (mm) cc_final: 0.7862 (tp)
REVERT: C   65 SER cc_start: 0.6897 (t) cc_final: 0.6324 (p)
REVERT: C   73 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7726 (mt)
  outliers start: 17
  outliers final: 9
  residues processed: 76
  average time/residue: 0.4106
  time to fit residues: 32.5462
Evaluate side-chains
  77 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    8.9990
   chunk 44 optimal weight:   20.0000
   chunk 57 optimal weight:    0.5980
   chunk 48 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    1.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.169373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.094974 restraints weight = 5238.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.34
r_work: 0.2708 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4746  Z= 0.157
  Angle     :  0.533   5.625   6455  Z= 0.273
  Chirality :  0.040   0.127    762
  Planarity :  0.003   0.026    794
  Dihedral  :  4.302  22.033    652
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 11.79 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.99 (0.34), residues: 606
  helix:  2.19 (0.31), residues: 288
  sheet:  1.74 (0.49), residues: 109
  loop : -0.14 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 203 
 TYR   0.013   0.001   TYR C  49 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.007   0.001   TRP C  35 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.16 ( 4744)
  covalent geometry    : angle       0.53276 /  0.27 ( 6451)
  SS BOND              : bond        0.00242 /  0.12 (    2)
  SS BOND              : angle       0.25396 /  0.14 (    4)
  hydrogen bonds       : bond        0.04121 /  2.89 (  286)
  hydrogen bonds       : angle       4.76453 /  3.50 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7226 (tp) cc_final: 0.6658 (mt)
REVERT: A   82 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7488 (mp0)
REVERT: A   84 MET cc_start: 0.8342 (mtp) cc_final: 0.8093 (mmp)
REVERT: A  119 ASP cc_start: 0.8437 (t0) cc_final: 0.8149 (t0)
REVERT: A  313 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7133 (mmm160)
REVERT: A  315 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8416 (mmtm)
REVERT: A  356 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7388 (pm20)
REVERT: A  383 ARG cc_start: 0.8043 (mmp80) cc_final: 0.7576 (mtp85)
REVERT: B   81 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5220 (tpt)
REVERT: B  107 TYR cc_start: 0.7484 (m-10) cc_final: 0.7178 (m-10)
REVERT: C   54 LEU cc_start: 0.8204 (mm) cc_final: 0.7916 (tp)
REVERT: C   65 SER cc_start: 0.7010 (t) cc_final: 0.6413 (p)
REVERT: C   73 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7677 (mt)
  outliers start: 18
  outliers final: 11
  residues processed: 75
  average time/residue: 0.4753
  time to fit residues: 37.1584
Evaluate side-chains
  78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 14 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.169172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.094998 restraints weight = 5208.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.33
r_work: 0.2719 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4746  Z= 0.149
  Angle     :  0.525   5.645   6455  Z= 0.270
  Chirality :  0.039   0.131    762
  Planarity :  0.003   0.026    794
  Dihedral  :  4.312  22.183    652
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 11.38 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.98 (0.34), residues: 606
  helix:  2.18 (0.30), residues: 288
  sheet:  1.75 (0.49), residues: 109
  loop : -0.15 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 203 
 TYR   0.013   0.001   TYR C  49 
 PHE   0.013   0.001   PHE A  72 
 TRP   0.009   0.001   TRP C  35 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 4744)
  covalent geometry    : angle       0.52492 /  0.27 ( 6451)
  SS BOND              : bond        0.00236 /  0.11 (    2)
  SS BOND              : angle       0.28290 /  0.16 (    4)
  hydrogen bonds       : bond        0.04010 /  2.81 (  286)
  hydrogen bonds       : angle       4.73699 /  3.49 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7220 (tp) cc_final: 0.6649 (mt)
REVERT: A   82 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7402 (mp0)
REVERT: A   84 MET cc_start: 0.8339 (mtp) cc_final: 0.8096 (mmp)
REVERT: A  119 ASP cc_start: 0.8444 (t0) cc_final: 0.8157 (t0)
REVERT: A  313 ARG cc_start: 0.7685 (ttt180) cc_final: 0.7107 (mmm160)
REVERT: A  315 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8416 (mmtm)
REVERT: A  356 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7419 (pm20)
REVERT: A  383 ARG cc_start: 0.8024 (mmp80) cc_final: 0.7524 (mtp85)
REVERT: B   81 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5257 (tpt)
REVERT: B  107 TYR cc_start: 0.7518 (m-10) cc_final: 0.7151 (m-10)
REVERT: C   54 LEU cc_start: 0.8189 (mm) cc_final: 0.7928 (tp)
REVERT: C   65 SER cc_start: 0.7064 (t) cc_final: 0.6443 (p)
REVERT: C   73 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (mt)
REVERT: C   89 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6975 (tp)
  outliers start: 20
  outliers final: 10
  residues processed: 79
  average time/residue: 0.4495
  time to fit residues: 37.0647
Evaluate side-chains
  83 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 55 optimal weight:   30.0000
   chunk 47 optimal weight:   20.0000
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    1.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.168593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.094481 restraints weight = 5304.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.34
r_work: 0.2716 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2583 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4746  Z= 0.165
  Angle     :  0.541   5.638   6455  Z= 0.277
  Chirality :  0.040   0.127    762
  Planarity :  0.003   0.026    794
  Dihedral  :  4.392  22.979    652
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.60 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.93 (0.34), residues: 606
  helix:  2.15 (0.31), residues: 287
  sheet:  1.75 (0.49), residues: 109
  loop : -0.20 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 203 
 TYR   0.014   0.001   TYR C  49 
 PHE   0.013   0.001   PHE A  72 
 TRP   0.008   0.001   TRP C  35 
 HIS   0.004   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.16 ( 4744)
  covalent geometry    : angle       0.54120 /  0.28 ( 6451)
  SS BOND              : bond        0.00269 /  0.13 (    2)
  SS BOND              : angle       0.22513 /  0.12 (    4)
  hydrogen bonds       : bond        0.04165 /  2.92 (  286)
  hydrogen bonds       : angle       4.75962 /  3.51 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7179 (tp) cc_final: 0.6674 (mt)
REVERT: A   82 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7424 (mp0)
REVERT: A   84 MET cc_start: 0.8320 (mtp) cc_final: 0.8096 (mmp)
REVERT: A  119 ASP cc_start: 0.8430 (t0) cc_final: 0.8160 (t0)
REVERT: A  313 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7085 (mmm160)
REVERT: A  315 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8421 (mmtm)
REVERT: A  356 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7434 (pm20)
REVERT: B   81 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5238 (tpt)
REVERT: B  107 TYR cc_start: 0.7516 (m-10) cc_final: 0.7182 (m-10)
REVERT: C   54 LEU cc_start: 0.8213 (mm) cc_final: 0.7959 (tp)
REVERT: C   65 SER cc_start: 0.7067 (t) cc_final: 0.6434 (p)
REVERT: C   73 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7617 (mt)
REVERT: C   89 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6984 (tp)
  outliers start: 18
  outliers final: 10
  residues processed: 75
  average time/residue: 0.4405
  time to fit residues: 34.5401
Evaluate side-chains
  82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  103 ASN
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0470
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.170998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.098066 restraints weight = 5174.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.27
r_work: 0.2754 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4746  Z= 0.101
  Angle     :  0.486   5.678   6455  Z= 0.251
  Chirality :  0.038   0.129    762
  Planarity :  0.003   0.027    794
  Dihedral  :  4.124  22.428    652
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 13.82 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.09 (0.34), residues: 606
  helix:  2.30 (0.30), residues: 288
  sheet:  1.81 (0.49), residues: 109
  loop : -0.16 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  81 
 TYR   0.010   0.001   TYR C  49 
 PHE   0.008   0.001   PHE A  72 
 TRP   0.011   0.001   TRP A 216 
 HIS   0.002   0.000   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 ( 4744)
  covalent geometry    : angle       0.48582 /  0.25 ( 6451)
  SS BOND              : bond        0.00245 /  0.12 (    2)
  SS BOND              : angle       0.22523 /  0.10 (    4)
  hydrogen bonds       : bond        0.03531 /  2.51 (  286)
  hydrogen bonds       : angle       4.63862 /  3.42 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7239 (tp) cc_final: 0.6731 (mt)
REVERT: A   82 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7452 (mp0)
REVERT: A  119 ASP cc_start: 0.8479 (t0) cc_final: 0.8203 (t0)
REVERT: A  181 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8195 (mmp)
REVERT: A  313 ARG cc_start: 0.7742 (ttt180) cc_final: 0.7138 (mmm160)
REVERT: A  315 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8435 (mmtm)
REVERT: A  356 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7449 (pm20)
REVERT: B   81 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5230 (tpt)
REVERT: B  107 TYR cc_start: 0.7493 (m-10) cc_final: 0.7190 (m-10)
REVERT: C   54 LEU cc_start: 0.8153 (mm) cc_final: 0.7919 (tp)
REVERT: C   65 SER cc_start: 0.6859 (t) cc_final: 0.6240 (p)
REVERT: C   73 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7689 (mt)
REVERT: C   89 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6915 (tp)
  outliers start: 13
  outliers final: 4
  residues processed: 73
  average time/residue: 0.3692
  time to fit residues: 28.0469
Evaluate side-chains
  78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.170712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.097055 restraints weight = 5199.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 2.33
r_work: 0.2741 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4746  Z= 0.109
  Angle     :  0.489   5.697   6455  Z= 0.251
  Chirality :  0.038   0.127    762
  Planarity :  0.003   0.026    794
  Dihedral  :  4.099  21.736    652
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.62 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.09 (0.34), residues: 606
  helix:  2.30 (0.30), residues: 288
  sheet:  1.82 (0.49), residues: 109
  loop : -0.15 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.010   0.001   TYR C  49 
 PHE   0.009   0.001   PHE A  72 
 TRP   0.009   0.001   TRP C  35 
 HIS   0.002   0.000   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 4744)
  covalent geometry    : angle       0.48929 /  0.25 ( 6451)
  SS BOND              : bond        0.00243 /  0.12 (    2)
  SS BOND              : angle       0.20092 /  0.11 (    4)
  hydrogen bonds       : bond        0.03569 /  2.54 (  286)
  hydrogen bonds       : angle       4.62084 /  3.41 (  831)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   53 LEU cc_start: 0.7224 (tp) cc_final: 0.6700 (mt)
REVERT: A   82 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7453 (mp0)
REVERT: A  119 ASP cc_start: 0.8450 (t0) cc_final: 0.8158 (t0)
REVERT: A  181 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8205 (mmp)
REVERT: A  313 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7138 (mmm160)
REVERT: A  315 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8423 (mmtm)
REVERT: A  356 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7407 (pm20)
REVERT: B   81 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5221 (tpt)
REVERT: B  107 TYR cc_start: 0.7468 (m-10) cc_final: 0.7106 (m-10)
REVERT: C   54 LEU cc_start: 0.8127 (mm) cc_final: 0.7892 (tp)
REVERT: C   65 SER cc_start: 0.6855 (t) cc_final: 0.6219 (p)
REVERT: C   73 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7639 (mt)
REVERT: C   89 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6863 (tp)
  outliers start: 12
  outliers final: 4
  residues processed: 73
  average time/residue: 0.4041
  time to fit residues: 30.7044
Evaluate side-chains
  79 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   89 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0570
   chunk 36 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.9502

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.170204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.097077 restraints weight = 5228.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 2.27
r_work: 0.2734 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4746  Z= 0.116
  Angle     :  0.495   5.714   6455  Z= 0.254
  Chirality :  0.038   0.127    762
  Planarity :  0.003   0.026    794
  Dihedral  :  4.107  21.329    652
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.21 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.08 (0.34), residues: 606
  helix:  2.29 (0.30), residues: 288
  sheet:  1.78 (0.49), residues: 109
  loop : -0.14 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 203 
 TYR   0.011   0.001   TYR C  49 
 PHE   0.009   0.001   PHE A  72 
 TRP   0.012   0.001   TRP C  35 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 4744)
  covalent geometry    : angle       0.49530 /  0.25 ( 6451)
  SS BOND              : bond        0.00249 /  0.12 (    2)
  SS BOND              : angle       0.27887 /  0.14 (    4)
  hydrogen bonds       : bond        0.03657 /  2.60 (  286)
  hydrogen bonds       : angle       4.62664 /  3.41 (  831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1784.89 seconds
wall clock time: 31 minutes 4.09 seconds (1864.09 seconds total)