Starting phenix.real_space_refine
on Tue Aug  4 15:59:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rhd_53966/08_2026/9rhd_53966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rhd_53966/08_2026/9rhd_53966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rhd_53966/08_2026/9rhd_53966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rhd_53966/08_2026/9rhd_53966.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rhd_53966/08_2026/9rhd_53966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rhd_53966/08_2026/9rhd_53966.cif"
  }
  resolution = 3.2
  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      19      5.16       5
     C    2989      2.51       5
     N     744      2.21       5
     O     832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  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: 4584
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2861
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 15, 'TRANS': 366}
    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: 1.19, per 1000 atoms: 0.26
  Number of scatterers: 4584
  At special positions: 0
  Unit cell: (69.471, 79.515, 100.44, 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      19     16.00
     O     832      8.00
     N     744      7.00
     C    2989      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: 0.38
  Conformation dependent library (CDL) restraints added in 164.9 milliseconds
  

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      53.6% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 31
      removed outlier: 4.229A  pdb=" N   GLY A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 43
      removed outlier: 4.605A  pdb=" N   GLY A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
      removed outlier: 4.891A  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 90 through 117
      removed outlier: 4.810A  pdb=" N   PHE A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      removed outlier: 3.588A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
      removed outlier: 3.925A  pdb=" N   PHE A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.553A  pdb=" N   GLU A 124 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP A 126 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 131
      removed outlier: 3.508A  pdb=" N   ALA A 131 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
      removed outlier: 3.955A  pdb=" N   LEU A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 148
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 3.512A  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: 3.587A  pdb=" N   TYR A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 237
      removed outlier: 3.763A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (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: 3.680A  pdb=" N   VAL A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.953A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.340A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.525A  pdb=" N   CYS B  96 " --> pdb=" O   TRP B 108 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   TRP B 108 " --> pdb=" O   CYS B  96 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   LYS B  98 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 5
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.843A  pdb=" N   LEU C  33 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   TYR C  49 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    825 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: 0.69

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1424
        1.35 -     1.46: 1132
        1.46 -     1.58: 2099
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 4686
  Sorted by residual:
  bond pdb=" N   VAL A 148 "
       pdb=" CA  VAL A 148 "
    ideal  model  delta    sigma   weight residual
    1.462  1.496 -0.035 1.04e-02 9.25e+03 1.12e+01
  bond pdb=" N   GLU B 100 "
       pdb=" CA  GLU B 100 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.23e-02 6.61e+03 8.49e+00
  bond pdb=" N   LEU A 144 "
       pdb=" CA  LEU A 144 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.18e-02 7.18e+03 7.82e+00
  bond pdb=" N   GLU B  99 "
       pdb=" CA  GLU B  99 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.21e-02 6.83e+03 7.33e+00
  bond pdb=" N   ARG A 147 "
       pdb=" CA  ARG A 147 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.032 1.32e-02 5.74e+03 5.81e+00
  ... (remaining 4681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 6257
        2.30 -     4.60: 95
        4.60 -     6.90: 20
        6.90 -     9.20: 2
        9.20 -    11.50: 1
  Bond angle restraints: 6375
  Sorted by residual:
  angle pdb=" C   TYR B 101 "
        pdb=" CA  TYR B 101 "
        pdb=" CB  TYR B 101 "
      ideal   model   delta    sigma   weight residual
     110.42  118.00   -7.58 1.99e+00 2.53e-01 1.45e+01
  angle pdb=" N   ASP B 104 "
        pdb=" CA  ASP B 104 "
        pdb=" C   ASP B 104 "
      ideal   model   delta    sigma   weight residual
     110.80  118.88   -8.08 2.13e+00 2.20e-01 1.44e+01
  angle pdb=" N   GLU B 100 "
        pdb=" CA  GLU B 100 "
        pdb=" C   GLU B 100 "
      ideal   model   delta    sigma   weight residual
     109.24  103.06    6.18 1.63e+00 3.76e-01 1.44e+01
  angle pdb=" C   ILE A 106 "
        pdb=" N   VAL A 107 "
        pdb=" CA  VAL A 107 "
      ideal   model   delta    sigma   weight residual
     120.24  122.33   -2.09 6.30e-01 2.52e+00 1.10e+01
  angle pdb=" CA  GLU B 100 "
        pdb=" C   GLU B 100 "
        pdb=" N   TYR B 101 "
      ideal   model   delta    sigma   weight residual
     116.25  120.30   -4.05 1.23e+00 6.61e-01 1.08e+01
  ... (remaining 6370 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.12: 2529
       18.12 -    36.24: 166
       36.24 -    54.36: 41
       54.36 -    72.48: 5
       72.48 -    90.60: 1
  Dihedral angle restraints: 2742
    sinusoidal: 1016
      harmonic: 1726
  Sorted by residual:
  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   51.77   41.23     1      1.00e+01 1.00e-02 2.38e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.04   31.96     1      1.00e+01 1.00e-02 1.46e+01
  dihedral pdb=" CA  TYR C  49 "
           pdb=" C   TYR C  49 "
           pdb=" N   ALA C  50 "
           pdb=" CA  ALA C  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.30  -18.70     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 2739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 550
       0.044 -    0.087: 157
       0.087 -    0.131: 38
       0.131 -    0.174: 8
       0.174 -    0.218: 2
  Chirality restraints: 755
  Sorted by residual:
  chirality pdb=" CA  ASP B 104 "
            pdb=" N   ASP B 104 "
            pdb=" C   ASP B 104 "
            pdb=" CB  ASP B 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  THR C   7 "
            pdb=" N   THR C   7 "
            pdb=" C   THR C   7 "
            pdb=" CB  THR C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 9.11e-01
  chirality pdb=" CG  LEU A 144 "
            pdb=" CB  LEU A 144 "
            pdb=" CD1 LEU A 144 "
            pdb=" CD2 LEU A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.41e-01
  ... (remaining 752 not shown)

  Planarity restraints: 785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  35 "    0.018 2.00e-02 2.50e+03   2.05e-02 1.05e+01
        pdb=" CG  TRP C  35 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  35 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  35 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  35 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  35 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  35 "    0.010 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=" CD  ARG C  46 "    0.277 9.50e-02 1.11e+02   1.24e-01 9.51e+00
        pdb=" NE  ARG C  46 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  46 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  46 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  46 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 119 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO A 120 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 120 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 120 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 782 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 656
        2.76 -     3.29: 4427
        3.29 -     3.83: 7646
        3.83 -     4.36: 9049
        4.36 -     4.90: 15821
  Nonbonded interactions: 37599
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  47 "
            pdb=" OE2 GLU A  54 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" CD2 LEU B  83 "
            pdb=" CD2 LEU B  86 "
     model   vdw
     2.289 3.880
  nonbonded pdb=" OH  TYR A  38 "
            pdb=" O   PHE A 269 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   PRO C   8 "
            pdb=" OG1 THR C 102 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" OD2 ASP B  73 "
            pdb=" OG  SER B  76 "
     model   vdw
     2.376 3.040
  ... (remaining 37594 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:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.200
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
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      :  0.003   0.036   4688  Z= 0.209
  Angle     :  0.737  11.502   6379  Z= 0.433
  Chirality :  0.044   0.218    755
  Planarity :  0.006   0.124    785
  Dihedral  : 13.179  90.598   1636
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 10.08 %
    Favored  : 89.51 %
  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:  0.85 (0.33), residues: 600
  helix:  0.96 (0.29), residues: 280
  sheet:  1.12 (0.46), residues: 118
  loop : -0.20 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  46 
 TYR   0.011   0.001   TYR C  87 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.052   0.002   TRP C  35 
 HIS   0.002   0.001   HIS B  52 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.21 ( 4686)
  covalent geometry    : angle       0.73642 /  0.43 ( 6375)
  SS BOND              : bond        0.00241 /  0.12 (    2)
  SS BOND              : angle       1.29585 /  1.14 (    4)
  hydrogen bonds       : bond        0.20500 / 14.04 (  287)
  hydrogen bonds       : angle       7.90317 /  5.61 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8677 (mmm) cc_final: 0.8399 (ttm)
REVERT: A   52 SER cc_start: 0.8395 (t) cc_final: 0.8158 (p)
REVERT: A   58 ASN cc_start: 0.8165 (m110) cc_final: 0.7936 (m110)
REVERT: A  157 MET cc_start: 0.8263 (ttp) cc_final: 0.7915 (tmm)
REVERT: A  240 LYS cc_start: 0.8177 (tttp) cc_final: 0.6923 (mptt)
REVERT: B   28 THR cc_start: 0.7360 (m) cc_final: 0.7069 (t)
REVERT: B   33 GLU cc_start: 0.7735 (pt0) cc_final: 0.7531 (pt0)
REVERT: B   55 SER cc_start: 0.7903 (m) cc_final: 0.7619 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 99
  average time/residue: 0.0882
  time to fit residues: 10.8576
Evaluate side-chains
  76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0270
   chunk 58 optimal weight:    0.2980
   overall best weight:    0.5440

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A 116 ASN
A 327 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.183251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.118537 restraints weight = 5749.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.52
r_work: 0.3138 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4688  Z= 0.120
  Angle     :  0.545   5.733   6379  Z= 0.284
  Chirality :  0.040   0.186    755
  Planarity :  0.004   0.040    785
  Dihedral  :  4.871  41.198    648
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.91 %
    Favored  : 87.24 %
  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:  1.72 (0.34), residues: 600
  helix:  2.01 (0.30), residues: 284
  sheet:  1.36 (0.50), residues: 108
  loop : -0.16 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  81 
 TYR   0.013   0.001   TYR C  49 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.021   0.001   TRP C  35 
 HIS   0.004   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 4686)
  covalent geometry    : angle       0.54524 /  0.28 ( 6375)
  SS BOND              : bond        0.00366 /  0.18 (    2)
  SS BOND              : angle       0.26690 /  0.24 (    4)
  hydrogen bonds       : bond        0.04100 /  2.75 (  287)
  hydrogen bonds       : angle       5.14917 /  3.69 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8654 (mmm) cc_final: 0.8339 (ttm)
REVERT: A   40 ASP cc_start: 0.7942 (m-30) cc_final: 0.7633 (m-30)
REVERT: A   52 SER cc_start: 0.8564 (t) cc_final: 0.8330 (p)
REVERT: A   58 ASN cc_start: 0.8359 (m110) cc_final: 0.8148 (m110)
REVERT: A  157 MET cc_start: 0.8356 (ttp) cc_final: 0.8044 (tmm)
REVERT: A  240 LYS cc_start: 0.8237 (tttp) cc_final: 0.6866 (mptt)
REVERT: A  309 TRP cc_start: 0.8520 (t-100) cc_final: 0.7773 (t60)
REVERT: A  313 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.6958 (mtm180)
REVERT: B   28 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7035 (t)
REVERT: B   31 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6720 (t0)
REVERT: B   55 SER cc_start: 0.7837 (m) cc_final: 0.7538 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 89
  average time/residue: 0.0681
  time to fit residues: 7.8084
Evaluate side-chains
  85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   72 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.181296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.115476 restraints weight = 5650.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.50
r_work: 0.3100 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4688  Z= 0.128
  Angle     :  0.538   5.250   6379  Z= 0.274
  Chirality :  0.040   0.178    755
  Planarity :  0.003   0.026    785
  Dihedral  :  4.759  44.563    648
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 11.52 %
    Favored  : 85.80 %
  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:  1.85 (0.34), residues: 600
  helix:  2.16 (0.30), residues: 284
  sheet:  1.46 (0.48), residues: 108
  loop : -0.19 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.019   0.002   TYR A 117 
 PHE   0.007   0.001   PHE C  62 
 TRP   0.017   0.001   TRP C  35 
 HIS   0.004   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 4686)
  covalent geometry    : angle       0.53801 /  0.27 ( 6375)
  SS BOND              : bond        0.00321 /  0.17 (    2)
  SS BOND              : angle       0.25836 /  0.24 (    4)
  hydrogen bonds       : bond        0.03796 /  2.56 (  287)
  hydrogen bonds       : angle       4.82317 /  3.44 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8659 (mmm) cc_final: 0.8266 (ttm)
REVERT: A   40 ASP cc_start: 0.7989 (m-30) cc_final: 0.7629 (m-30)
REVERT: A   52 SER cc_start: 0.8525 (t) cc_final: 0.8315 (p)
REVERT: A   58 ASN cc_start: 0.8353 (m110) cc_final: 0.8108 (m110)
REVERT: A   92 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7650 (tpp80)
REVERT: A  117 TYR cc_start: 0.8284 (p90) cc_final: 0.8083 (p90)
REVERT: A  240 LYS cc_start: 0.8247 (tttp) cc_final: 0.6987 (mppt)
REVERT: A  309 TRP cc_start: 0.8526 (t-100) cc_final: 0.7770 (t60)
REVERT: A  313 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6925 (mtm180)
REVERT: B   31 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6724 (t0)
REVERT: B   33 GLU cc_start: 0.7973 (pt0) cc_final: 0.6950 (pm20)
REVERT: B   55 SER cc_start: 0.7930 (m) cc_final: 0.7573 (p)
  outliers start: 13
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0759
  time to fit residues: 8.9623
Evaluate side-chains
  86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PHE
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   99 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 27 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 55 optimal weight:    9.9990
   chunk 49 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A  47 GLN
A 253 HIS
A 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.180353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.114599 restraints weight = 5677.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.51
r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4688  Z= 0.129
  Angle     :  0.534   5.215   6379  Z= 0.271
  Chirality :  0.040   0.171    755
  Planarity :  0.003   0.038    785
  Dihedral  :  4.730  44.454    648
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 10.91 %
    Favored  : 85.39 %
  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: 600
  helix:  2.23 (0.30), residues: 284
  sheet:  1.60 (0.50), residues: 106
  loop : -0.19 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.015   0.002   TYR A 117 
 PHE   0.007   0.001   PHE C  62 
 TRP   0.015   0.001   TRP C  35 
 HIS   0.010   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 4686)
  covalent geometry    : angle       0.53373 /  0.27 ( 6375)
  SS BOND              : bond        0.00201 /  0.10 (    2)
  SS BOND              : angle       0.58493 /  0.35 (    4)
  hydrogen bonds       : bond        0.03554 /  2.40 (  287)
  hydrogen bonds       : angle       4.72772 /  3.36 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   40 ASP cc_start: 0.7952 (m-30) cc_final: 0.7593 (m-30)
REVERT: A   58 ASN cc_start: 0.8444 (m110) cc_final: 0.8153 (m110)
REVERT: A   92 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7638 (tpp80)
REVERT: A  170 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8320 (mp)
REVERT: A  240 LYS cc_start: 0.8339 (tttp) cc_final: 0.7092 (mppt)
REVERT: A  245 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6712 (ttm110)
REVERT: A  313 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.7123 (mtm180)
REVERT: B   31 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6793 (t0)
REVERT: B   33 GLU cc_start: 0.7892 (pt0) cc_final: 0.6996 (pm20)
REVERT: B   34 MET cc_start: 0.6964 (ptm) cc_final: 0.6484 (ppp)
REVERT: B   55 SER cc_start: 0.8037 (m) cc_final: 0.7664 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0854
  time to fit residues: 10.1768
Evaluate side-chains
  93 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   99 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 38 optimal weight:   30.0000
   chunk 30 optimal weight:    0.1980
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A 253 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.181570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.116578 restraints weight = 5671.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.48
r_work: 0.3086 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4688  Z= 0.107
  Angle     :  0.505   6.611   6379  Z= 0.257
  Chirality :  0.039   0.188    755
  Planarity :  0.003   0.042    785
  Dihedral  :  4.647  44.737    648
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.76 %
    Favored  : 84.36 %
  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:  2.03 (0.34), residues: 600
  helix:  2.31 (0.30), residues: 284
  sheet:  1.76 (0.49), residues: 104
  loop : -0.22 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.016   0.001   TYR C  71 
 PHE   0.009   0.001   PHE C  62 
 TRP   0.014   0.001   TRP C  35 
 HIS   0.009   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 4686)
  covalent geometry    : angle       0.50557 /  0.26 ( 6375)
  SS BOND              : bond        0.00226 /  0.11 (    2)
  SS BOND              : angle       0.32507 /  0.19 (    4)
  hydrogen bonds       : bond        0.03287 /  2.22 (  287)
  hydrogen bonds       : angle       4.59037 /  3.26 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   40 ASP cc_start: 0.7946 (m-30) cc_final: 0.7532 (m-30)
REVERT: A   58 ASN cc_start: 0.8354 (m110) cc_final: 0.8103 (m110)
REVERT: A   92 ARG cc_start: 0.7879 (tpp-160) cc_final: 0.7599 (tpp80)
REVERT: A  111 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8848 (mt)
REVERT: A  170 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8250 (mp)
REVERT: A  245 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6738 (ttm110)
REVERT: A  309 TRP cc_start: 0.8547 (t-100) cc_final: 0.7803 (t60)
REVERT: A  313 ARG cc_start: 0.7457 (ttp-170) cc_final: 0.6966 (mtm180)
REVERT: B   31 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6719 (t0)
REVERT: B   33 GLU cc_start: 0.7837 (pt0) cc_final: 0.7103 (pm20)
REVERT: B   34 MET cc_start: 0.6736 (ptm) cc_final: 0.6321 (ppp)
REVERT: B   55 SER cc_start: 0.8083 (m) cc_final: 0.7712 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0757
  time to fit residues: 8.7639
Evaluate side-chains
  88 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PHE
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 46 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 253 HIS
A 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.180412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125715 restraints weight = 5710.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.48
r_work: 0.3065 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4688  Z= 0.127
  Angle     :  0.519   5.643   6379  Z= 0.264
  Chirality :  0.040   0.187    755
  Planarity :  0.003   0.041    785
  Dihedral  :  4.651  44.310    648
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 12.14 %
    Favored  : 84.16 %
  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:  1.99 (0.34), residues: 600
  helix:  2.27 (0.30), residues: 285
  sheet:  1.68 (0.50), residues: 104
  loop : -0.20 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.013   0.001   TYR C  71 
 PHE   0.011   0.001   PHE C  62 
 TRP   0.016   0.001   TRP C  35 
 HIS   0.009   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 4686)
  covalent geometry    : angle       0.51946 /  0.26 ( 6375)
  SS BOND              : bond        0.00229 /  0.11 (    2)
  SS BOND              : angle       0.29339 /  0.18 (    4)
  hydrogen bonds       : bond        0.03393 /  2.29 (  287)
  hydrogen bonds       : angle       4.57855 /  3.26 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.8460 (m110) cc_final: 0.8152 (m110)
REVERT: A   92 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7635 (tpp80)
REVERT: A  111 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8938 (mt)
REVERT: A  170 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8388 (mp)
REVERT: A  309 TRP cc_start: 0.8622 (t-100) cc_final: 0.7931 (t60)
REVERT: A  313 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7003 (mtm180)
REVERT: B   31 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6666 (t0)
REVERT: B   32 TYR cc_start: 0.7827 (m-80) cc_final: 0.7513 (m-80)
REVERT: B   33 GLU cc_start: 0.7789 (pt0) cc_final: 0.7116 (pm20)
REVERT: B   34 MET cc_start: 0.6787 (ptm) cc_final: 0.6422 (ppp)
REVERT: B   55 SER cc_start: 0.8280 (m) cc_final: 0.7904 (p)
REVERT: B   81 MET cc_start: 0.4727 (tmm) cc_final: 0.4523 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 90
  average time/residue: 0.0710
  time to fit residues: 8.2259
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PHE
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 253 HIS
A 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.179779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.113421 restraints weight = 5672.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.59
r_work: 0.3064 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4688  Z= 0.140
  Angle     :  0.527   5.732   6379  Z= 0.268
  Chirality :  0.040   0.187    755
  Planarity :  0.003   0.043    785
  Dihedral  :  4.694  43.917    648
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 11.93 %
    Favored  : 84.16 %
  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:  1.91 (0.34), residues: 600
  helix:  2.22 (0.30), residues: 285
  sheet:  1.58 (0.49), residues: 104
  loop : -0.21 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.016   0.001   TYR C  71 
 PHE   0.012   0.001   PHE C  62 
 TRP   0.021   0.002   TRP C  35 
 HIS   0.009   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.14 ( 4686)
  covalent geometry    : angle       0.52669 /  0.27 ( 6375)
  SS BOND              : bond        0.00155 /  0.07 (    2)
  SS BOND              : angle       0.27436 /  0.16 (    4)
  hydrogen bonds       : bond        0.03489 /  2.35 (  287)
  hydrogen bonds       : angle       4.57724 /  3.27 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.8331 (m110) cc_final: 0.7963 (m110)
REVERT: A   92 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7621 (tpp80)
REVERT: A  111 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8784 (mt)
REVERT: A  245 ARG cc_start: 0.7432 (ttm110) cc_final: 0.7130 (ttp80)
REVERT: A  313 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7053 (mtm180)
REVERT: B   31 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6518 (t0)
REVERT: B   33 GLU cc_start: 0.7719 (pt0) cc_final: 0.6993 (pm20)
REVERT: B   34 MET cc_start: 0.6589 (ptm) cc_final: 0.6182 (ppp)
REVERT: B   55 SER cc_start: 0.8137 (m) cc_final: 0.7741 (p)
  outliers start: 19
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0738
  time to fit residues: 8.3942
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0040
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 253 HIS
A 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.181289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115846 restraints weight = 5743.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.55
r_work: 0.3090 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4688  Z= 0.108
  Angle     :  0.505   5.958   6379  Z= 0.257
  Chirality :  0.039   0.185    755
  Planarity :  0.003   0.043    785
  Dihedral  :  4.582  43.819    648
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 12.96 %
    Favored  : 83.95 %
  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:  1.92 (0.34), residues: 600
  helix:  2.25 (0.30), residues: 285
  sheet:  1.53 (0.49), residues: 104
  loop : -0.21 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.016   0.001   TYR A 112 
 PHE   0.012   0.001   PHE C  62 
 TRP   0.017   0.001   TRP C  35 
 HIS   0.009   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 4686)
  covalent geometry    : angle       0.50476 /  0.26 ( 6375)
  SS BOND              : bond        0.00263 /  0.13 (    2)
  SS BOND              : angle       0.23051 /  0.20 (    4)
  hydrogen bonds       : bond        0.03224 /  2.18 (  287)
  hydrogen bonds       : angle       4.51398 /  3.23 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   30 ASN cc_start: 0.8306 (m110) cc_final: 0.7975 (m-40)
REVERT: A   58 ASN cc_start: 0.8339 (m110) cc_final: 0.8002 (m110)
REVERT: A   59 MET cc_start: 0.8745 (tpp) cc_final: 0.8522 (ttm)
REVERT: A   92 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7610 (tpp80)
REVERT: A  111 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8781 (mt)
REVERT: A  309 TRP cc_start: 0.8466 (t-100) cc_final: 0.7928 (t60)
REVERT: B   31 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6647 (t0)
REVERT: B   33 GLU cc_start: 0.7722 (pt0) cc_final: 0.7358 (pt0)
REVERT: B   55 SER cc_start: 0.8094 (m) cc_final: 0.7708 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0574
  time to fit residues: 6.4254
Evaluate side-chains
  85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0170
   overall best weight:    0.6418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 253 HIS
A 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.181988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.116745 restraints weight = 5589.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.51
r_work: 0.3101 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4688  Z= 0.102
  Angle     :  0.500   5.635   6379  Z= 0.254
  Chirality :  0.039   0.185    755
  Planarity :  0.003   0.043    785
  Dihedral  :  4.535  43.931    648
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 12.76 %
    Favored  : 83.95 %
  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:  1.95 (0.34), residues: 600
  helix:  2.28 (0.30), residues: 285
  sheet:  1.54 (0.49), residues: 104
  loop : -0.21 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.014   0.001   TYR A 112 
 PHE   0.012   0.001   PHE C  62 
 TRP   0.017   0.001   TRP C  35 
 HIS   0.009   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.10 ( 4686)
  covalent geometry    : angle       0.49993 /  0.25 ( 6375)
  SS BOND              : bond        0.00296 /  0.14 (    2)
  SS BOND              : angle       0.23431 /  0.21 (    4)
  hydrogen bonds       : bond        0.03139 /  2.12 (  287)
  hydrogen bonds       : angle       4.48137 /  3.21 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   30 ASN cc_start: 0.8293 (m110) cc_final: 0.7977 (m-40)
REVERT: A   43 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6267 (pt0)
REVERT: A   58 ASN cc_start: 0.8355 (m110) cc_final: 0.8035 (m110)
REVERT: A   59 MET cc_start: 0.8721 (tpp) cc_final: 0.8516 (ttm)
REVERT: A   92 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7626 (tpp80)
REVERT: A  111 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8666 (mt)
REVERT: A  170 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8113 (mp)
REVERT: A  309 TRP cc_start: 0.8461 (t-100) cc_final: 0.7933 (t60)
REVERT: B   31 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6496 (t0)
REVERT: B   32 TYR cc_start: 0.7660 (m-80) cc_final: 0.7261 (m-80)
REVERT: B   33 GLU cc_start: 0.7646 (pt0) cc_final: 0.7317 (pt0)
REVERT: B   55 SER cc_start: 0.8079 (m) cc_final: 0.7696 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0495
  time to fit residues: 5.7153
Evaluate side-chains
  83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   99 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0770
   chunk 57 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 277 GLN
A 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.182099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117098 restraints weight = 5615.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.52
r_work: 0.3107 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4688  Z= 0.102
  Angle     :  0.495   5.647   6379  Z= 0.251
  Chirality :  0.039   0.184    755
  Planarity :  0.003   0.045    785
  Dihedral  :  4.458  42.115    648
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 12.76 %
    Favored  : 83.95 %
  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:  1.96 (0.34), residues: 600
  helix:  2.25 (0.30), residues: 285
  sheet:  1.54 (0.50), residues: 104
  loop : -0.12 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.015   0.001   TYR A 112 
 PHE   0.013   0.001   PHE C  62 
 TRP   0.021   0.001   TRP C  35 
 HIS   0.004   0.001   HIS A 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.10 ( 4686)
  covalent geometry    : angle       0.49482 /  0.25 ( 6375)
  SS BOND              : bond        0.00284 /  0.14 (    2)
  SS BOND              : angle       0.22867 /  0.21 (    4)
  hydrogen bonds       : bond        0.03118 /  2.10 (  287)
  hydrogen bonds       : angle       4.44591 /  3.19 (  825)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A   43 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6355 (pt0)
REVERT: A   58 ASN cc_start: 0.8324 (m110) cc_final: 0.8006 (m110)
REVERT: A   92 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.7611 (tpp80)
REVERT: A  111 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8661 (mt)
REVERT: A  309 TRP cc_start: 0.8454 (t-100) cc_final: 0.7929 (t60)
REVERT: B   31 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6493 (t0)
REVERT: B   33 GLU cc_start: 0.7540 (pt0) cc_final: 0.7234 (pt0)
REVERT: B   55 SER cc_start: 0.8104 (m) cc_final: 0.7704 (p)
REVERT: C   70 ASP cc_start: 0.7786 (p0) cc_final: 0.6521 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 82
  average time/residue: 0.0537
  time to fit residues: 5.9539
Evaluate side-chains
  86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain C residue    2 ILE
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:   20.0000
   chunk 34 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:   20.0000
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 277 GLN
A 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.181033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115676 restraints weight = 5756.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.57
r_work: 0.3078 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4688  Z= 0.123
  Angle     :  0.515   5.635   6379  Z= 0.260
  Chirality :  0.040   0.184    755
  Planarity :  0.003   0.044    785
  Dihedral  :  4.502  39.861    648
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 12.55 %
    Favored  : 83.95 %
  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:  1.90 (0.34), residues: 600
  helix:  2.16 (0.30), residues: 285
  sheet:  1.56 (0.51), residues: 103
  loop : -0.11 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 250 
 TYR   0.014   0.002   TYR A 117 
 PHE   0.013   0.001   PHE C  62 
 TRP   0.037   0.002   TRP C  35 
 HIS   0.003   0.001   HIS B  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.12 ( 4686)
  covalent geometry    : angle       0.51497 /  0.26 ( 6375)
  SS BOND              : bond        0.00228 /  0.11 (    2)
  SS BOND              : angle       0.39423 /  0.34 (    4)
  hydrogen bonds       : bond        0.03311 /  2.24 (  287)
  hydrogen bonds       : angle       4.51660 /  3.24 (  825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1567.59 seconds
wall clock time: 27 minutes 27.75 seconds (1647.75 seconds total)