Starting phenix.real_space_refine
on Wed Sep 17 04:46:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gcm_51234/09_2025/9gcm_51234.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gcm_51234/09_2025/9gcm_51234.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gcm_51234/09_2025/9gcm_51234.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gcm_51234/09_2025/9gcm_51234.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gcm_51234/09_2025/9gcm_51234.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gcm_51234/09_2025/9gcm_51234.cif"
  }
  resolution = 3.1
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      11      5.16       5
     C    2553      2.51       5
     N     811      2.21       5
     O    1025      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4466
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 1413
          Classifications: {'RNA': 66}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 13, 'rna3p': 52}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1032
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1032
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
    Chain: "C"
      Number of atoms: 1261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1261
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 6, 'TRANS': 148}
    Chain: "D"
      Number of atoms: 760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 760
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
  Time building chain proxies: 1.16, per 1000 atoms: 0.26
  Number of scatterers: 4466
  At special positions: 0
  Unit cell: (86.87, 89.06, 84.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      11     16.00
     P      66     15.00
     O    1025      8.00
     N     811      7.00
     C    2553      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 121.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  700

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 4 sheets defined
      53.1% alpha, 12.5% beta
      25 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 13
      removed outlier: 4.288A  pdb=" N   GLU B   6 " --> pdb=" O   ASP B   2 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY B   7 " --> pdb=" O   VAL B   3 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN B  13 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 18
      removed outlier: 3.847A  pdb=" N   CYS B  18 " --> pdb=" O   PRO B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
      removed outlier: 3.618A  pdb=" N   VAL B  29 " --> pdb=" O   THR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 82
      removed outlier: 3.609A  pdb=" N   ARG B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 95
    Processing helix  chain 'C' and resid 12 through 17
      removed outlier: 3.920A  pdb=" N   GLY C  17 " --> pdb=" O   PRO C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 37
    Processing helix  chain 'C' and resid 48 through 50
      No H-bonds generated for 'chain 'C' and resid 48 through 50'
    Processing helix  chain 'C' and resid 63 through 72
    Processing helix  chain 'C' and resid 73 through 75
      No H-bonds generated for 'chain 'C' and resid 73 through 75'
    Processing helix  chain 'C' and resid 101 through 113
      removed outlier: 4.063A  pdb=" N   VAL C 105 " --> pdb=" O   GLU C 101 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ASP C 113 " --> pdb=" O   TYR C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 151
      removed outlier: 3.802A  pdb=" N   GLY C 151 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 148 through 151'
    Processing helix  chain 'D' and resid 292 through 332
      removed outlier: 3.730A  pdb=" N   VAL D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   GLU D 304 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   MET D 315 " --> pdb=" O   ASP D 311 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   VAL D 316 " --> pdb=" O   THR D 312 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP D 317 " --> pdb=" O   LYS D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 332 through 337
      removed outlier: 4.116A  pdb=" N   LYS D 336 " --> pdb=" O   ALA D 332 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 384
      removed outlier: 3.744A  pdb=" N   ALA D 344 " --> pdb=" O   PRO D 340 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   HIS D 351 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU D 352 " --> pdb=" O   PHE D 348 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN D 353 " --> pdb=" O   THR D 349 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG D 354 " --> pdb=" O   HIS D 350 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN D 381 " --> pdb=" O   LEU D 377 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU D 382 " --> pdb=" O   GLU D 378 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLU D 383 " --> pdb=" O   GLY D 379 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58
      removed outlier: 3.600A  pdb=" N   ASP B 121 " --> pdb=" O   THR B  42 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   CYS B  46 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE B 125 " --> pdb=" O   CYS B  46 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE B 126 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 84
      removed outlier: 5.272A  pdb=" N   ILE C  77 " --> pdb=" O   GLU C  98 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   GLU C  98 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ARG C  79 " --> pdb=" O   PHE C  96 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   PHE C  96 " --> pdb=" O   ARG C  79 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ARG C  81 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   TYR C  94 " --> pdb=" O   ARG C  81 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   VAL C  83 " --> pdb=" O   LYS C  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117
    Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 147
      removed outlier: 4.078A  pdb=" N   LYS C 147 " --> pdb=" O   GLN C 152 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   GLN C 152 " --> pdb=" O   LYS C 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    142 hydrogen bonds defined for protein.
    414 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      62 hydrogen bonds
      108 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 0.61

  Time building geometry restraints manager: 0.51 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: 1113
        1.33 -     1.45: 1238
        1.45 -     1.58: 2176
        1.58 -     1.70: 131
        1.70 -     1.82: 19
  Bond restraints: 4677
  Sorted by residual:
  bond pdb=" CB  PRO C  26 "
       pdb=" CG  PRO C  26 "
    ideal  model  delta    sigma   weight residual
    1.492  1.579 -0.087 5.00e-02 4.00e+02 3.05e+00
  bond pdb=" CB  LYS D 295 "
       pdb=" CG  LYS D 295 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.07e-01
  bond pdb=" CB  GLU C 129 "
       pdb=" CG  GLU C 129 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.65e-01
  bond pdb=" CB  ARG D 314 "
       pdb=" CG  ARG D 314 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.60e-01
  bond pdb=" CG  ARG D 314 "
       pdb=" CD  ARG D 314 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.33e-01
  ... (remaining 4672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 6460
        1.77 -     3.54: 121
        3.54 -     5.32: 21
        5.32 -     7.09: 9
        7.09 -     8.86: 2
  Bond angle restraints: 6613
  Sorted by residual:
  angle pdb=" CA  PRO C  26 "
        pdb=" N   PRO C  26 "
        pdb=" CD  PRO C  26 "
      ideal   model   delta    sigma   weight residual
     112.00  106.80    5.20 1.40e+00 5.10e-01 1.38e+01
  angle pdb=" CA  LYS D 336 "
        pdb=" CB  LYS D 336 "
        pdb=" CG  LYS D 336 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.32e+00
  angle pdb=" CB  ARG D 314 "
        pdb=" CG  ARG D 314 "
        pdb=" CD  ARG D 314 "
      ideal   model   delta    sigma   weight residual
     111.30  118.10   -6.80 2.30e+00 1.89e-01 8.73e+00
  angle pdb=" CB  MET D 376 "
        pdb=" CG  MET D 376 "
        pdb=" SD  MET D 376 "
      ideal   model   delta    sigma   weight residual
     112.70  121.56   -8.86 3.00e+00 1.11e-01 8.72e+00
  angle pdb=" CA  LYS D 295 "
        pdb=" CB  LYS D 295 "
        pdb=" CG  LYS D 295 "
      ideal   model   delta    sigma   weight residual
     114.10  119.81   -5.71 2.00e+00 2.50e-01 8.16e+00
  ... (remaining 6608 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.08: 2516
       23.08 -    46.16: 301
       46.16 -    69.23: 113
       69.23 -    92.31: 19
       92.31 -   115.39: 2
  Dihedral angle restraints: 2951
    sinusoidal: 1864
      harmonic: 1087
  Sorted by residual:
  dihedral pdb=" O4'   U A  22 "
           pdb=" C1'   U A  22 "
           pdb=" N1    U A  22 "
           pdb=" C2    U A  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -64.15  -63.85     1      1.70e+01 3.46e-03 1.86e+01
  dihedral pdb=" O4'   G A  55 "
           pdb=" C1'   G A  55 "
           pdb=" N9    G A  55 "
           pdb=" C4    G A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -159.65   53.65     1      1.70e+01 3.46e-03 1.35e+01
  dihedral pdb=" O4'   A A  20 "
           pdb=" C1'   A A  20 "
           pdb=" N9    A A  20 "
           pdb=" C4    A A  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -29.93  -60.07     1      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2948 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 514
       0.024 -    0.048: 151
       0.048 -    0.073: 65
       0.073 -    0.097: 40
       0.097 -    0.121: 13
  Chirality restraints: 783
  Sorted by residual:
  chirality pdb=" CA  ILE C  97 "
            pdb=" N   ILE C  97 "
            pdb=" C   ILE C  97 "
            pdb=" CB  ILE C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality pdb=" CA  ILE C 136 "
            pdb=" N   ILE C 136 "
            pdb=" C   ILE C 136 "
            pdb=" CB  ILE C 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  ILE B 126 "
            pdb=" N   ILE B 126 "
            pdb=" C   ILE B 126 "
            pdb=" CB  ILE B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  ... (remaining 780 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  25 "    0.058 5.00e-02 4.00e+02   8.61e-02 1.19e+01
        pdb=" N   PRO C  26 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO C  26 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO C  26 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A  78 "   -0.030 2.00e-02 2.50e+03   1.51e-02 5.13e+00
        pdb=" N1    C A  78 "    0.031 2.00e-02 2.50e+03
        pdb=" C2    C A  78 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C A  78 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    C A  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    C A  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C A  78 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    C A  78 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C A  78 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  12 "    0.030 5.00e-02 4.00e+02   4.63e-02 3.42e+00
        pdb=" N   PRO C  13 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C  13 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C  13 "    0.026 5.00e-02 4.00e+02
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 215
        2.69 -     3.24: 4546
        3.24 -     3.80: 7861
        3.80 -     4.35: 10332
        4.35 -     4.90: 14833
  Nonbonded interactions: 37787
  Sorted by model distance:
  nonbonded pdb=" O2'   G A  63 "
            pdb=" OG  SER C 150 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" O   LYS D 308 "
            pdb=" OG1 THR D 312 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" N   GLU C 102 "
            pdb=" OE1 GLU C 102 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" O2'   C A  62 "
            pdb=" OE2 GLU C 149 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   LYS C  68 "
            pdb=" OG  SER C  72 "
     model   vdw
     2.260 3.040
  ... (remaining 37782 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:             5.570
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.270
  Find NCS groups from input model:        0.010
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
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   0.087   4677  Z= 0.170
  Angle     :  0.651   8.859   6613  Z= 0.332
  Chirality :  0.034   0.121    783
  Planarity :  0.006   0.086    604
  Dihedral  : 20.804 115.389   2251
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.23 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 25.08 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.45), residues: 371
  helix:  0.74 (0.41), residues: 162
  sheet: -1.76 (1.03), residues: 21
  loop : -0.43 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 109 
 TYR   0.023   0.003   TYR C  39 
 PHE   0.010   0.002   PHE C  54 
 TRP   0.021   0.003   TRP C  32 
 HIS   0.006   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 4677)
  covalent geometry    : angle       0.65087 ( 6613)
  hydrogen bonds       : bond        0.22820 (  204)
  hydrogen bonds       : angle       7.45579 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 73
  average time/residue: 0.1213
  time to fit residues: 10.2212
Evaluate side-chains
  74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN

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 = 0.106297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.081592 restraints weight = 13565.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 3.25
r_work: 0.3404 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4677  Z= 0.137
  Angle     :  0.587   7.991   6613  Z= 0.303
  Chirality :  0.036   0.206    783
  Planarity :  0.005   0.047    604
  Dihedral  : 20.022 109.898   1462
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  2.70 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.12 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.45), residues: 371
  helix:  0.96 (0.39), residues: 173
  sheet: -2.39 (0.92), residues: 28
  loop : -0.05 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 109 
 TYR   0.015   0.002   TYR C 126 
 PHE   0.010   0.001   PHE C 123 
 TRP   0.013   0.002   TRP C  32 
 HIS   0.010   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4677)
  covalent geometry    : angle       0.58681 ( 6613)
  hydrogen bonds       : bond        0.04370 (  204)
  hydrogen bonds       : angle       4.19454 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8698 (mmm) cc_final: 0.8421 (mmm)
REVERT: B   59 GLN cc_start: 0.8544 (mt0) cc_final: 0.8290 (mt0)
REVERT: C   29 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7373 (ttm110)
REVERT: D  314 ARG cc_start: 0.8560 (tpp80) cc_final: 0.7988 (tpt90)
REVERT: D  320 ARG cc_start: 0.8292 (tpt90) cc_final: 0.7939 (tpt90)
  outliers start: 11
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1131
  time to fit residues: 11.4017
Evaluate side-chains
  72 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.5958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.107032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.083419 restraints weight = 13498.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 3.07
r_work: 0.3475 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4677  Z= 0.121
  Angle     :  0.551   9.567   6613  Z= 0.278
  Chirality :  0.035   0.187    783
  Planarity :  0.004   0.038    604
  Dihedral  : 19.875 109.296   1456
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  2.70 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 21.98 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.45), residues: 371
  helix:  1.17 (0.40), residues: 173
  sheet: -2.05 (0.91), residues: 28
  loop :  0.04 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 109 
 TYR   0.015   0.002   TYR C  39 
 PHE   0.008   0.001   PHE C  54 
 TRP   0.010   0.002   TRP B  89 
 HIS   0.008   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4677)
  covalent geometry    : angle       0.55073 ( 6613)
  hydrogen bonds       : bond        0.03962 (  204)
  hydrogen bonds       : angle       3.85036 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8824 (mmm) cc_final: 0.8519 (mmm)
REVERT: B   39 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7354 (tp40)
REVERT: B   59 GLN cc_start: 0.8453 (mt0) cc_final: 0.8136 (mt0)
REVERT: C   29 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7340 (ttm110)
REVERT: D  320 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7912 (tpt90)
  outliers start: 17
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1106
  time to fit residues: 11.8706
Evaluate side-chains
  80 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 24 optimal weight:    0.1980
   chunk 25 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.106850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.082786 restraints weight = 13346.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 3.17
r_work: 0.3421 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4677  Z= 0.121
  Angle     :  0.556  10.887   6613  Z= 0.275
  Chirality :  0.034   0.177    783
  Planarity :  0.004   0.037    604
  Dihedral  : 19.860 108.609   1456
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  2.96 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 21.67 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.45), residues: 371
  helix:  1.34 (0.40), residues: 173
  sheet: -1.57 (0.96), residues: 28
  loop :  0.14 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  78 
 TYR   0.015   0.002   TYR C  39 
 PHE   0.009   0.001   PHE C  54 
 TRP   0.010   0.002   TRP C  32 
 HIS   0.009   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4677)
  covalent geometry    : angle       0.55612 ( 6613)
  hydrogen bonds       : bond        0.03674 (  204)
  hydrogen bonds       : angle       3.70785 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8878 (mmm) cc_final: 0.8537 (mmm)
REVERT: B   39 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7526 (tp40)
REVERT: B   59 GLN cc_start: 0.8552 (mt0) cc_final: 0.8151 (mt0)
REVERT: C   29 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7489 (ttm110)
REVERT: D  320 ARG cc_start: 0.8234 (tpt90) cc_final: 0.7885 (tpt90)
REVERT: D  329 ARG cc_start: 0.7318 (mtt180) cc_final: 0.7100 (ttm170)
REVERT: D  362 ARG cc_start: 0.6861 (tpt170) cc_final: 0.6143 (mmp80)
  outliers start: 14
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1201
  time to fit residues: 12.6726
Evaluate side-chains
  83 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.105083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.081075 restraints weight = 13426.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.04
r_work: 0.3432 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4677  Z= 0.174
  Angle     :  0.616  11.049   6613  Z= 0.309
  Chirality :  0.036   0.159    783
  Planarity :  0.004   0.034    604
  Dihedral  : 20.052 107.554   1456
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.77 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.15 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.45), residues: 371
  helix:  0.96 (0.39), residues: 178
  sheet: -1.54 (0.96), residues: 28
  loop :  0.02 (0.51), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  80 
 TYR   0.018   0.002   TYR C  39 
 PHE   0.010   0.002   PHE C  54 
 TRP   0.013   0.002   TRP C  32 
 HIS   0.010   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4677)
  covalent geometry    : angle       0.61557 ( 6613)
  hydrogen bonds       : bond        0.04157 (  204)
  hydrogen bonds       : angle       3.88171 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8914 (mmm) cc_final: 0.8582 (mmm)
REVERT: B   39 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7311 (tp40)
REVERT: B   46 CYS cc_start: 0.7580 (m) cc_final: 0.7335 (m)
REVERT: B   59 GLN cc_start: 0.8490 (mt0) cc_final: 0.7979 (mt0)
REVERT: C   29 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7637 (ttm110)
REVERT: D  314 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8266 (tpt90)
REVERT: D  320 ARG cc_start: 0.8272 (tpt90) cc_final: 0.7918 (tpt90)
REVERT: D  329 ARG cc_start: 0.7361 (mtt180) cc_final: 0.7004 (ttm170)
REVERT: D  358 LEU cc_start: 0.8612 (tp) cc_final: 0.8252 (tp)
REVERT: D  362 ARG cc_start: 0.6974 (tpt170) cc_final: 0.6172 (mmp80)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1195
  time to fit residues: 12.0393
Evaluate side-chains
  86 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   77 ILE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 41 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0670
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
B  71 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.107775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.083599 restraints weight = 13852.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 3.16
r_work: 0.3484 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4677  Z= 0.114
  Angle     :  0.589  12.500   6613  Z= 0.287
  Chirality :  0.034   0.172    783
  Planarity :  0.004   0.034    604
  Dihedral  : 19.895 109.503   1456
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.23 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 26.32 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.45), residues: 371
  helix:  1.01 (0.40), residues: 179
  sheet: -1.21 (0.97), residues: 28
  loop :  0.17 (0.52), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 314 
 TYR   0.013   0.002   TYR B 115 
 PHE   0.008   0.001   PHE C  54 
 TRP   0.012   0.002   TRP C  32 
 HIS   0.009   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4677)
  covalent geometry    : angle       0.58895 ( 6613)
  hydrogen bonds       : bond        0.03723 (  204)
  hydrogen bonds       : angle       3.66020 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8934 (mmm) cc_final: 0.8595 (mmm)
REVERT: B   39 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7344 (tp40)
REVERT: B   46 CYS cc_start: 0.7531 (m) cc_final: 0.7251 (m)
REVERT: B   59 GLN cc_start: 0.8487 (mt0) cc_final: 0.8085 (mt0)
REVERT: C   29 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7484 (ttm110)
REVERT: C   61 GLN cc_start: 0.8873 (mp10) cc_final: 0.8531 (mp10)
REVERT: D  314 ARG cc_start: 0.9097 (tpp80) cc_final: 0.8292 (tpt90)
REVERT: D  329 ARG cc_start: 0.7349 (mtt180) cc_final: 0.7014 (ttm170)
REVERT: D  358 LEU cc_start: 0.8624 (tp) cc_final: 0.8241 (tp)
REVERT: D  362 ARG cc_start: 0.6935 (tpt170) cc_final: 0.6160 (mmp80)
  outliers start: 11
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1172
  time to fit residues: 12.4355
Evaluate side-chains
  83 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue  319 LEU
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.0010
   chunk 32 optimal weight:    0.0980
   chunk 8 optimal weight:    0.1980
   chunk 20 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.2786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.109856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.086086 restraints weight = 13713.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.15
r_work: 0.3530 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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      :  0.002   0.031   4677  Z= 0.108
  Angle     :  0.591  13.340   6613  Z= 0.287
  Chirality :  0.034   0.171    783
  Planarity :  0.004   0.034    604
  Dihedral  : 19.724 108.213   1456
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  2.70 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 27.24 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.45), residues: 371
  helix:  1.07 (0.40), residues: 179
  sheet: -0.86 (1.02), residues: 28
  loop :  0.16 (0.52), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  80 
 TYR   0.024   0.002   TYR B  73 
 PHE   0.007   0.001   PHE C  54 
 TRP   0.016   0.002   TRP C  32 
 HIS   0.009   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4677)
  covalent geometry    : angle       0.59053 ( 6613)
  hydrogen bonds       : bond        0.03668 (  204)
  hydrogen bonds       : angle       3.55935 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8933 (mmm) cc_final: 0.8572 (mmm)
REVERT: B   27 GLU cc_start: 0.8360 (mp0) cc_final: 0.8072 (pm20)
REVERT: B   39 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7498 (tp40)
REVERT: B   59 GLN cc_start: 0.8444 (mt0) cc_final: 0.8081 (mt0)
REVERT: B  115 TYR cc_start: 0.6219 (m-80) cc_final: 0.6002 (m-80)
REVERT: B  120 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7839 (mmm-85)
REVERT: C   29 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7349 (ttm110)
REVERT: C   61 GLN cc_start: 0.8878 (mp10) cc_final: 0.8506 (mp10)
REVERT: C   69 GLU cc_start: 0.8036 (tp30) cc_final: 0.7815 (tp30)
REVERT: D  314 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8272 (tpt90)
REVERT: D  320 ARG cc_start: 0.8203 (tpt90) cc_final: 0.7873 (tpt90)
REVERT: D  329 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6900 (ttm170)
REVERT: D  358 LEU cc_start: 0.8635 (tp) cc_final: 0.8385 (tp)
REVERT: D  362 ARG cc_start: 0.6962 (tpt170) cc_final: 0.6248 (mmp80)
  outliers start: 9
  outliers final: 6
  residues processed: 97
  average time/residue: 0.1207
  time to fit residues: 13.5799
Evaluate side-chains
  90 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue  319 LEU
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.107588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.083061 restraints weight = 13618.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 3.21
r_work: 0.3471 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4677  Z= 0.146
  Angle     :  0.628  13.106   6613  Z= 0.310
  Chirality :  0.035   0.154    783
  Planarity :  0.004   0.034    604
  Dihedral  : 19.841 107.490   1456
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.23 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 27.55 %
    Favored  : 69.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.45), residues: 371
  helix:  1.00 (0.40), residues: 179
  sheet: -0.84 (1.04), residues: 28
  loop :  0.07 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 139 
 TYR   0.020   0.002   TYR C  39 
 PHE   0.011   0.001   PHE C 123 
 TRP   0.018   0.003   TRP C  32 
 HIS   0.010   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4677)
  covalent geometry    : angle       0.62797 ( 6613)
  hydrogen bonds       : bond        0.03945 (  204)
  hydrogen bonds       : angle       3.69614 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8971 (mmm) cc_final: 0.8602 (mmm)
REVERT: B   39 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7348 (tp40)
REVERT: B   46 CYS cc_start: 0.7519 (m) cc_final: 0.7295 (m)
REVERT: B   59 GLN cc_start: 0.8467 (mt0) cc_final: 0.8045 (mt0)
REVERT: C   29 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7397 (ttm110)
REVERT: C   61 GLN cc_start: 0.8876 (mp10) cc_final: 0.8504 (mp10)
REVERT: D  314 ARG cc_start: 0.9078 (tpp80) cc_final: 0.8328 (tpt90)
REVERT: D  362 ARG cc_start: 0.7022 (tpt170) cc_final: 0.6233 (mmp80)
  outliers start: 11
  outliers final: 7
  residues processed: 86
  average time/residue: 0.1227
  time to fit residues: 12.1962
Evaluate side-chains
  85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
B  71 GLN
B  97 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.105586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.081706 restraints weight = 13377.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 3.03
r_work: 0.3437 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4677  Z= 0.189
  Angle     :  0.674  13.665   6613  Z= 0.333
  Chirality :  0.036   0.142    783
  Planarity :  0.004   0.033    604
  Dihedral  : 20.064 107.437   1456
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.31 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 28.48 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.44), residues: 371
  helix:  0.80 (0.39), residues: 179
  sheet: -0.88 (1.03), residues: 28
  loop : -0.04 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  80 
 TYR   0.023   0.003   TYR C  74 
 PHE   0.013   0.002   PHE C 123 
 TRP   0.019   0.003   TRP C  32 
 HIS   0.011   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4677)
  covalent geometry    : angle       0.67441 ( 6613)
  hydrogen bonds       : bond        0.04236 (  204)
  hydrogen bonds       : angle       3.87676 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8998 (mmm) cc_final: 0.8633 (mmm)
REVERT: B   39 GLN cc_start: 0.7744 (tp-100) cc_final: 0.7435 (tp40)
REVERT: B   46 CYS cc_start: 0.7529 (m) cc_final: 0.7225 (m)
REVERT: B   59 GLN cc_start: 0.8474 (mt0) cc_final: 0.8037 (mt0)
REVERT: C   29 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7587 (ttm110)
REVERT: C   61 GLN cc_start: 0.8839 (mp10) cc_final: 0.8506 (mp10)
REVERT: D  329 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6904 (ttm170)
REVERT: D  362 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6338 (mmp80)
  outliers start: 11
  outliers final: 8
  residues processed: 87
  average time/residue: 0.1260
  time to fit residues: 12.7336
Evaluate side-chains
  86 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.105634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.081313 restraints weight = 13615.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 3.13
r_work: 0.3433 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4677  Z= 0.174
  Angle     :  0.677  14.031   6613  Z= 0.332
  Chirality :  0.036   0.148    783
  Planarity :  0.004   0.034    604
  Dihedral  : 20.063 107.528   1456
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.77 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 29.10 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.44), residues: 371
  helix:  0.75 (0.39), residues: 179
  sheet: -0.87 (1.04), residues: 28
  loop : -0.06 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  80 
 TYR   0.023   0.002   TYR C  74 
 PHE   0.011   0.002   PHE C 123 
 TRP   0.024   0.003   TRP C  32 
 HIS   0.011   0.002   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4677)
  covalent geometry    : angle       0.67744 ( 6613)
  hydrogen bonds       : bond        0.04181 (  204)
  hydrogen bonds       : angle       3.88646 (  522)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 MET cc_start: 0.8987 (mmm) cc_final: 0.8617 (mmm)
REVERT: B   39 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7428 (tp40)
REVERT: B   46 CYS cc_start: 0.7582 (m) cc_final: 0.7298 (m)
REVERT: B   59 GLN cc_start: 0.8465 (mt0) cc_final: 0.8027 (mt0)
REVERT: C   29 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7586 (ttm110)
REVERT: C   61 GLN cc_start: 0.8836 (mp10) cc_final: 0.8490 (mp10)
REVERT: D  329 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6948 (ttm170)
REVERT: D  346 GLU cc_start: 0.7652 (tp30) cc_final: 0.7445 (tp30)
REVERT: D  362 ARG cc_start: 0.7238 (tpt170) cc_final: 0.6474 (mmp80)
  outliers start: 8
  outliers final: 8
  residues processed: 81
  average time/residue: 0.1193
  time to fit residues: 11.3100
Evaluate side-chains
  84 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain D residue  366 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.106380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.082006 restraints weight = 13639.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 3.11
r_work: 0.3449 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4677  Z= 0.157
  Angle     :  0.672  14.292   6613  Z= 0.331
  Chirality :  0.036   0.151    783
  Planarity :  0.004   0.033    604
  Dihedral  : 20.032 107.473   1456
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.04 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 28.79 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.44), residues: 371
  helix:  0.82 (0.39), residues: 178
  sheet: -0.88 (1.03), residues: 28
  loop : -0.06 (0.51), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  80 
 TYR   0.021   0.002   TYR C  74 
 PHE   0.011   0.001   PHE C 123 
 TRP   0.027   0.003   TRP C  32 
 HIS   0.014   0.003   HIS D 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4677)
  covalent geometry    : angle       0.67161 ( 6613)
  hydrogen bonds       : bond        0.04099 (  204)
  hydrogen bonds       : angle       3.82686 (  522)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1748.35 seconds
wall clock time: 30 minutes 34.21 seconds (1834.21 seconds total)