Starting phenix.real_space_refine
on Tue Mar  3 12:19:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kjr_22898/03_2026/7kjr_22898.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kjr_22898/03_2026/7kjr_22898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_2026/7kjr_22898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_2026/7kjr_22898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_2026/7kjr_22898.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_2026/7kjr_22898.cif"
  }
  resolution = 2.08
  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=   0.002 sd=   0.067
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       2      5.49       5
     S      18      5.16       5
     C    2446      2.51       5
     N     580      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3840
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1575
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 4, 'TRANS': 188}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1575
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 4, 'TRANS': 188}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 261
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
    Chain: "D"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 261
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 28
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 28
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 61
          Classifications: {'water': 61}
          Link IDs: {None: 60}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 61
          Classifications: {'water': 61}
          Link IDs: {None: 60}
  Time building chain proxies: 1.06, per 1000 atoms: 0.28
  Number of scatterers: 3840
  At special positions: 0
  Unit cell: (77.789, 67.611, 90.148, 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      18     16.00
     P       2     15.00
     O     794      8.00
     N     580      7.00
     C    2446      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: 0.32
  Conformation dependent library (CDL) restraints added in 129.3 milliseconds
  

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  848

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 2 sheets defined
      57.4% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 61
      removed outlier: 3.596A  pdb=" N   ILE A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 100
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 105 through 134
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 219 through 224
    Processing helix  chain 'B' and resid 43 through 61
      removed outlier: 3.716A  pdb=" N   ILE B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 100
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 105 through 134
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 219 through 224
    Processing helix  chain 'C' and resid 26 through 55
      Proline residue:  C  34  - end of helix
      removed outlier: 5.027A  pdb=" N   GLY C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 5.263A  pdb=" N   LEU C  50 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 47
      Proline residue:  D  34  - end of helix
    Processing helix  chain 'D' and resid 47 through 55
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160
      removed outlier: 5.965A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   CYS A 200 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 5.445A  pdb=" N   LEU A 214 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASN A 234 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160
      removed outlier: 5.963A  pdb=" N   HIS B 150 " --> pdb=" O   CYS B 200 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   CYS B 200 " --> pdb=" O   HIS B 150 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   LEU B 214 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ASN B 234 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)

    253 hydrogen bonds defined for protein.
    741 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: 0.59

  Time building geometry restraints manager: 0.39 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: 857
        1.33 -     1.45: 906
        1.45 -     1.57: 2029
        1.57 -     1.69: 2
        1.69 -     1.81: 24
  Bond restraints: 3818
  Sorted by residual:
  bond pdb=" O4P PEE B 301 "
       pdb=" P   PEE B 301 "
    ideal  model  delta    sigma   weight residual
    1.653  1.769 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" O4P PEE A 301 "
       pdb=" P   PEE A 301 "
    ideal  model  delta    sigma   weight residual
    1.653  1.769 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" C4  PEE A 301 "
       pdb=" O4P PEE A 301 "
    ideal  model  delta    sigma   weight residual
    1.409  1.365  0.044 2.00e-02 2.50e+03 4.76e+00
  bond pdb=" C4  PEE B 301 "
       pdb=" O4P PEE B 301 "
    ideal  model  delta    sigma   weight residual
    1.409  1.366  0.043 2.00e-02 2.50e+03 4.70e+00
  bond pdb=" C   ILE B  62 "
       pdb=" O   ILE B  62 "
    ideal  model  delta    sigma   weight residual
    1.236  1.218  0.018 1.19e-02 7.06e+03 2.25e+00
  ... (remaining 3813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 5035
        1.99 -     3.98: 113
        3.98 -     5.97: 27
        5.97 -     7.96: 5
        7.96 -     9.95: 6
  Bond angle restraints: 5186
  Sorted by residual:
  angle pdb=" CB  GLN C  37 "
        pdb=" CG  GLN C  37 "
        pdb=" CD  GLN C  37 "
      ideal   model   delta    sigma   weight residual
     112.60  118.61   -6.01 1.70e+00 3.46e-01 1.25e+01
  angle pdb=" CB  GLU B 226 "
        pdb=" CG  GLU B 226 "
        pdb=" CD  GLU B 226 "
      ideal   model   delta    sigma   weight residual
     112.60  118.44   -5.84 1.70e+00 3.46e-01 1.18e+01
  angle pdb=" O1P PEE A 301 "
        pdb=" P   PEE A 301 "
        pdb=" O4P PEE A 301 "
      ideal   model   delta    sigma   weight residual
     109.92   99.97    9.95 3.00e+00 1.11e-01 1.10e+01
  angle pdb=" O1P PEE B 301 "
        pdb=" P   PEE B 301 "
        pdb=" O4P PEE B 301 "
      ideal   model   delta    sigma   weight residual
     109.92   99.99    9.93 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" O1P PEE A 301 "
        pdb=" P   PEE A 301 "
        pdb=" O2P PEE A 301 "
      ideal   model   delta    sigma   weight residual
     119.43  129.00   -9.57 3.00e+00 1.11e-01 1.02e+01
  ... (remaining 5181 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.46: 2076
       30.46 -    60.92: 93
       60.92 -    91.39: 14
       91.39 -   121.85: 1
      121.85 -   152.31: 6
  Dihedral angle restraints: 2190
    sinusoidal: 868
      harmonic: 1322
  Sorted by residual:
  dihedral pdb=" C4  PEE A 301 "
           pdb=" O4P PEE A 301 "
           pdb=" P   PEE A 301 "
           pdb=" O2P PEE A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     284.22  131.91  152.31     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C4  PEE B 301 "
           pdb=" O4P PEE B 301 "
           pdb=" P   PEE B 301 "
           pdb=" O2P PEE B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     284.22  132.36  151.86     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C3  PEE B 301 "
           pdb=" C1  PEE B 301 "
           pdb=" C2  PEE B 301 "
           pdb=" O3P PEE B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73  -63.97  126.70     1      3.00e+01 1.11e-03 1.70e+01
  ... (remaining 2187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 352
       0.036 -    0.071: 156
       0.071 -    0.107: 47
       0.107 -    0.142: 15
       0.142 -    0.178: 6
  Chirality restraints: 576
  Sorted by residual:
  chirality pdb=" CG  LEU A 147 "
            pdb=" CB  LEU A 147 "
            pdb=" CD1 LEU A 147 "
            pdb=" CD2 LEU A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CG  LEU B 147 "
            pdb=" CB  LEU B 147 "
            pdb=" CD1 LEU B 147 "
            pdb=" CD2 LEU B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.81e-01
  chirality pdb=" CG  LEU A 101 "
            pdb=" CB  LEU A 101 "
            pdb=" CD1 LEU A 101 "
            pdb=" CD2 LEU A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.68e-01
  ... (remaining 573 not shown)

  Planarity restraints: 626
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 113 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.27e+00
        pdb=" C   TYR B 113 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   TYR B 113 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PHE B 114 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN D  37 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" CD  GLN D  37 "    0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN D  37 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 GLN D  37 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 114 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.82e+00
        pdb=" C   PHE B 114 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   PHE B 114 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU B 115 "    0.011 2.00e-02 2.50e+03
  ... (remaining 623 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 914
        2.78 -     3.31: 3567
        3.31 -     3.84: 7367
        3.84 -     4.37: 8430
        4.37 -     4.90: 13680
  Nonbonded interactions: 33958
  Sorted by model distance:
  nonbonded pdb=" O   HOH A 424 "
            pdb=" O   HOH A 451 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   HOH B 401 "
            pdb=" O   HOH B 433 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER A 216 "
            pdb=" OE1 GLN A 218 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER B 216 "
            pdb=" OE1 GLN B 218 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   HOH A 401 "
            pdb=" O   HOH A 437 "
     model   vdw
     2.294 3.040
  ... (remaining 33953 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.680
  Find NCS groups from input model:        0.060
  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:8.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
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      :  0.006   0.116   3818  Z= 0.288
  Angle     :  0.843   9.946   5186  Z= 0.426
  Chirality :  0.047   0.178    576
  Planarity :  0.005   0.036    626
  Dihedral  : 19.500 152.312   1342
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 13.05 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.37), residues: 436
  helix:  1.81 (0.31), residues: 234
  sheet:  0.02 (0.48), residues: 90
  loop : -0.81 (0.53), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  29 
 TYR   0.011   0.002   TYR B 109 
 PHE   0.015   0.003   PHE B 146 
 TRP   0.013   0.002   TRP B 149 
 HIS   0.003   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 ( 3818)
  covalent geometry    : angle       0.84253 ( 5186)
  hydrogen bonds       : bond        0.10825 (  253)
  hydrogen bonds       : angle       5.94981 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7754 (m-10) cc_final: 0.6681 (t80)
REVERT: A  136 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7714 (mmtm)
REVERT: B  136 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7686 (mmtm)
REVERT: B  192 LYS cc_start: 0.8741 (tttm) cc_final: 0.8044 (tptt)
  outliers start: 1
  outliers final: 1
  residues processed: 69
  average time/residue: 0.6266
  time to fit residues: 44.5336
Evaluate side-chains
  69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.134277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.098249 restraints weight = 3702.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.60
r_work: 0.3049 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.0781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3818  Z= 0.136
  Angle     :  0.538   6.613   5186  Z= 0.287
  Chirality :  0.041   0.131    576
  Planarity :  0.003   0.035    626
  Dihedral  : 17.740 170.216    525
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.58 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.37), residues: 436
  helix:  2.88 (0.31), residues: 224
  sheet:  0.15 (0.45), residues: 86
  loop : -0.57 (0.48), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  29 
 TYR   0.010   0.001   TYR B 109 
 PHE   0.011   0.002   PHE B  87 
 TRP   0.013   0.001   TRP A 149 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3818)
  covalent geometry    : angle       0.53760 ( 5186)
  hydrogen bonds       : bond        0.04396 (  253)
  hydrogen bonds       : angle       4.64538 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7949 (m-10) cc_final: 0.6472 (t80)
REVERT: A  136 LYS cc_start: 0.8498 (mtpt) cc_final: 0.7703 (mmpt)
REVERT: B  136 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7645 (mmpt)
REVERT: B  152 ASN cc_start: 0.8257 (m-40) cc_final: 0.7114 (p0)
REVERT: B  192 LYS cc_start: 0.8959 (tttm) cc_final: 0.8002 (tptt)
  outliers start: 9
  outliers final: 5
  residues processed: 74
  average time/residue: 0.5920
  time to fit residues: 45.1398
Evaluate side-chains
  75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.133641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.098415 restraints weight = 3604.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.55
r_work: 0.3045 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3818  Z= 0.146
  Angle     :  0.519   6.984   5186  Z= 0.279
  Chirality :  0.041   0.130    576
  Planarity :  0.003   0.036    626
  Dihedral  : 16.888 176.403    522
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.32 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.38), residues: 436
  helix:  3.14 (0.31), residues: 224
  sheet: -0.22 (0.44), residues: 90
  loop : -0.42 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  29 
 TYR   0.009   0.001   TYR B 109 
 PHE   0.012   0.002   PHE B  87 
 TRP   0.012   0.002   TRP B 149 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3818)
  covalent geometry    : angle       0.51873 ( 5186)
  hydrogen bonds       : bond        0.04257 (  253)
  hydrogen bonds       : angle       4.55658 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7929 (m-10) cc_final: 0.6449 (t80)
REVERT: A   68 ARG cc_start: 0.8252 (ttt-90) cc_final: 0.7830 (ttt90)
REVERT: A  136 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7693 (mmpt)
REVERT: B  136 LYS cc_start: 0.8471 (mtpt) cc_final: 0.7673 (mmpt)
REVERT: B  192 LYS cc_start: 0.8958 (tttm) cc_final: 0.7985 (tptt)
  outliers start: 5
  outliers final: 6
  residues processed: 70
  average time/residue: 0.6158
  time to fit residues: 44.3636
Evaluate side-chains
  75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.133091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.096593 restraints weight = 3594.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.60
r_work: 0.3001 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3818  Z= 0.143
  Angle     :  0.507   6.912   5186  Z= 0.273
  Chirality :  0.041   0.128    576
  Planarity :  0.003   0.037    626
  Dihedral  : 16.052 166.287    522
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.07 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.38), residues: 436
  helix:  3.20 (0.31), residues: 224
  sheet: -0.36 (0.44), residues: 90
  loop : -0.42 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  29 
 TYR   0.009   0.001   TYR A 109 
 PHE   0.013   0.002   PHE B 114 
 TRP   0.012   0.002   TRP B 149 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3818)
  covalent geometry    : angle       0.50738 ( 5186)
  hydrogen bonds       : bond        0.04126 (  253)
  hydrogen bonds       : angle       4.51448 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7860 (m-10) cc_final: 0.6274 (t80)
REVERT: A   68 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7732 (ttt90)
REVERT: A  136 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7502 (mmpt)
REVERT: B  136 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7498 (mmpt)
REVERT: B  152 ASN cc_start: 0.8218 (m-40) cc_final: 0.6995 (p0)
REVERT: B  192 LYS cc_start: 0.8919 (tttm) cc_final: 0.7872 (tptt)
  outliers start: 6
  outliers final: 5
  residues processed: 69
  average time/residue: 0.6261
  time to fit residues: 44.4457
Evaluate side-chains
  71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.132981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.096529 restraints weight = 3601.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.60
r_work: 0.2997 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3818  Z= 0.142
  Angle     :  0.506   6.969   5186  Z= 0.271
  Chirality :  0.041   0.130    576
  Planarity :  0.003   0.037    626
  Dihedral  : 14.809 148.270    522
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.30 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.38), residues: 436
  helix:  3.20 (0.31), residues: 224
  sheet: -0.39 (0.45), residues: 90
  loop : -0.45 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  29 
 TYR   0.009   0.001   TYR A 109 
 PHE   0.012   0.002   PHE B  87 
 TRP   0.011   0.002   TRP B 149 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3818)
  covalent geometry    : angle       0.50603 ( 5186)
  hydrogen bonds       : bond        0.04098 (  253)
  hydrogen bonds       : angle       4.50286 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7871 (m-10) cc_final: 0.6258 (t80)
REVERT: A   68 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7734 (ttt90)
REVERT: A  136 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7493 (mmpt)
REVERT: B  101 LEU cc_start: 0.7638 (mm) cc_final: 0.7432 (mm)
REVERT: B  136 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7494 (mmpt)
REVERT: B  152 ASN cc_start: 0.8237 (m-40) cc_final: 0.7004 (p0)
REVERT: B  192 LYS cc_start: 0.8895 (tttm) cc_final: 0.7860 (tptt)
  outliers start: 4
  outliers final: 5
  residues processed: 67
  average time/residue: 0.6432
  time to fit residues: 44.3341
Evaluate side-chains
  71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.133741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.097252 restraints weight = 3617.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.60
r_work: 0.3009 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3818  Z= 0.125
  Angle     :  0.485   6.413   5186  Z= 0.261
  Chirality :  0.040   0.130    576
  Planarity :  0.003   0.037    626
  Dihedral  : 14.043 127.758    522
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.30 %
    Favored  : 85.47 %
  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 are not related in a simple way.
  whole:  2.27 (0.38), residues: 436
  helix:  3.30 (0.31), residues: 224
  sheet: -0.40 (0.44), residues: 90
  loop : -0.47 (0.52), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  29 
 TYR   0.008   0.001   TYR B 109 
 PHE   0.010   0.001   PHE A  87 
 TRP   0.012   0.002   TRP A 149 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3818)
  covalent geometry    : angle       0.48522 ( 5186)
  hydrogen bonds       : bond        0.03876 (  253)
  hydrogen bonds       : angle       4.41280 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7867 (m-10) cc_final: 0.6270 (t80)
REVERT: A   68 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7718 (ttt90)
REVERT: A  136 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7488 (mmpt)
REVERT: B  136 LYS cc_start: 0.8374 (mtpt) cc_final: 0.7480 (mmpt)
REVERT: B  152 ASN cc_start: 0.8240 (m-40) cc_final: 0.7009 (p0)
REVERT: B  192 LYS cc_start: 0.8867 (tttm) cc_final: 0.7908 (tptt)
REVERT: C   29 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6359 (ttt180)
REVERT: C   36 THR cc_start: 0.7355 (m) cc_final: 0.7066 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.6631
  time to fit residues: 48.3934
Evaluate side-chains
  72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain C residue   29 ARG
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.133388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.096829 restraints weight = 3650.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.62
r_work: 0.3003 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3818  Z= 0.135
  Angle     :  0.508   6.749   5186  Z= 0.269
  Chirality :  0.041   0.130    576
  Planarity :  0.003   0.037    626
  Dihedral  : 13.657 118.169    522
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.81 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.38), residues: 436
  helix:  3.27 (0.31), residues: 224
  sheet: -0.42 (0.45), residues: 90
  loop : -0.45 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  29 
 TYR   0.009   0.001   TYR A 109 
 PHE   0.011   0.002   PHE A  87 
 TRP   0.013   0.002   TRP B 128 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3818)
  covalent geometry    : angle       0.50779 ( 5186)
  hydrogen bonds       : bond        0.03964 (  253)
  hydrogen bonds       : angle       4.44340 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7862 (m-10) cc_final: 0.6254 (t80)
REVERT: A   68 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7724 (ttt90)
REVERT: A  136 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7501 (mmpt)
REVERT: A  226 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7803 (mm-30)
REVERT: B  136 LYS cc_start: 0.8389 (mtpt) cc_final: 0.7497 (mmpt)
REVERT: B  152 ASN cc_start: 0.8232 (m-40) cc_final: 0.7005 (p0)
REVERT: B  192 LYS cc_start: 0.8876 (tttm) cc_final: 0.7902 (tptt)
REVERT: C   29 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6354 (ttt180)
REVERT: C   36 THR cc_start: 0.7341 (m) cc_final: 0.7047 (p)
REVERT: D   36 THR cc_start: 0.7316 (m) cc_final: 0.7039 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 69
  average time/residue: 0.6146
  time to fit residues: 43.6258
Evaluate side-chains
  70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain C residue   29 ARG
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.136800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.100629 restraints weight = 3680.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.63
r_work: 0.3098 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3818  Z= 0.116
  Angle     :  0.488   6.007   5186  Z= 0.260
  Chirality :  0.040   0.131    576
  Planarity :  0.003   0.037    626
  Dihedral  : 13.262 123.016    522
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.56 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.38), residues: 436
  helix:  3.33 (0.31), residues: 224
  sheet: -0.41 (0.44), residues: 90
  loop : -0.50 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  29 
 TYR   0.008   0.001   TYR A 109 
 PHE   0.009   0.001   PHE B  87 
 TRP   0.018   0.002   TRP B 128 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3818)
  covalent geometry    : angle       0.48764 ( 5186)
  hydrogen bonds       : bond        0.03728 (  253)
  hydrogen bonds       : angle       4.35926 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7919 (m-10) cc_final: 0.6483 (t80)
REVERT: A   68 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7870 (ttt90)
REVERT: A  136 LYS cc_start: 0.8529 (mtpt) cc_final: 0.7686 (mmpt)
REVERT: A  226 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7964 (mm-30)
REVERT: B   64 THR cc_start: 0.8466 (m) cc_final: 0.8085 (p)
REVERT: B  136 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7673 (mmpt)
REVERT: B  152 ASN cc_start: 0.8321 (m-40) cc_final: 0.7186 (p0)
REVERT: B  192 LYS cc_start: 0.8894 (tttm) cc_final: 0.8052 (tptt)
REVERT: C   36 THR cc_start: 0.7511 (m) cc_final: 0.7255 (p)
REVERT: D   36 THR cc_start: 0.7496 (m) cc_final: 0.7262 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 69
  average time/residue: 0.5905
  time to fit residues: 41.9162
Evaluate side-chains
  70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.136437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.100272 restraints weight = 3648.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.60
r_work: 0.3091 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3818  Z= 0.124
  Angle     :  0.498   6.363   5186  Z= 0.264
  Chirality :  0.040   0.132    576
  Planarity :  0.003   0.036    626
  Dihedral  : 12.847 127.647    522
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.30 %
    Favored  : 85.47 %
  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 are not related in a simple way.
  whole:  2.26 (0.38), residues: 436
  helix:  3.33 (0.31), residues: 224
  sheet: -0.41 (0.44), residues: 90
  loop : -0.55 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  68 
 TYR   0.009   0.001   TYR A 109 
 PHE   0.010   0.001   PHE B  87 
 TRP   0.024   0.002   TRP B 128 
 HIS   0.003   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3818)
  covalent geometry    : angle       0.49795 ( 5186)
  hydrogen bonds       : bond        0.03797 (  253)
  hydrogen bonds       : angle       4.40418 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7900 (m-10) cc_final: 0.6413 (t80)
REVERT: A   64 THR cc_start: 0.8363 (m) cc_final: 0.8056 (p)
REVERT: A   68 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7817 (ttt90)
REVERT: A  136 LYS cc_start: 0.8475 (mtpt) cc_final: 0.7600 (mmpt)
REVERT: A  226 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7916 (mm-30)
REVERT: B   64 THR cc_start: 0.8413 (m) cc_final: 0.8029 (p)
REVERT: B  136 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7604 (mmpt)
REVERT: B  152 ASN cc_start: 0.8292 (m-40) cc_final: 0.7127 (p0)
REVERT: B  192 LYS cc_start: 0.8888 (tttm) cc_final: 0.7986 (tptt)
REVERT: C   36 THR cc_start: 0.7486 (m) cc_final: 0.7200 (p)
REVERT: D   36 THR cc_start: 0.7433 (m) cc_final: 0.7191 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 70
  average time/residue: 0.5682
  time to fit residues: 41.0172
Evaluate side-chains
  72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.133316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.096533 restraints weight = 3620.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.62
r_work: 0.3002 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3818  Z= 0.141
  Angle     :  0.524   6.886   5186  Z= 0.277
  Chirality :  0.041   0.131    576
  Planarity :  0.003   0.037    626
  Dihedral  : 12.768 130.264    522
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.30 %
    Favored  : 85.47 %
  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 are not related in a simple way.
  whole:  2.23 (0.38), residues: 436
  helix:  3.29 (0.31), residues: 224
  sheet: -0.40 (0.44), residues: 90
  loop : -0.54 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  29 
 TYR   0.009   0.001   TYR B 109 
 PHE   0.011   0.002   PHE B  87 
 TRP   0.030   0.002   TRP B 128 
 HIS   0.003   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3818)
  covalent geometry    : angle       0.52352 ( 5186)
  hydrogen bonds       : bond        0.03965 (  253)
  hydrogen bonds       : angle       4.49135 (  741)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   43 PHE cc_start: 0.7903 (m-10) cc_final: 0.6295 (t80)
REVERT: A   64 THR cc_start: 0.8329 (m) cc_final: 0.7952 (p)
REVERT: A   68 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7727 (ttt90)
REVERT: A  136 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7487 (mmpt)
REVERT: A  226 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: B   64 THR cc_start: 0.8314 (m) cc_final: 0.7891 (p)
REVERT: B  136 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7499 (mmpt)
REVERT: B  152 ASN cc_start: 0.8234 (m-40) cc_final: 0.7015 (p0)
REVERT: B  192 LYS cc_start: 0.8883 (tttm) cc_final: 0.7869 (tptt)
  outliers start: 5
  outliers final: 4
  residues processed: 69
  average time/residue: 0.5991
  time to fit residues: 42.5706
Evaluate side-chains
  71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain D residue   38 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS
C  42 ASN
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.133754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.097063 restraints weight = 3622.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.60
r_work: 0.3011 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3818  Z= 0.131
  Angle     :  0.514   6.514   5186  Z= 0.273
  Chirality :  0.041   0.131    576
  Planarity :  0.003   0.037    626
  Dihedral  : 12.718 131.706    522
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.05 %
    Favored  : 85.47 %
  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 are not related in a simple way.
  whole:  2.22 (0.38), residues: 436
  helix:  3.28 (0.31), residues: 224
  sheet: -0.41 (0.44), residues: 90
  loop : -0.55 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  29 
 TYR   0.009   0.001   TYR B 109 
 PHE   0.010   0.001   PHE B  87 
 TRP   0.034   0.002   TRP B 128 
 HIS   0.003   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3818)
  covalent geometry    : angle       0.51377 ( 5186)
  hydrogen bonds       : bond        0.03862 (  253)
  hydrogen bonds       : angle       4.46010 (  741)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2035.42 seconds
wall clock time: 35 minutes 25.24 seconds (2125.24 seconds total)