Starting phenix.real_space_refine
on Tue Feb  3 12:20:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j4d_61132/02_2026/9j4d_61132.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j4d_61132/02_2026/9j4d_61132.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j4d_61132/02_2026/9j4d_61132.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j4d_61132/02_2026/9j4d_61132.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j4d_61132/02_2026/9j4d_61132.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j4d_61132/02_2026/9j4d_61132.cif"
  }
  resolution = 2.93
  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=   0.001 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: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    1044      2.51       5
     N     294      2.21       5
     O     312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1668
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 278
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
  Restraints were copied for chains:
    C, D, E, A, B
  Time building chain proxies: 0.38, per 1000 atoms: 0.23
  Number of scatterers: 1668
  At special positions: 0
  Unit cell: (79.5, 77.38, 36.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     312      8.00
     N     294      7.00
     C    1044      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  80 " - pdb=" SG  CYS F  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS C  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  80 " - pdb=" SG  CYS E  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS B  83 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.12
  Conformation dependent library (CDL) restraints added in 68.7 milliseconds
  

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  396

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 34.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 71 through 72
      removed outlier: 6.656A  pdb=" N   MET F  71 " --> pdb=" O   HIS D  72 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 79 through 85
      removed outlier: 6.823A  pdb=" N   CYS C  83 " --> pdb=" O   ASP F  82 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   GLN F  84 " --> pdb=" O   CYS C  83 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL C  85 " --> pdb=" O   GLN F  84 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU F  79 " --> pdb=" O   CYS D  80 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   ASP D  82 " --> pdb=" O   LEU F  79 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   LYS F  81 " --> pdb=" O   ASP D  82 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   GLN D  84 " --> pdb=" O   LYS F  81 " (cutoff:3.500A)
      removed outlier: 9.254A  pdb=" N   CYS F  83 " --> pdb=" O   GLN D  84 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 90 through 94
      removed outlier: 6.328A  pdb=" N   ASN F  90 " --> pdb=" O   VAL C  91 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   VAL C  93 " --> pdb=" O   ASN F  90 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR F  92 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.247A  pdb=" N   LYS F 102 " --> pdb=" O   ILE D 103 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72
      removed outlier: 6.657A  pdb=" N   MET E  71 " --> pdb=" O   HIS B  72 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 79 through 85
      removed outlier: 6.824A  pdb=" N   CYS A  83 " --> pdb=" O   ASP E  82 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   GLN E  84 " --> pdb=" O   CYS A  83 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL A  85 " --> pdb=" O   GLN E  84 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU E  79 " --> pdb=" O   CYS B  80 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   ASP B  82 " --> pdb=" O   LEU E  79 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   LYS E  81 " --> pdb=" O   ASP B  82 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   GLN B  84 " --> pdb=" O   LYS E  81 " (cutoff:3.500A)
      removed outlier: 9.255A  pdb=" N   CYS E  83 " --> pdb=" O   GLN B  84 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.328A  pdb=" N   ASN E  90 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   VAL A  93 " --> pdb=" O   ASN E  90 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR E  92 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 103
      removed outlier: 6.247A  pdb=" N   LYS E 102 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)

    18 hydrogen bonds defined for protein.
    54 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: 0.21

  Time building geometry restraints manager: 0.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 540
        1.34 -     1.46: 272
        1.46 -     1.57: 850
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 1686
  Sorted by residual:
  bond pdb=" CZ  ARG E  89 "
       pdb=" NH2 ARG E  89 "
    ideal  model  delta    sigma   weight residual
    1.330  1.323  0.007 1.30e-02 5.92e+03 2.95e-01
  bond pdb=" CB  VAL E  93 "
       pdb=" CG2 VAL E  93 "
    ideal  model  delta    sigma   weight residual
    1.521  1.504  0.017 3.30e-02 9.18e+02 2.79e-01
  bond pdb=" CZ  ARG A  89 "
       pdb=" NH2 ARG A  89 "
    ideal  model  delta    sigma   weight residual
    1.330  1.323  0.007 1.30e-02 5.92e+03 2.61e-01
  bond pdb=" CB  VAL A  93 "
       pdb=" CG2 VAL A  93 "
    ideal  model  delta    sigma   weight residual
    1.521  1.504  0.017 3.30e-02 9.18e+02 2.60e-01
  bond pdb=" CB  VAL B  93 "
       pdb=" CG2 VAL B  93 "
    ideal  model  delta    sigma   weight residual
    1.521  1.504  0.017 3.30e-02 9.18e+02 2.57e-01
  ... (remaining 1681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 2021
        1.04 -     2.08: 181
        2.08 -     3.13: 33
        3.13 -     4.17: 3
        4.17 -     5.21: 18
  Bond angle restraints: 2256
  Sorted by residual:
  angle pdb=" C   LYS A  74 "
        pdb=" N   ASN A  75 "
        pdb=" CA  ASN A  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.73   -5.19 1.91e+00 2.74e-01 7.39e+00
  angle pdb=" C   LYS B  74 "
        pdb=" N   ASN B  75 "
        pdb=" CA  ASN B  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.72   -5.18 1.91e+00 2.74e-01 7.35e+00
  angle pdb=" C   LYS D  74 "
        pdb=" N   ASN D  75 "
        pdb=" CA  ASN D  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.68   -5.14 1.91e+00 2.74e-01 7.25e+00
  angle pdb=" C   LYS F  74 "
        pdb=" N   ASN F  75 "
        pdb=" CA  ASN F  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.68   -5.14 1.91e+00 2.74e-01 7.25e+00
  angle pdb=" C   LYS C  74 "
        pdb=" N   ASN C  75 "
        pdb=" CA  ASN C  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.68   -5.14 1.91e+00 2.74e-01 7.24e+00
  ... (remaining 2251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 852
       15.05 -    30.10: 156
       30.10 -    45.15: 24
       45.15 -    60.19: 6
       60.19 -    75.24: 6
  Dihedral angle restraints: 1044
    sinusoidal: 444
      harmonic: 600
  Sorted by residual:
  dihedral pdb=" CA  ASN E  75 "
           pdb=" C   ASN E  75 "
           pdb=" N   TRP E  76 "
           pdb=" CA  TRP E  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  ASN C  75 "
           pdb=" C   ASN C  75 "
           pdb=" N   TRP C  76 "
           pdb=" CA  TRP C  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  ASN A  75 "
           pdb=" C   ASN A  75 "
           pdb=" N   TRP A  76 "
           pdb=" CA  TRP A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 1041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 118
       0.027 -    0.054: 65
       0.054 -    0.082: 17
       0.082 -    0.109: 46
       0.109 -    0.136: 18
  Chirality restraints: 264
  Sorted by residual:
  chirality pdb=" CB  VAL B  93 "
            pdb=" CA  VAL B  93 "
            pdb=" CG1 VAL B  93 "
            pdb=" CG2 VAL B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CB  VAL A  93 "
            pdb=" CA  VAL A  93 "
            pdb=" CG1 VAL A  93 "
            pdb=" CG2 VAL A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CB  VAL E  93 "
            pdb=" CA  VAL E  93 "
            pdb=" CG1 VAL E  93 "
            pdb=" CG2 VAL E  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 261 not shown)

  Planarity restraints: 276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E  86 "    0.003 2.00e-02 2.50e+03   5.79e-03 3.35e-01
        pdb=" C   ILE E  86 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   ILE E  86 "    0.004 2.00e-02 2.50e+03
        pdb=" N   ASP E  87 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C  86 "    0.003 2.00e-02 2.50e+03   5.75e-03 3.31e-01
        pdb=" C   ILE C  86 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   ILE C  86 "    0.004 2.00e-02 2.50e+03
        pdb=" N   ASP C  87 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  86 "    0.003 2.00e-02 2.50e+03   5.73e-03 3.29e-01
        pdb=" C   ILE B  86 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   ILE B  86 "    0.004 2.00e-02 2.50e+03
        pdb=" N   ASP B  87 "    0.003 2.00e-02 2.50e+03
  ... (remaining 273 not shown)

  Histogram of nonbonded interaction distances:
        2.65 -     3.10: 1179
        3.10 -     3.55: 1583
        3.55 -     4.00: 2346
        4.00 -     4.45: 2713
        4.45 -     4.90: 4957
  Nonbonded interactions: 12778
  Sorted by model distance:
  nonbonded pdb=" O   ASP E  95 "
            pdb=" OD1 ASP E  95 "
     model   vdw
     2.655 3.040
  nonbonded pdb=" O   ASP F  95 "
            pdb=" OD1 ASP F  95 "
     model   vdw
     2.655 3.040
  nonbonded pdb=" O   ASP B  95 "
            pdb=" OD1 ASP B  95 "
     model   vdw
     2.656 3.040
  nonbonded pdb=" O   ASP D  95 "
            pdb=" OD1 ASP D  95 "
     model   vdw
     2.656 3.040
  nonbonded pdb=" O   ASP A  95 "
            pdb=" OD1 ASP A  95 "
     model   vdw
     2.656 3.040
  ... (remaining 12773 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 'F'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'A'
  selection = chain 'B'
}

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:             0.700
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.580
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:6.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1692  Z= 0.155
  Angle     :  0.756   5.210   2268  Z= 0.420
  Chirality :  0.058   0.136    264
  Planarity :  0.002   0.006    276
  Dihedral  : 16.105  75.243    630
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.19 %
    Favored  : 80.81 %
  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: -4.69 (0.32), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.24), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 PHE   0.005   0.002   PHE E 100 
 TRP   0.009   0.002   TRP A  76 
 HIS   0.001   0.000   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 1686)
  covalent geometry    : angle       0.75661 ( 2256)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       0.63815 (   12)
  hydrogen bonds       : bond        0.33595 (   18)
  hydrogen bonds       : angle      10.42138 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.078 
Fit side-chains
REVERT: C   74 LYS cc_start: 0.7184 (tptp) cc_final: 0.6368 (pptt)
REVERT: A   74 LYS cc_start: 0.6856 (tptp) cc_final: 0.6142 (pptt)
REVERT: A   81 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8266 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.5268
  time to fit residues: 25.7133
Evaluate side-chains
  38 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0070
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
F  84 GLN
C  84 GLN
D  84 GLN
E  84 GLN
A  84 GLN
B  84 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.227753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.187901 restraints weight = 1611.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.15
r_work: 0.4204 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.4091 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   1692  Z= 0.095
  Angle     :  0.690   5.779   2268  Z= 0.368
  Chirality :  0.052   0.123    264
  Planarity :  0.002   0.013    276
  Dihedral  :  6.914  20.651    210
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 29.80 %
    Favored  : 66.16 %
  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: -3.69 (0.39), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.30), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C  89 
 PHE   0.005   0.001   PHE A 100 
 TRP   0.034   0.005   TRP F  76 
 HIS   0.001   0.000   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 1686)
  covalent geometry    : angle       0.69153 ( 2256)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       0.44236 (   12)
  hydrogen bonds       : bond        0.02889 (   18)
  hydrogen bonds       : angle       8.03559 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.074 
Fit side-chains
REVERT: C   76 TRP cc_start: 0.7941 (m-90) cc_final: 0.7627 (m-90)
REVERT: A   76 TRP cc_start: 0.7793 (m-90) cc_final: 0.7404 (m-90)
REVERT: A   81 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8325 (ttmt)
  outliers start: 8
  outliers final: 3
  residues processed: 46
  average time/residue: 0.5092
  time to fit residues: 23.8555
Evaluate side-chains
  42 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   74 LYS
Chi-restraints excluded: chain D residue  101 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 17 optimal weight:    0.4980
   chunk 12 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
** D  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  75 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.221696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.184343 restraints weight = 1641.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.4321 rms_B_bonded: 2.12
r_work: 0.4207 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.4098 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1692  Z= 0.122
  Angle     :  0.693   6.567   2268  Z= 0.368
  Chirality :  0.052   0.180    264
  Planarity :  0.002   0.014    276
  Dihedral  :  6.711  17.528    210
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.13 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.80 %
    Favored  : 64.65 %
  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: -3.23 (0.43), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.33), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.006   0.002   PHE A 100 
 TRP   0.036   0.004   TRP F  76 
 HIS   0.001   0.001   HIS F  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 1686)
  covalent geometry    : angle       0.69369 ( 2256)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       0.42229 (   12)
  hydrogen bonds       : bond        0.03492 (   18)
  hydrogen bonds       : angle       7.88566 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.073 
Fit side-chains
REVERT: C   75 ASN cc_start: 0.7015 (m-40) cc_final: 0.6750 (m110)
REVERT: A   75 ASN cc_start: 0.6994 (m-40) cc_final: 0.6698 (m110)
REVERT: A   78 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7800 (ptpt)
  outliers start: 11
  outliers final: 4
  residues processed: 49
  average time/residue: 0.4916
  time to fit residues: 24.5223
Evaluate side-chains
  45 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain B residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.4691 r_free = 0.4691 target = 0.219229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.182302 restraints weight = 1557.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.4293 rms_B_bonded: 1.98
r_work: 0.4184 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.4076 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1692  Z= 0.168
  Angle     :  0.761   6.337   2268  Z= 0.404
  Chirality :  0.053   0.174    264
  Planarity :  0.003   0.015    276
  Dihedral  :  6.936  17.911    210
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 30.30 %
    Favored  : 63.64 %
  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: -3.16 (0.44), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.34), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  89 
 PHE   0.010   0.003   PHE F 100 
 TRP   0.038   0.005   TRP F  76 
 HIS   0.002   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 1686)
  covalent geometry    : angle       0.76218 ( 2256)
  SS BOND              : bond        0.00403 (    6)
  SS BOND              : angle       0.50237 (   12)
  hydrogen bonds       : bond        0.03938 (   18)
  hydrogen bonds       : angle       7.96087 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.077 
Fit side-chains
REVERT: E  104 LYS cc_start: 0.7982 (tppt) cc_final: 0.7782 (tppt)
REVERT: B  104 LYS cc_start: 0.8008 (tptp) cc_final: 0.7755 (tppp)
  outliers start: 12
  outliers final: 7
  residues processed: 46
  average time/residue: 0.5219
  time to fit residues: 24.4247
Evaluate side-chains
  45 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   79 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0170
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.4024

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.225935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.188307 restraints weight = 1589.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.4356 rms_B_bonded: 2.00
r_work: 0.4252 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.4144 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   1692  Z= 0.117
  Angle     :  0.701   5.138   2268  Z= 0.367
  Chirality :  0.052   0.153    264
  Planarity :  0.002   0.015    276
  Dihedral  :  6.517  17.357    210
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.13 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 32.32 %
    Favored  : 62.12 %
  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: -3.10 (0.45), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.35), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.006   0.002   PHE A 100 
 TRP   0.041   0.004   TRP F  76 
 HIS   0.001   0.000   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 1686)
  covalent geometry    : angle       0.70233 ( 2256)
  SS BOND              : bond        0.00333 (    6)
  SS BOND              : angle       0.46231 (   12)
  hydrogen bonds       : bond        0.03284 (   18)
  hydrogen bonds       : angle       7.58613 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 LYS cc_start: 0.7727 (tmmt) cc_final: 0.7417 (tmmt)
REVERT: A   78 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7596 (ptpt)
REVERT: A  104 LYS cc_start: 0.5197 (tppt) cc_final: 0.4890 (tppt)
  outliers start: 11
  outliers final: 6
  residues processed: 49
  average time/residue: 0.4818
  time to fit residues: 24.0459
Evaluate side-chains
  49 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   79 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    0.0270
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   overall best weight:    2.6044

-------------------------------------------------------------------------------
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 = 0.4716 r_free = 0.4716 target = 0.219728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.184019 restraints weight = 1576.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.4312 rms_B_bonded: 2.00
r_work: 0.4190 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.4078 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1692  Z= 0.165
  Angle     :  0.764   6.311   2268  Z= 0.402
  Chirality :  0.052   0.132    264
  Planarity :  0.003   0.017    276
  Dihedral  :  6.915  17.382    210
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.65 %
    Favored  : 85.35 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 35.86 %
    Favored  : 58.08 %
  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: -3.09 (0.46), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.35), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.011   0.002   PHE F 100 
 TRP   0.045   0.005   TRP F  76 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 1686)
  covalent geometry    : angle       0.76494 ( 2256)
  SS BOND              : bond        0.00414 (    6)
  SS BOND              : angle       0.48408 (   12)
  hydrogen bonds       : bond        0.03600 (   18)
  hydrogen bonds       : angle       7.88512 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: D  104 LYS cc_start: 0.7886 (tptt) cc_final: 0.7267 (tttm)
REVERT: E  104 LYS cc_start: 0.7809 (tppt) cc_final: 0.7566 (tppt)
REVERT: A  104 LYS cc_start: 0.4923 (OUTLIER) cc_final: 0.4602 (tppt)
  outliers start: 12
  outliers final: 6
  residues processed: 49
  average time/residue: 0.4264
  time to fit residues: 21.2852
Evaluate side-chains
  46 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain B residue   74 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 4 optimal weight:    0.3980
   chunk 14 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
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 = 0.4736 r_free = 0.4736 target = 0.220594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.184453 restraints weight = 1521.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 1.91
r_work: 0.4222 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.4114 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   1692  Z= 0.166
  Angle     :  0.778   6.098   2268  Z= 0.406
  Chirality :  0.053   0.130    264
  Planarity :  0.003   0.019    276
  Dihedral  :  6.957  18.064    210
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.15 %
    Favored  : 84.85 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 39.90 %
    Favored  : 54.55 %
  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: -3.15 (0.46), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.35), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.010   0.003   PHE F 100 
 TRP   0.051   0.005   TRP F  76 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 1686)
  covalent geometry    : angle       0.77895 ( 2256)
  SS BOND              : bond        0.00412 (    6)
  SS BOND              : angle       0.52108 (   12)
  hydrogen bonds       : bond        0.03331 (   18)
  hydrogen bonds       : angle       7.83975 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.043 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 LYS cc_start: 0.7641 (tmmt) cc_final: 0.7351 (tmmt)
REVERT: E  104 LYS cc_start: 0.7800 (tppt) cc_final: 0.7554 (tppt)
REVERT: A  104 LYS cc_start: 0.5002 (OUTLIER) cc_final: 0.3674 (tttp)
  outliers start: 11
  outliers final: 5
  residues processed: 47
  average time/residue: 0.2918
  time to fit residues: 13.9807
Evaluate side-chains
  45 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  104 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.4773 r_free = 0.4773 target = 0.223764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.185812 restraints weight = 1530.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 1.95
r_work: 0.4213 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.4102 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1692  Z= 0.162
  Angle     :  0.791   6.156   2268  Z= 0.410
  Chirality :  0.053   0.130    264
  Planarity :  0.003   0.021    276
  Dihedral  :  6.988  18.518    210
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.65 %
    Favored  : 85.35 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 41.41 %
    Favored  : 53.54 %
  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: -3.17 (0.47), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.010   0.002   PHE F 100 
 TRP   0.054   0.006   TRP F  76 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 1686)
  covalent geometry    : angle       0.79202 ( 2256)
  SS BOND              : bond        0.00399 (    6)
  SS BOND              : angle       0.52245 (   12)
  hydrogen bonds       : bond        0.03244 (   18)
  hydrogen bonds       : angle       7.83270 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.043 
Fit side-chains
   revert: symmetry clash
REVERT: D  104 LYS cc_start: 0.8090 (tptt) cc_final: 0.7842 (tptm)
REVERT: E  104 LYS cc_start: 0.7818 (tppt) cc_final: 0.7593 (tppt)
REVERT: A   78 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7669 (ptpt)
REVERT: A  104 LYS cc_start: 0.5091 (OUTLIER) cc_final: 0.3726 (tttp)
  outliers start: 10
  outliers final: 5
  residues processed: 47
  average time/residue: 0.3154
  time to fit residues: 15.0930
Evaluate side-chains
  44 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  104 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.4767 r_free = 0.4767 target = 0.222166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.185221 restraints weight = 1561.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.4351 rms_B_bonded: 1.93
r_work: 0.4242 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.4137 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1692  Z= 0.143
  Angle     :  0.779   5.753   2268  Z= 0.404
  Chirality :  0.052   0.129    264
  Planarity :  0.003   0.024    276
  Dihedral  :  6.730  18.432    210
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.15 %
    Favored  : 84.85 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 42.42 %
    Favored  : 53.54 %
  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: -3.18 (0.47), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.007   0.002   PHE A 100 
 TRP   0.063   0.006   TRP F  76 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 1686)
  covalent geometry    : angle       0.78030 ( 2256)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       0.49970 (   12)
  hydrogen bonds       : bond        0.03007 (   18)
  hydrogen bonds       : angle       7.66990 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.044 
Fit side-chains
REVERT: F  104 LYS cc_start: 0.7497 (tmmt) cc_final: 0.7210 (tmmt)
REVERT: E  104 LYS cc_start: 0.7902 (tppt) cc_final: 0.7660 (tppt)
REVERT: A   78 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7704 (ptpt)
REVERT: A  104 LYS cc_start: 0.4994 (OUTLIER) cc_final: 0.3618 (tttp)
  outliers start: 8
  outliers final: 6
  residues processed: 44
  average time/residue: 0.4060
  time to fit residues: 18.2150
Evaluate side-chains
  44 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  104 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0870
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.2166

-------------------------------------------------------------------------------
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 = 0.4759 r_free = 0.4759 target = 0.221453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.184823 restraints weight = 1557.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.4344 rms_B_bonded: 1.93
r_work: 0.4235 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.4127 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   1692  Z= 0.154
  Angle     :  0.807   5.978   2268  Z= 0.417
  Chirality :  0.052   0.128    264
  Planarity :  0.003   0.024    276
  Dihedral  :  6.856  20.095    210
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.66 %
    Favored  : 84.34 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 40.91 %
    Favored  : 54.04 %
  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 are not related in a simple way.
  whole: -3.17 (0.47), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  89 
 PHE   0.009   0.002   PHE F 100 
 TRP   0.063   0.007   TRP F  76 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 1686)
  covalent geometry    : angle       0.80853 ( 2256)
  SS BOND              : bond        0.00363 (    6)
  SS BOND              : angle       0.54533 (   12)
  hydrogen bonds       : bond        0.03096 (   18)
  hydrogen bonds       : angle       7.79706 (   54)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.069 
Fit side-chains
REVERT: D  104 LYS cc_start: 0.8139 (tptt) cc_final: 0.7805 (tptm)
REVERT: E  104 LYS cc_start: 0.7906 (tppt) cc_final: 0.7665 (tppt)
REVERT: A   78 LYS cc_start: 0.8033 (ptpt) cc_final: 0.7636 (ptpp)
REVERT: A  104 LYS cc_start: 0.4989 (OUTLIER) cc_final: 0.3625 (tttp)
  outliers start: 10
  outliers final: 5
  residues processed: 45
  average time/residue: 0.3192
  time to fit residues: 14.6612
Evaluate side-chains
  43 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  104 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.4715 r_free = 0.4715 target = 0.217630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.181783 restraints weight = 1539.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.4312 rms_B_bonded: 1.86
r_work: 0.4205 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4099 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   1692  Z= 0.206
  Angle     :  0.922  11.370   2268  Z= 0.470
  Chirality :  0.056   0.165    264
  Planarity :  0.004   0.024    276
  Dihedral  :  7.218  20.617    210
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.66 %
    Favored  : 84.34 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 42.42 %
    Favored  : 53.54 %
  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: -3.21 (0.47), residues: 198
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  89 
 PHE   0.013   0.003   PHE F 100 
 TRP   0.063   0.007   TRP F  76 
 HIS   0.002   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 1686)
  covalent geometry    : angle       0.92348 ( 2256)
  SS BOND              : bond        0.00447 (    6)
  SS BOND              : angle       0.63940 (   12)
  hydrogen bonds       : bond        0.03436 (   18)
  hydrogen bonds       : angle       8.06001 (   54)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 904.10 seconds
wall clock time: 16 minutes 2.84 seconds (962.84 seconds total)