Starting phenix.real_space_refine
on Tue Feb  3 12:56:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jc4_61356/02_2026/9jc4_61356.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jc4_61356/02_2026/9jc4_61356.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jc4_61356/02_2026/9jc4_61356.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jc4_61356/02_2026/9jc4_61356.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jc4_61356/02_2026/9jc4_61356.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jc4_61356/02_2026/9jc4_61356.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 3
    Type Number    sf(0)   Gaussians
     C    1632      2.51       5
     N     444      2.21       5
     O     534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 2610
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 435
          Classifications: {'peptide': 62}
          Link IDs: {'TRANS': 61}
  Restraints were copied for chains:
    F, C, G, D, H
  Time building chain proxies: 0.36, per 1000 atoms: 0.14
  Number of scatterers: 2610
  At special positions: 0
  Unit cell: (86.32, 122.01, 33.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     534      8.00
     N     444      7.00
     C    1632      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: 0.11
  Conformation dependent library (CDL) restraints added in 65.2 milliseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 39 through 40
      removed outlier: 6.350A  pdb=" N   TYR C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 50
      removed outlier: 6.512A  pdb=" N   LYS B  45 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   VAL D  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   GLY B  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   HIS D  50 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 8.888A  pdb=" N   VAL B  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL C  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL D  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   HIS C  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 74 through 78
      removed outlier: 6.609A  pdb=" N   THR B  75 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   ALA D  78 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL B  77 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 82
      removed outlier: 6.891A  pdb=" N   THR C  81 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 89
      removed outlier: 6.440A  pdb=" N   ILE C  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 96
      removed outlier: 6.529A  pdb=" N   VAL B  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 39 through 40
      removed outlier: 6.323A  pdb=" N   TYR G  39 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 45 through 50
      removed outlier: 6.507A  pdb=" N   LYS F  45 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   VAL H  48 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   GLY F  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 10.158A  pdb=" N   HIS H  50 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.884A  pdb=" N   VAL F  49 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL G  48 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL H  49 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   HIS G  50 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 74 through 78
      removed outlier: 6.628A  pdb=" N   THR F  75 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ALA H  78 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL F  77 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 81 through 82
      removed outlier: 6.882A  pdb=" N   THR G  81 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 88 through 89
      removed outlier: 6.416A  pdb=" N   ILE G  88 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 94 through 96
      removed outlier: 6.535A  pdb=" N   VAL F  95 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)

    22 hydrogen bonds defined for protein.
    66 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: 0.18

  Time building geometry restraints manager: 0.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 462
        1.29 -     1.35: 399
        1.35 -     1.42: 102
        1.42 -     1.48: 435
        1.48 -     1.54: 1224
  Bond restraints: 2622
  Sorted by residual:
  bond pdb=" CB  THR G  92 "
       pdb=" CG2 THR G  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.71e+00
  bond pdb=" CB  THR H  92 "
       pdb=" CG2 THR H  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.71e+00
  bond pdb=" CB  THR F  92 "
       pdb=" CG2 THR F  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.70e+00
  bond pdb=" CB  THR D  92 "
       pdb=" CG2 THR D  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.68e+00
  bond pdb=" CB  THR B  92 "
       pdb=" CG2 THR B  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.67e+00
  ... (remaining 2617 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.64: 2916
        0.64 -     1.28: 470
        1.28 -     1.91: 130
        1.91 -     2.55: 12
        2.55 -     3.19: 24
  Bond angle restraints: 3552
  Sorted by residual:
  angle pdb=" C   VAL F  49 "
        pdb=" N   HIS F  50 "
        pdb=" CA  HIS F  50 "
      ideal   model   delta    sigma   weight residual
     121.87  118.68    3.19 1.64e+00 3.72e-01 3.78e+00
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     121.87  118.68    3.19 1.64e+00 3.72e-01 3.78e+00
  angle pdb=" C   VAL H  49 "
        pdb=" N   HIS H  50 "
        pdb=" CA  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     121.87  118.72    3.15 1.64e+00 3.72e-01 3.69e+00
  angle pdb=" C   VAL D  49 "
        pdb=" N   HIS D  50 "
        pdb=" CA  HIS D  50 "
      ideal   model   delta    sigma   weight residual
     121.87  118.72    3.15 1.64e+00 3.72e-01 3.68e+00
  angle pdb=" C   VAL G  49 "
        pdb=" N   HIS G  50 "
        pdb=" CA  HIS G  50 "
      ideal   model   delta    sigma   weight residual
     121.87  118.74    3.13 1.64e+00 3.72e-01 3.63e+00
  ... (remaining 3547 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.46: 1242
        9.46 -    18.92: 191
       18.92 -    28.37: 67
       28.37 -    37.83: 24
       37.83 -    47.29: 18
  Dihedral angle restraints: 1542
    sinusoidal: 522
      harmonic: 1020
  Sorted by residual:
  dihedral pdb=" CA  GLY B  47 "
           pdb=" C   GLY B  47 "
           pdb=" N   VAL B  48 "
           pdb=" CA  VAL B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -167.00  -13.00     0      5.00e+00 4.00e-02 6.76e+00
  dihedral pdb=" CA  GLY C  47 "
           pdb=" C   GLY C  47 "
           pdb=" N   VAL C  48 "
           pdb=" CA  VAL C  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -167.00  -13.00     0      5.00e+00 4.00e-02 6.76e+00
  dihedral pdb=" CA  GLY D  47 "
           pdb=" C   GLY D  47 "
           pdb=" N   VAL D  48 "
           pdb=" CA  VAL D  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -167.01  -12.99     0      5.00e+00 4.00e-02 6.75e+00
  ... (remaining 1539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 282
       0.041 -    0.082: 92
       0.082 -    0.123: 88
       0.123 -    0.165: 6
       0.165 -    0.206: 6
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CB  THR D  92 "
            pdb=" CA  THR D  92 "
            pdb=" OG1 THR D  92 "
            pdb=" CG2 THR D  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  THR F  92 "
            pdb=" CA  THR F  92 "
            pdb=" OG1 THR F  92 "
            pdb=" CG2 THR F  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  THR B  92 "
            pdb=" CA  THR B  92 "
            pdb=" OG1 THR B  92 "
            pdb=" CG2 THR B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 471 not shown)

  Planarity restraints: 438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU G  46 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" CD  GLU G  46 "    0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLU G  46 "   -0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU G  46 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H  46 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.56e+00
        pdb=" CD  GLU H  46 "    0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLU H  46 "   -0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU H  46 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU F  46 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" CD  GLU F  46 "    0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLU F  46 "   -0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU F  46 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 435 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 918
        2.87 -     3.37: 2161
        3.37 -     3.88: 4086
        3.88 -     4.39: 4520
        4.39 -     4.90: 8607
  Nonbonded interactions: 20292
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS C  50 "
            pdb=" OD2 ASP C  51 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" ND1 HIS D  50 "
            pdb=" OD2 ASP D  51 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" ND1 HIS F  50 "
            pdb=" OD2 ASP F  51 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" ND1 HIS G  50 "
            pdb=" OD2 ASP G  51 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" ND1 HIS H  50 "
            pdb=" OD2 ASP H  51 "
     model   vdw
     2.358 3.120
  ... (remaining 20287 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 'B'
  selection = chain 'F'
  selection = chain 'C'
  selection = chain 'G'
  selection = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     2.770
  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:5.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
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   0.054   2622  Z= 0.280
  Angle     :  0.574   3.188   3552  Z= 0.340
  Chirality :  0.060   0.206    474
  Planarity :  0.003   0.013    438
  Dihedral  : 13.108  47.287    894
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  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: -4.95 (0.31), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.23), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR C  39 
 PHE   0.011   0.003   PHE C  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 ( 2622)
  covalent geometry    : angle       0.57383 ( 3552)
  hydrogen bonds       : bond        0.15882 (   22)
  hydrogen bonds       : angle       8.47371 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.060 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8328 (tttt) cc_final: 0.7362 (mptt)
REVERT: F   43 LYS cc_start: 0.8196 (tttt) cc_final: 0.7895 (tmtp)
REVERT: C   43 LYS cc_start: 0.8362 (tttt) cc_final: 0.7695 (mttm)
REVERT: G   43 LYS cc_start: 0.8374 (tttt) cc_final: 0.7705 (tmtt)
REVERT: D   43 LYS cc_start: 0.8275 (tttt) cc_final: 0.7367 (mttm)
REVERT: H   43 LYS cc_start: 0.8213 (tttt) cc_final: 0.7326 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.3834
  time to fit residues: 16.4782
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
F  79 GLN
C  79 GLN
G  79 GLN
D  79 GLN
H  79 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.139654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.106528 restraints weight = 2933.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.76
r_work: 0.3527 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   2622  Z= 0.208
  Angle     :  0.490   2.873   3552  Z= 0.291
  Chirality :  0.056   0.143    474
  Planarity :  0.002   0.008    438
  Dihedral  :  5.067  11.525    372
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 14.13 %
    Favored  : 85.51 %
  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: -3.85 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR B  39 
 PHE   0.012   0.003   PHE D  94 
 HIS   0.005   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 2622)
  covalent geometry    : angle       0.49041 ( 3552)
  hydrogen bonds       : bond        0.02437 (   22)
  hydrogen bonds       : angle       5.78020 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8060 (tttt) cc_final: 0.7004 (mptt)
REVERT: B   61 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8359 (mt-10)
REVERT: F   43 LYS cc_start: 0.7900 (tttt) cc_final: 0.6964 (mptt)
REVERT: C   43 LYS cc_start: 0.8242 (tttt) cc_final: 0.7445 (tmtt)
REVERT: G   43 LYS cc_start: 0.8245 (tttt) cc_final: 0.7510 (tmtt)
REVERT: G   83 GLU cc_start: 0.8064 (mp0) cc_final: 0.7610 (mp0)
REVERT: D   43 LYS cc_start: 0.8058 (tttt) cc_final: 0.6969 (mttm)
REVERT: H   43 LYS cc_start: 0.8054 (tttt) cc_final: 0.7077 (mptt)
  outliers start: 1
  outliers final: 1
  residues processed: 37
  average time/residue: 0.4978
  time to fit residues: 18.8996
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.138298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.105069 restraints weight = 2962.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.82
r_work: 0.3518 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   2622  Z= 0.251
  Angle     :  0.512   2.944   3552  Z= 0.306
  Chirality :  0.057   0.143    474
  Planarity :  0.002   0.008    438
  Dihedral  :  5.135  12.140    372
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.96 %
    Favored  : 85.51 %
  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: -3.37 (0.39), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR D  39 
 PHE   0.015   0.004   PHE B  94 
 HIS   0.005   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 2622)
  covalent geometry    : angle       0.51158 ( 3552)
  hydrogen bonds       : bond        0.02190 (   22)
  hydrogen bonds       : angle       5.07562 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.097 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8118 (tttt) cc_final: 0.7139 (mptt)
REVERT: F   43 LYS cc_start: 0.7977 (tttt) cc_final: 0.7072 (mptt)
REVERT: C   43 LYS cc_start: 0.8224 (tttt) cc_final: 0.7452 (tmtt)
REVERT: C   83 GLU cc_start: 0.8181 (mp0) cc_final: 0.7749 (mp0)
REVERT: G   43 LYS cc_start: 0.8288 (tttt) cc_final: 0.7543 (tmtt)
REVERT: D   43 LYS cc_start: 0.8096 (tttt) cc_final: 0.7078 (mptt)
REVERT: H   43 LYS cc_start: 0.8081 (tttt) cc_final: 0.7147 (mptt)
  outliers start: 7
  outliers final: 5
  residues processed: 40
  average time/residue: 0.5567
  time to fit residues: 22.8152
Evaluate side-chains
  43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0570
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.9704

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

Flipped N/Q/H residues before XYZ refinement:
D  79 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.143303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.110981 restraints weight = 2827.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 2.68
r_work: 0.3637 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2622  Z= 0.084
  Angle     :  0.368   2.094   3552  Z= 0.220
  Chirality :  0.053   0.134    474
  Planarity :  0.001   0.006    438
  Dihedral  :  3.983   9.369    372
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.96 %
    Favored  : 86.23 %
  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: -3.03 (0.41), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR H  39 
 PHE   0.005   0.001   PHE B  94 
 HIS   0.003   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00180 ( 2622)
  covalent geometry    : angle       0.36845 ( 3552)
  hydrogen bonds       : bond        0.01230 (   22)
  hydrogen bonds       : angle       4.52210 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8098 (tttt) cc_final: 0.7136 (mptt)
REVERT: F   43 LYS cc_start: 0.7937 (tttt) cc_final: 0.7040 (mptt)
REVERT: C   43 LYS cc_start: 0.8216 (tttt) cc_final: 0.7427 (tmtt)
REVERT: G   43 LYS cc_start: 0.8214 (tttt) cc_final: 0.7499 (mptp)
REVERT: G   83 GLU cc_start: 0.8069 (mp0) cc_final: 0.7653 (mp0)
REVERT: D   43 LYS cc_start: 0.8024 (tttt) cc_final: 0.7061 (mptt)
REVERT: H   43 LYS cc_start: 0.8043 (tttt) cc_final: 0.7166 (mptt)
  outliers start: 5
  outliers final: 2
  residues processed: 34
  average time/residue: 0.5532
  time to fit residues: 19.3255
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain G residue   72 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
C  79 GLN
G  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.138802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.105743 restraints weight = 2935.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.78
r_work: 0.3518 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   2622  Z= 0.253
  Angle     :  0.494   2.959   3552  Z= 0.298
  Chirality :  0.057   0.141    474
  Planarity :  0.002   0.008    438
  Dihedral  :  4.841  11.767    372
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.68 %
    Favored  : 85.51 %
  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: -2.95 (0.42), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR B  39 
 PHE   0.015   0.004   PHE B  94 
 HIS   0.006   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 2622)
  covalent geometry    : angle       0.49365 ( 3552)
  hydrogen bonds       : bond        0.01770 (   22)
  hydrogen bonds       : angle       4.60213 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8154 (tttt) cc_final: 0.7184 (mptt)
REVERT: F   43 LYS cc_start: 0.8032 (tttt) cc_final: 0.7114 (mptt)
REVERT: C   43 LYS cc_start: 0.8218 (tttt) cc_final: 0.7437 (tmtt)
REVERT: C   83 GLU cc_start: 0.8158 (mp0) cc_final: 0.7697 (mp0)
REVERT: G   43 LYS cc_start: 0.8284 (tttt) cc_final: 0.7616 (tmtt)
REVERT: G   83 GLU cc_start: 0.8106 (mp0) cc_final: 0.7662 (mp0)
REVERT: D   43 LYS cc_start: 0.8158 (tttt) cc_final: 0.7101 (mptt)
REVERT: H   43 LYS cc_start: 0.8089 (tttt) cc_final: 0.7155 (mptt)
  outliers start: 5
  outliers final: 5
  residues processed: 39
  average time/residue: 0.5904
  time to fit residues: 23.5880
Evaluate side-chains
  43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.138541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.105650 restraints weight = 2970.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.75
r_work: 0.3542 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2622  Z= 0.241
  Angle     :  0.491   2.913   3552  Z= 0.296
  Chirality :  0.057   0.143    474
  Planarity :  0.002   0.008    438
  Dihedral  :  4.899  12.157    372
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.77 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.42), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR H  39 
 PHE   0.014   0.004   PHE B  94 
 HIS   0.006   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 2622)
  covalent geometry    : angle       0.49128 ( 3552)
  hydrogen bonds       : bond        0.01705 (   22)
  hydrogen bonds       : angle       4.59397 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.062 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8186 (tttt) cc_final: 0.7222 (mptt)
REVERT: F   43 LYS cc_start: 0.8056 (tttt) cc_final: 0.7172 (mptt)
REVERT: C   43 LYS cc_start: 0.8207 (tttt) cc_final: 0.7438 (tmtt)
REVERT: G   43 LYS cc_start: 0.8248 (tttt) cc_final: 0.7609 (mptp)
REVERT: D   43 LYS cc_start: 0.8194 (tttt) cc_final: 0.7169 (mptt)
REVERT: H   43 LYS cc_start: 0.8079 (tttt) cc_final: 0.7239 (mptt)
  outliers start: 5
  outliers final: 5
  residues processed: 35
  average time/residue: 0.5162
  time to fit residues: 18.5440
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0020
   chunk 18 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
C  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.141267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.109060 restraints weight = 2894.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.69
r_work: 0.3585 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2622  Z= 0.118
  Angle     :  0.392   2.226   3552  Z= 0.236
  Chirality :  0.054   0.139    474
  Planarity :  0.001   0.005    438
  Dihedral  :  4.146  10.612    372
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.22 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.43), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR H  39 
 PHE   0.007   0.002   PHE B  94 
 HIS   0.004   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 2622)
  covalent geometry    : angle       0.39151 ( 3552)
  hydrogen bonds       : bond        0.01252 (   22)
  hydrogen bonds       : angle       4.43675 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.104 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8171 (tttt) cc_final: 0.7196 (mptt)
REVERT: F   43 LYS cc_start: 0.8056 (tttt) cc_final: 0.7147 (mptt)
REVERT: C   43 LYS cc_start: 0.8180 (tttt) cc_final: 0.7421 (tmtt)
REVERT: C   83 GLU cc_start: 0.8167 (mp0) cc_final: 0.7735 (mp0)
REVERT: G   43 LYS cc_start: 0.8239 (tttt) cc_final: 0.7566 (mptp)
REVERT: D   43 LYS cc_start: 0.8147 (tttt) cc_final: 0.7126 (mptt)
REVERT: H   43 LYS cc_start: 0.8076 (tttt) cc_final: 0.7212 (mptt)
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.5561
  time to fit residues: 21.1199
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    0.0570
   chunk 8 optimal weight:    0.0970
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 25 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6096

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.145679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.114250 restraints weight = 2931.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 2.66
r_work: 0.3665 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.010   2622  Z= 0.065
  Angle     :  0.333   1.894   3552  Z= 0.201
  Chirality :  0.053   0.131    474
  Planarity :  0.001   0.005    438
  Dihedral  :  3.450   8.914    372
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.94 %
    Favored  : 82.25 %
  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: -2.50 (0.43), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR H  39 
 PHE   0.004   0.001   PHE B  94 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00133 ( 2622)
  covalent geometry    : angle       0.33290 ( 3552)
  hydrogen bonds       : bond        0.00887 (   22)
  hydrogen bonds       : angle       4.18714 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.063 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8211 (tttt) cc_final: 0.7247 (mptt)
REVERT: F   43 LYS cc_start: 0.8089 (tttt) cc_final: 0.7181 (mptt)
REVERT: C   43 LYS cc_start: 0.8181 (tttt) cc_final: 0.7418 (tmtt)
REVERT: G   43 LYS cc_start: 0.8259 (tttt) cc_final: 0.7602 (mttp)
REVERT: G   83 GLU cc_start: 0.8014 (mp0) cc_final: 0.7576 (mp0)
REVERT: D   43 LYS cc_start: 0.8180 (tttt) cc_final: 0.7200 (mptp)
REVERT: H   43 LYS cc_start: 0.8075 (tttt) cc_final: 0.7245 (mptt)
  outliers start: 5
  outliers final: 4
  residues processed: 33
  average time/residue: 0.4481
  time to fit residues: 15.2182
Evaluate side-chains
  35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
F  79 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.135797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.102580 restraints weight = 3079.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.83
r_work: 0.3483 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.042   2622  Z= 0.421
  Angle     :  0.624   3.588   3552  Z= 0.377
  Chirality :  0.062   0.160    474
  Planarity :  0.004   0.011    438
  Dihedral  :  5.525  14.086    372
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.67 %
    Favored  : 81.16 %
  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: -2.95 (0.42), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  39 
 PHE   0.022   0.006   PHE B  94 
 HIS   0.009   0.005   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00946 ( 2622)
  covalent geometry    : angle       0.62433 ( 3552)
  hydrogen bonds       : bond        0.02238 (   22)
  hydrogen bonds       : angle       4.45714 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.063 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8155 (tttt) cc_final: 0.7199 (mptt)
REVERT: F   43 LYS cc_start: 0.8053 (tttt) cc_final: 0.7138 (mptt)
REVERT: C   43 LYS cc_start: 0.8205 (tttt) cc_final: 0.7550 (mttm)
REVERT: G   43 LYS cc_start: 0.8260 (tttt) cc_final: 0.7669 (mptt)
REVERT: D   43 LYS cc_start: 0.8175 (tttt) cc_final: 0.7178 (mptt)
REVERT: H   43 LYS cc_start: 0.8095 (tttt) cc_final: 0.7279 (mptt)
  outliers start: 6
  outliers final: 5
  residues processed: 36
  average time/residue: 0.5196
  time to fit residues: 19.1829
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4097 r_free = 0.4097 target = 0.142846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.110655 restraints weight = 2945.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.72
r_work: 0.3620 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2622  Z= 0.087
  Angle     :  0.375   2.062   3552  Z= 0.227
  Chirality :  0.054   0.136    474
  Planarity :  0.001   0.007    438
  Dihedral  :  4.002  10.951    372
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.75 %
    Favored  : 80.80 %
  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: -2.73 (0.42), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR H  39 
 PHE   0.006   0.002   PHE B  94 
 HIS   0.004   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 ( 2622)
  covalent geometry    : angle       0.37481 ( 3552)
  hydrogen bonds       : bond        0.01082 (   22)
  hydrogen bonds       : angle       4.29305 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.111 
Fit side-chains
REVERT: B   43 LYS cc_start: 0.8219 (tttt) cc_final: 0.7214 (mptt)
REVERT: F   43 LYS cc_start: 0.8092 (tttt) cc_final: 0.7191 (mptt)
REVERT: C   43 LYS cc_start: 0.8182 (tttt) cc_final: 0.7392 (tmtt)
REVERT: G   43 LYS cc_start: 0.8211 (tttt) cc_final: 0.7587 (mptp)
REVERT: D   43 LYS cc_start: 0.8133 (tttt) cc_final: 0.7129 (mptt)
REVERT: H   43 LYS cc_start: 0.8081 (tttt) cc_final: 0.7285 (mptt)
  outliers start: 4
  outliers final: 2
  residues processed: 33
  average time/residue: 0.5606
  time to fit residues: 19.0123
Evaluate side-chains
  34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    3.9586

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.138358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.105673 restraints weight = 3000.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.74
r_work: 0.3533 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2622  Z= 0.268
  Angle     :  0.517   3.788   3552  Z= 0.312
  Chirality :  0.057   0.144    474
  Planarity :  0.003   0.012    438
  Dihedral  :  4.873  12.777    372
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 17.75 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.42), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR F  39 
 PHE   0.016   0.004   PHE B  94 
 HIS   0.006   0.004   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 2622)
  covalent geometry    : angle       0.51691 ( 3552)
  hydrogen bonds       : bond        0.01790 (   22)
  hydrogen bonds       : angle       4.47255 (   66)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 969.17 seconds
wall clock time: 17 minutes 18.38 seconds (1038.38 seconds total)