Starting phenix.real_space_refine
on Wed Sep 17 03:23:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e7j_47678/09_2025/9e7j_47678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e7j_47678/09_2025/9e7j_47678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e7j_47678/09_2025/9e7j_47678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e7j_47678/09_2025/9e7j_47678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e7j_47678/09_2025/9e7j_47678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e7j_47678/09_2025/9e7j_47678.cif"
  }
  resolution = 2.98
  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=   0.021
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      64      5.16       5
     C    1912      2.51       5
     N     528      2.21       5
     O     608      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3112
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 778
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 107}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 0.84, per 1000 atoms: 0.27
  Number of scatterers: 3112
  At special positions: 0
  Unit cell: (56.4021, 70.6647, 61.5885, 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      64     16.00
     O     608      8.00
     N     528      7.00
     C    1912      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: 0.29
  Conformation dependent library (CDL) restraints added in 86.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  832

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      86.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 42
    Processing helix  chain 'A' and resid 48 through 71
      removed outlier: 3.514A  pdb=" N   THR A  52 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR A  71 " --> pdb=" O   LYS A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 95
      removed outlier: 4.196A  pdb=" N   VAL A  82 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ASP A  85 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 122
      removed outlier: 3.599A  pdb=" N   ALA A 122 " --> pdb=" O   HIS A 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 42
    Processing helix  chain 'B' and resid 48 through 71
      removed outlier: 3.514A  pdb=" N   THR B  52 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR B  71 " --> pdb=" O   LYS B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 95
      removed outlier: 4.196A  pdb=" N   VAL B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ASP B  85 " --> pdb=" O   LYS B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 122
      removed outlier: 3.599A  pdb=" N   ALA B 122 " --> pdb=" O   HIS B 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 42
    Processing helix  chain 'C' and resid 48 through 71
      removed outlier: 3.514A  pdb=" N   THR C  52 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR C  71 " --> pdb=" O   LYS C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 95
      removed outlier: 4.196A  pdb=" N   VAL C  82 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ASP C  85 " --> pdb=" O   LYS C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 122
      removed outlier: 3.599A  pdb=" N   ALA C 122 " --> pdb=" O   HIS C 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 42
    Processing helix  chain 'D' and resid 48 through 71
      removed outlier: 3.514A  pdb=" N   THR D  52 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR D  71 " --> pdb=" O   LYS D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 95
      removed outlier: 4.196A  pdb=" N   VAL D  82 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ASP D  85 " --> pdb=" O   LYS D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 122
      removed outlier: 3.599A  pdb=" N   ALA D 122 " --> pdb=" O   HIS D 118 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    888 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: 0.54

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 916
        1.33 -     1.45: 388
        1.45 -     1.57: 1772
        1.57 -     1.68: 0
        1.68 -     1.80: 76
  Bond restraints: 3152
  Sorted by residual:
  bond pdb=" C   CYS D 110 "
       pdb=" N   GLN D 111 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 1.27e-02 6.20e+03 6.74e+00
  bond pdb=" C   CYS B 110 "
       pdb=" N   GLN B 111 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 1.27e-02 6.20e+03 6.74e+00
  bond pdb=" C   CYS A 110 "
       pdb=" N   GLN A 111 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 1.27e-02 6.20e+03 6.74e+00
  bond pdb=" C   CYS C 110 "
       pdb=" N   GLN C 111 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 1.27e-02 6.20e+03 6.74e+00
  bond pdb=" CB  CYS C  26 "
       pdb=" SG  CYS C  26 "
    ideal  model  delta    sigma   weight residual
    1.808  1.735  0.073 3.30e-02 9.18e+02 4.85e+00
  ... (remaining 3147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 3860
        1.44 -     2.87: 316
        2.87 -     4.31: 48
        4.31 -     5.74: 16
        5.74 -     7.18: 4
  Bond angle restraints: 4244
  Sorted by residual:
  angle pdb=" N   ALA C  54 "
        pdb=" CA  ALA C  54 "
        pdb=" C   ALA C  54 "
      ideal   model   delta    sigma   weight residual
     111.28  114.48   -3.20 1.09e+00 8.42e-01 8.59e+00
  angle pdb=" N   ALA B  54 "
        pdb=" CA  ALA B  54 "
        pdb=" C   ALA B  54 "
      ideal   model   delta    sigma   weight residual
     111.28  114.48   -3.20 1.09e+00 8.42e-01 8.59e+00
  angle pdb=" N   ALA A  54 "
        pdb=" CA  ALA A  54 "
        pdb=" C   ALA A  54 "
      ideal   model   delta    sigma   weight residual
     111.28  114.48   -3.20 1.09e+00 8.42e-01 8.59e+00
  angle pdb=" N   ALA D  54 "
        pdb=" CA  ALA D  54 "
        pdb=" C   ALA D  54 "
      ideal   model   delta    sigma   weight residual
     111.28  114.48   -3.20 1.09e+00 8.42e-01 8.59e+00
  angle pdb=" C   GLN B 111 "
        pdb=" N   ALA B 112 "
        pdb=" CA  ALA B 112 "
      ideal   model   delta    sigma   weight residual
     120.28  123.74   -3.46 1.34e+00 5.57e-01 6.65e+00
  ... (remaining 4239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.72: 1732
       15.72 -    31.43: 148
       31.43 -    47.15: 48
       47.15 -    62.87: 0
       62.87 -    78.58: 8
  Dihedral angle restraints: 1936
    sinusoidal: 660
      harmonic: 1276
  Sorted by residual:
  dihedral pdb=" N   MET D  48 "
           pdb=" CA  MET D  48 "
           pdb=" CB  MET D  48 "
           pdb=" CG  MET D  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.35  -42.65     3      1.50e+01 4.44e-03 7.66e+00
  dihedral pdb=" N   MET B  48 "
           pdb=" CA  MET B  48 "
           pdb=" CB  MET B  48 "
           pdb=" CG  MET B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.35  -42.65     3      1.50e+01 4.44e-03 7.66e+00
  dihedral pdb=" N   MET C  48 "
           pdb=" CA  MET C  48 "
           pdb=" CB  MET C  48 "
           pdb=" CG  MET C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.35  -42.65     3      1.50e+01 4.44e-03 7.66e+00
  ... (remaining 1933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 208
       0.030 -    0.060: 172
       0.060 -    0.089: 80
       0.089 -    0.119: 24
       0.119 -    0.149: 8
  Chirality restraints: 492
  Sorted by residual:
  chirality pdb=" CA  THR C  76 "
            pdb=" N   THR C  76 "
            pdb=" C   THR C  76 "
            pdb=" CB  THR C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  THR A  76 "
            pdb=" N   THR A  76 "
            pdb=" C   THR A  76 "
            pdb=" CB  THR A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  THR B  76 "
            pdb=" N   THR B  76 "
            pdb=" C   THR B  76 "
            pdb=" CB  THR B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.55e-01
  ... (remaining 489 not shown)

  Planarity restraints: 552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  76 "   -0.022 5.00e-02 4.00e+02   3.29e-02 1.74e+00
        pdb=" N   PRO D  77 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO D  77 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  77 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  76 "   -0.022 5.00e-02 4.00e+02   3.29e-02 1.74e+00
        pdb=" N   PRO B  77 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B  77 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  77 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  76 "    0.022 5.00e-02 4.00e+02   3.29e-02 1.74e+00
        pdb=" N   PRO A  77 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A  77 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  77 "    0.019 5.00e-02 4.00e+02
  ... (remaining 549 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1592
        2.97 -     3.46: 3394
        3.46 -     3.94: 5044
        3.94 -     4.42: 6504
        4.42 -     4.90: 9876
  Nonbonded interactions: 26410
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  68 "
            pdb=" OG1 THR A  76 "
     model   vdw
     2.493 3.040
  nonbonded pdb=" O   LEU B  68 "
            pdb=" OG1 THR B  76 "
     model   vdw
     2.493 3.040
  nonbonded pdb=" O   LEU C  68 "
            pdb=" OG1 THR C  76 "
     model   vdw
     2.493 3.040
  nonbonded pdb=" O   LEU D  68 "
            pdb=" OG1 THR D  76 "
     model   vdw
     2.493 3.040
  nonbonded pdb=" NZ  LYS A  91 "
            pdb=" OD2 ASP A  95 "
     model   vdw
     2.595 3.120
  ... (remaining 26405 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.690
  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:7.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
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      :  0.011   0.073   3152  Z= 0.500
  Angle     :  0.898   7.180   4244  Z= 0.528
  Chirality :  0.050   0.149    492
  Planarity :  0.005   0.033    552
  Dihedral  : 14.352  78.585   1104
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.37), residues: 432
  helix: -0.30 (0.25), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.05 (0.68), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D  35 
 TYR   0.021   0.003   TYR A  16 
 PHE   0.012   0.003   PHE D  97 
 HIS   0.003   0.001   HIS D  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.01104 ( 3152)
  covalent geometry    : angle       0.89824 ( 4244)
  hydrogen bonds       : bond        0.12262 (  296)
  hydrogen bonds       : angle       5.87766 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A   43 MET cc_start: 0.7292 (mtt) cc_final: 0.7063 (mtp)
REVERT: A   81 LYS cc_start: 0.8452 (tttt) cc_final: 0.8008 (tppt)
REVERT: B   43 MET cc_start: 0.7289 (mtt) cc_final: 0.7060 (mtp)
REVERT: B   68 LEU cc_start: 0.8328 (mt) cc_final: 0.8123 (mm)
REVERT: B   81 LYS cc_start: 0.8456 (tttt) cc_final: 0.8012 (tppt)
REVERT: C   43 MET cc_start: 0.7288 (mtt) cc_final: 0.7060 (mtp)
REVERT: C   68 LEU cc_start: 0.8314 (mt) cc_final: 0.8109 (mm)
REVERT: C   81 LYS cc_start: 0.8456 (tttt) cc_final: 0.8015 (tppt)
REVERT: D   43 MET cc_start: 0.7290 (mtt) cc_final: 0.7061 (mtp)
REVERT: D   81 LYS cc_start: 0.8452 (tttt) cc_final: 0.8010 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.7238
  time to fit residues: 35.5574
Evaluate side-chains
  44 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0010
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.4386

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.180978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.165803 restraints weight = 2926.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 1.63
r_work: 0.3974 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3836 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3152  Z= 0.141
  Angle     :  0.513   5.557   4244  Z= 0.263
  Chirality :  0.034   0.108    492
  Planarity :  0.003   0.025    552
  Dihedral  :  6.890  63.098    452
  Min Nonbonded Distance : 2.676

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.23 %
    Favored  : 90.51 %
  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 aren not related in a simple way.
  whole:  1.76 (0.39), residues: 432
  helix:  1.32 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.72 (0.76), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  35 
 TYR   0.009   0.001   TYR D  16 
 PHE   0.005   0.001   PHE B  79 
 HIS   0.001   0.001   HIS C  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3152)
  covalent geometry    : angle       0.51309 ( 4244)
  hydrogen bonds       : bond        0.05186 (  296)
  hydrogen bonds       : angle       3.39851 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8487 (tttt) cc_final: 0.7655 (tppt)
REVERT: B   81 LYS cc_start: 0.8489 (tttt) cc_final: 0.7640 (tppt)
REVERT: C   81 LYS cc_start: 0.8488 (tttt) cc_final: 0.7652 (tppt)
REVERT: D   81 LYS cc_start: 0.8496 (tttt) cc_final: 0.7666 (tppt)
  outliers start: 4
  outliers final: 0
  residues processed: 46
  average time/residue: 0.6779
  time to fit residues: 31.9742
Evaluate side-chains
  38 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4136 r_free = 0.4136 target = 0.173030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.159173 restraints weight = 3054.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 1.57
r_work: 0.3884 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3748 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3152  Z= 0.175
  Angle     :  0.546   5.967   4244  Z= 0.277
  Chirality :  0.036   0.111    492
  Planarity :  0.003   0.024    552
  Dihedral  :  6.249  55.853    452
  Min Nonbonded Distance : 2.666

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 12.66 %
    Favored  : 83.54 %
  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 aren not related in a simple way.
  whole:  2.16 (0.40), residues: 432
  helix:  1.61 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.68 (0.76), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.012   0.002   TYR A  16 
 PHE   0.009   0.001   PHE B  79 
 HIS   0.002   0.001   HIS B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3152)
  covalent geometry    : angle       0.54570 ( 4244)
  hydrogen bonds       : bond        0.05491 (  296)
  hydrogen bonds       : angle       3.42451 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8618 (tttt) cc_final: 0.7750 (tppt)
REVERT: B   68 LEU cc_start: 0.7962 (mp) cc_final: 0.7645 (mm)
REVERT: B   81 LYS cc_start: 0.8589 (tttt) cc_final: 0.7699 (tppt)
REVERT: C   68 LEU cc_start: 0.7950 (mp) cc_final: 0.7626 (mm)
REVERT: C   81 LYS cc_start: 0.8581 (tttt) cc_final: 0.7704 (tppt)
REVERT: D   81 LYS cc_start: 0.8610 (tttt) cc_final: 0.7744 (tppt)
  outliers start: 12
  outliers final: 0
  residues processed: 44
  average time/residue: 0.7670
  time to fit residues: 34.4982
Evaluate side-chains
  38 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.176463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.163048 restraints weight = 3002.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 1.52
r_work: 0.3933 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3797 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3152  Z= 0.149
  Angle     :  0.501   5.374   4244  Z= 0.253
  Chirality :  0.035   0.107    492
  Planarity :  0.003   0.023    552
  Dihedral  :  5.145  42.921    452
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.46 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.40), residues: 432
  helix:  1.94 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.76 (0.76), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C  35 
 TYR   0.009   0.001   TYR D  16 
 PHE   0.008   0.001   PHE B  79 
 HIS   0.001   0.001   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3152)
  covalent geometry    : angle       0.50063 ( 4244)
  hydrogen bonds       : bond        0.05076 (  296)
  hydrogen bonds       : angle       3.20804 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8575 (tttt) cc_final: 0.7716 (tppt)
REVERT: B   68 LEU cc_start: 0.7976 (mp) cc_final: 0.7685 (mm)
REVERT: B   81 LYS cc_start: 0.8527 (tttt) cc_final: 0.7656 (tppt)
REVERT: C   68 LEU cc_start: 0.7976 (mp) cc_final: 0.7682 (mm)
REVERT: C   81 LYS cc_start: 0.8527 (tttt) cc_final: 0.7654 (tppt)
REVERT: D   81 LYS cc_start: 0.8559 (tttt) cc_final: 0.7699 (tppt)
  outliers start: 10
  outliers final: 0
  residues processed: 46
  average time/residue: 0.6542
  time to fit residues: 30.8720
Evaluate side-chains
  42 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.175659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162070 restraints weight = 2975.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 1.55
r_work: 0.3924 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3790 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3152  Z= 0.152
  Angle     :  0.514   5.433   4244  Z= 0.257
  Chirality :  0.035   0.106    492
  Planarity :  0.003   0.021    552
  Dihedral  :  4.170  28.798    452
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 20.25 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.40), residues: 432
  helix:  2.08 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.86 (0.75), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.010   0.002   TYR A  16 
 PHE   0.008   0.001   PHE C  79 
 HIS   0.001   0.001   HIS D 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3152)
  covalent geometry    : angle       0.51408 ( 4244)
  hydrogen bonds       : bond        0.05081 (  296)
  hydrogen bonds       : angle       3.21399 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8574 (tttt) cc_final: 0.7732 (tppt)
REVERT: A   98 PRO cc_start: 0.8492 (Cg_endo) cc_final: 0.8234 (Cg_exo)
REVERT: B   68 LEU cc_start: 0.7990 (mp) cc_final: 0.7720 (mm)
REVERT: B   81 LYS cc_start: 0.8555 (tttt) cc_final: 0.7671 (tppt)
REVERT: B   98 PRO cc_start: 0.8494 (Cg_endo) cc_final: 0.8235 (Cg_exo)
REVERT: C   68 LEU cc_start: 0.7977 (mp) cc_final: 0.7703 (mm)
REVERT: C   81 LYS cc_start: 0.8552 (tttt) cc_final: 0.7676 (tppt)
REVERT: C   98 PRO cc_start: 0.8487 (Cg_endo) cc_final: 0.8230 (Cg_exo)
REVERT: D   81 LYS cc_start: 0.8567 (tttt) cc_final: 0.7722 (tppt)
REVERT: D   98 PRO cc_start: 0.8487 (Cg_endo) cc_final: 0.8227 (Cg_exo)
  outliers start: 2
  outliers final: 0
  residues processed: 50
  average time/residue: 0.6107
  time to fit residues: 31.3356
Evaluate side-chains
  46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0670
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.177708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.164287 restraints weight = 2953.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 1.53
r_work: 0.3952 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3816 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3152  Z= 0.140
  Angle     :  0.500   5.424   4244  Z= 0.249
  Chirality :  0.034   0.106    492
  Planarity :  0.002   0.019    552
  Dihedral  :  3.506  17.750    452
  Min Nonbonded Distance : 2.666

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.25 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.16 (0.40), residues: 432
  helix:  2.31 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop :  0.78 (0.75), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  35 
 TYR   0.009   0.001   TYR B  16 
 PHE   0.008   0.001   PHE C  79 
 HIS   0.001   0.000   HIS D 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3152)
  covalent geometry    : angle       0.49975 ( 4244)
  hydrogen bonds       : bond        0.04900 (  296)
  hydrogen bonds       : angle       3.11042 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8524 (tttt) cc_final: 0.7637 (tppt)
REVERT: A   98 PRO cc_start: 0.8467 (Cg_endo) cc_final: 0.8204 (Cg_exo)
REVERT: A  111 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6910 (tt0)
REVERT: B   68 LEU cc_start: 0.7913 (mp) cc_final: 0.7655 (mm)
REVERT: B   81 LYS cc_start: 0.8519 (tttt) cc_final: 0.7610 (tppt)
REVERT: B   98 PRO cc_start: 0.8472 (Cg_endo) cc_final: 0.8207 (Cg_exo)
REVERT: B  111 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6882 (tt0)
REVERT: C   68 LEU cc_start: 0.7894 (mp) cc_final: 0.7631 (mm)
REVERT: C   81 LYS cc_start: 0.8519 (tttt) cc_final: 0.7613 (tppt)
REVERT: C   98 PRO cc_start: 0.8468 (Cg_endo) cc_final: 0.8206 (Cg_exo)
REVERT: C  111 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6887 (tt0)
REVERT: D   81 LYS cc_start: 0.8529 (tttt) cc_final: 0.7632 (tppt)
REVERT: D   98 PRO cc_start: 0.8463 (Cg_endo) cc_final: 0.8198 (Cg_exo)
REVERT: D  111 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6865 (tt0)
  outliers start: 6
  outliers final: 0
  residues processed: 54
  average time/residue: 0.6452
  time to fit residues: 35.7676
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue  111 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.172412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.158918 restraints weight = 3047.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 1.55
r_work: 0.3880 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3749 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3152  Z= 0.175
  Angle     :  0.563   6.199   4244  Z= 0.281
  Chirality :  0.036   0.107    492
  Planarity :  0.003   0.018    552
  Dihedral  :  3.402  11.286    452
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.89 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.40), residues: 432
  helix:  2.17 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop :  0.16 (0.75), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.011   0.002   TYR D  16 
 PHE   0.010   0.001   PHE C  79 
 HIS   0.002   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3152)
  covalent geometry    : angle       0.56309 ( 4244)
  hydrogen bonds       : bond        0.05326 (  296)
  hydrogen bonds       : angle       3.33871 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8614 (tttt) cc_final: 0.7760 (tppt)
REVERT: A   98 PRO cc_start: 0.8498 (Cg_endo) cc_final: 0.8229 (Cg_exo)
REVERT: A  111 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6849 (tt0)
REVERT: B   68 LEU cc_start: 0.7973 (mp) cc_final: 0.7716 (mm)
REVERT: B   81 LYS cc_start: 0.8586 (tttt) cc_final: 0.7704 (tppt)
REVERT: B   98 PRO cc_start: 0.8495 (Cg_endo) cc_final: 0.8224 (Cg_exo)
REVERT: B  111 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6886 (tt0)
REVERT: C   68 LEU cc_start: 0.7961 (mp) cc_final: 0.7697 (mm)
REVERT: C   81 LYS cc_start: 0.8593 (tttt) cc_final: 0.7709 (tppt)
REVERT: C   98 PRO cc_start: 0.8490 (Cg_endo) cc_final: 0.8220 (Cg_exo)
REVERT: C  111 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6871 (tt0)
REVERT: D   81 LYS cc_start: 0.8602 (tttt) cc_final: 0.7743 (tppt)
REVERT: D   98 PRO cc_start: 0.8493 (Cg_endo) cc_final: 0.8223 (Cg_exo)
REVERT: D  111 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6845 (tt0)
  outliers start: 6
  outliers final: 0
  residues processed: 52
  average time/residue: 0.6703
  time to fit residues: 35.7741
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue  111 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0050
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0020
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.4402

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.177608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.163630 restraints weight = 3067.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 1.64
r_work: 0.3945 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3805 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3152  Z= 0.134
  Angle     :  0.504   5.457   4244  Z= 0.251
  Chirality :  0.034   0.105    492
  Planarity :  0.002   0.019    552
  Dihedral  :  3.131   9.118    452
  Min Nonbonded Distance : 2.671

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 22.15 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.32 (0.40), residues: 432
  helix:  2.53 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop :  0.21 (0.78), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.008   0.001   TYR A  16 
 PHE   0.008   0.001   PHE C  79 
 HIS   0.001   0.000   HIS D 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3152)
  covalent geometry    : angle       0.50360 ( 4244)
  hydrogen bonds       : bond        0.04809 (  296)
  hydrogen bonds       : angle       3.09835 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8547 (tttt) cc_final: 0.7656 (tppt)
REVERT: A   98 PRO cc_start: 0.8456 (Cg_endo) cc_final: 0.8186 (Cg_exo)
REVERT: A  111 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6897 (tt0)
REVERT: B   68 LEU cc_start: 0.7909 (mp) cc_final: 0.7661 (mm)
REVERT: B   81 LYS cc_start: 0.8531 (tttt) cc_final: 0.7618 (tppt)
REVERT: B   98 PRO cc_start: 0.8464 (Cg_endo) cc_final: 0.8194 (Cg_exo)
REVERT: C   68 LEU cc_start: 0.7902 (mp) cc_final: 0.7653 (mm)
REVERT: C   81 LYS cc_start: 0.8524 (tttt) cc_final: 0.7611 (tppt)
REVERT: C   98 PRO cc_start: 0.8458 (Cg_endo) cc_final: 0.8191 (Cg_exo)
REVERT: D   81 LYS cc_start: 0.8543 (tttt) cc_final: 0.7646 (tppt)
REVERT: D   98 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.8181 (Cg_exo)
REVERT: D  111 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6890 (tt0)
  outliers start: 2
  outliers final: 0
  residues processed: 50
  average time/residue: 0.6520
  time to fit residues: 33.4757
Evaluate side-chains
  48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain D residue  111 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.177662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.163809 restraints weight = 3046.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.4084 rms_B_bonded: 1.61
r_work: 0.3944 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3806 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3152  Z= 0.135
  Angle     :  0.535   5.353   4244  Z= 0.264
  Chirality :  0.034   0.106    492
  Planarity :  0.003   0.018    552
  Dihedral  :  3.052   8.851    452
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 22.15 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.40 (0.40), residues: 432
  helix:  2.58 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop :  0.24 (0.79), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.009   0.001   TYR C  16 
 PHE   0.008   0.001   PHE C  79 
 HIS   0.001   0.000   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3152)
  covalent geometry    : angle       0.53511 ( 4244)
  hydrogen bonds       : bond        0.04848 (  296)
  hydrogen bonds       : angle       3.08101 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8509 (tttt) cc_final: 0.7620 (tppt)
REVERT: A   98 PRO cc_start: 0.8460 (Cg_endo) cc_final: 0.8184 (Cg_exo)
REVERT: A  111 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6891 (tt0)
REVERT: B   68 LEU cc_start: 0.7902 (mp) cc_final: 0.7665 (mm)
REVERT: B   81 LYS cc_start: 0.8495 (tttt) cc_final: 0.7582 (tppt)
REVERT: B   98 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.8188 (Cg_exo)
REVERT: C   68 LEU cc_start: 0.7880 (mp) cc_final: 0.7636 (mm)
REVERT: C   81 LYS cc_start: 0.8495 (tttt) cc_final: 0.7584 (tppt)
REVERT: C   98 PRO cc_start: 0.8459 (Cg_endo) cc_final: 0.8185 (Cg_exo)
REVERT: D   81 LYS cc_start: 0.8517 (tttt) cc_final: 0.7623 (tppt)
REVERT: D   98 PRO cc_start: 0.8456 (Cg_endo) cc_final: 0.8179 (Cg_exo)
REVERT: D  111 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6882 (tt0)
  outliers start: 2
  outliers final: 0
  residues processed: 48
  average time/residue: 0.6562
  time to fit residues: 32.2852
Evaluate side-chains
  48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain D residue  111 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4161 r_free = 0.4161 target = 0.173549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.159722 restraints weight = 3023.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 1.62
r_work: 0.3911 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3773 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3152  Z= 0.156
  Angle     :  0.581   5.679   4244  Z= 0.289
  Chirality :  0.035   0.107    492
  Planarity :  0.003   0.018    552
  Dihedral  :  3.142   9.221    452
  Min Nonbonded Distance : 2.666

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.52 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.40), residues: 432
  helix:  2.36 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop :  0.35 (0.79), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.010   0.002   TYR A  16 
 PHE   0.010   0.001   PHE C  79 
 HIS   0.001   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3152)
  covalent geometry    : angle       0.58055 ( 4244)
  hydrogen bonds       : bond        0.05153 (  296)
  hydrogen bonds       : angle       3.25222 (  888)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.8514 (tttt) cc_final: 0.7598 (tppt)
REVERT: A   98 PRO cc_start: 0.8476 (Cg_endo) cc_final: 0.8198 (Cg_exo)
REVERT: A  111 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6791 (tt0)
REVERT: B   68 LEU cc_start: 0.7786 (mp) cc_final: 0.7542 (mm)
REVERT: B   81 LYS cc_start: 0.8496 (tttt) cc_final: 0.7562 (tppt)
REVERT: B   98 PRO cc_start: 0.8484 (Cg_endo) cc_final: 0.8207 (Cg_exo)
REVERT: B  111 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6819 (tt0)
REVERT: C   68 LEU cc_start: 0.7770 (mp) cc_final: 0.7524 (mm)
REVERT: C   81 LYS cc_start: 0.8501 (tttt) cc_final: 0.7565 (tppt)
REVERT: C   98 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.8203 (Cg_exo)
REVERT: C  111 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6802 (tt0)
REVERT: D   81 LYS cc_start: 0.8516 (tttt) cc_final: 0.7596 (tppt)
REVERT: D   98 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8197 (Cg_exo)
REVERT: D  111 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6785 (tt0)
  outliers start: 4
  outliers final: 0
  residues processed: 50
  average time/residue: 0.6992
  time to fit residues: 35.7590
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue  111 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4128 r_free = 0.4128 target = 0.171758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.158027 restraints weight = 3038.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 1.64
r_work: 0.3882 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3750 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3152  Z= 0.169
  Angle     :  0.627   7.050   4244  Z= 0.303
  Chirality :  0.036   0.107    492
  Planarity :  0.003   0.018    552
  Dihedral  :  3.286   9.363    452
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 24.05 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.40), residues: 432
  helix:  2.17 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop :  0.17 (0.77), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  35 
 TYR   0.011   0.002   TYR C  16 
 PHE   0.011   0.001   PHE B  79 
 HIS   0.002   0.001   HIS D 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 3152)
  covalent geometry    : angle       0.62733 ( 4244)
  hydrogen bonds       : bond        0.05379 (  296)
  hydrogen bonds       : angle       3.43678 (  888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1357.49 seconds
wall clock time: 24 minutes 17.12 seconds (1457.12 seconds total)