Starting phenix.real_space_refine
on Tue Feb  3 12:57:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9je2_61405/02_2026/9je2_61405.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9je2_61405/02_2026/9je2_61405.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9je2_61405/02_2026/9je2_61405.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9je2_61405/02_2026/9je2_61405.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9je2_61405/02_2026/9je2_61405.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9je2_61405/02_2026/9je2_61405.cif"
  }
  resolution = 3.06
  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    1650      2.51       5
     N     456      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2658
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 443
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    E, D, F, G, H
  Time building chain proxies: 0.47, per 1000 atoms: 0.18
  Number of scatterers: 2658
  At special positions: 0
  Unit cell: (118.69, 100.43, 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     552      8.00
     N     456      7.00
     C    1650      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: 0.23
  Conformation dependent library (CDL) restraints added in 114.5 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 40
      removed outlier: 6.721A  pdb=" N   LEU C  38 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 50
      removed outlier: 6.640A  pdb=" N   LYS C  45 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   VAL G  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   GLY C  47 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 10.098A  pdb=" N   HIS G  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.913A  pdb=" N   VAL C  49 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL D  48 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL G  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   HIS D  50 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 63 through 66
      removed outlier: 6.900A  pdb=" N   VAL D  63 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   VAL G  66 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ASN D  65 " --> pdb=" O   VAL G  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 70 through 71
      removed outlier: 6.700A  pdb=" N   VAL D  70 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 78
      removed outlier: 6.616A  pdb=" N   THR C  75 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ALA G  78 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL C  77 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 96
      removed outlier: 8.229A  pdb=" N   ALA C  89 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   THR G  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   ALA C  91 " --> pdb=" O   THR G  92 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   PHE G  94 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY C  93 " --> pdb=" O   PHE G  94 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   LYS G  96 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL C  95 " --> pdb=" O   LYS G  96 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ALA G  91 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   THR D  92 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLY G  93 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 38 through 40
      removed outlier: 6.711A  pdb=" N   LEU E  38 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 45 through 50
      removed outlier: 6.646A  pdb=" N   LYS E  45 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   VAL H  48 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   GLY E  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 10.088A  pdb=" N   HIS H  50 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.906A  pdb=" N   VAL E  49 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   VAL F  48 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   VAL H  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   HIS F  50 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 63 through 66
      removed outlier: 6.906A  pdb=" N   VAL F  63 " --> pdb=" O   THR H  64 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   VAL H  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASN F  65 " --> pdb=" O   VAL H  66 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 70 through 71
      removed outlier: 6.695A  pdb=" N   VAL F  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 75 through 78
      removed outlier: 6.624A  pdb=" N   THR E  75 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ALA H  78 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   VAL E  77 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 88 through 96
      removed outlier: 8.222A  pdb=" N   ALA E  89 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   THR H  92 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 8.872A  pdb=" N   ALA E  91 " --> pdb=" O   THR H  92 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   PHE H  94 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   GLY E  93 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   LYS H  96 " --> pdb=" O   GLY E  93 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL E  95 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ALA H  91 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   THR F  92 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   GLY H  93 " --> pdb=" O   THR F  92 " (cutoff:3.500A)

    32 hydrogen bonds defined for protein.
    96 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: 0.31

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 480
        1.28 -     1.35: 414
        1.35 -     1.41: 102
        1.41 -     1.48: 455
        1.48 -     1.54: 1219
  Bond restraints: 2670
  Sorted by residual:
  bond pdb=" CA  ALA C  91 "
       pdb=" CB  ALA C  91 "
    ideal  model  delta    sigma   weight residual
    1.529  1.506  0.023 1.38e-02 5.25e+03 2.66e+00
  bond pdb=" CA  ALA F  91 "
       pdb=" CB  ALA F  91 "
    ideal  model  delta    sigma   weight residual
    1.528  1.507  0.021 1.39e-02 5.18e+03 2.28e+00
  bond pdb=" CA  ALA H  91 "
       pdb=" CB  ALA H  91 "
    ideal  model  delta    sigma   weight residual
    1.528  1.507  0.021 1.39e-02 5.18e+03 2.24e+00
  bond pdb=" CA  ALA G  91 "
       pdb=" CB  ALA G  91 "
    ideal  model  delta    sigma   weight residual
    1.528  1.507  0.021 1.39e-02 5.18e+03 2.22e+00
  bond pdb=" CA  ALA E  91 "
       pdb=" CB  ALA E  91 "
    ideal  model  delta    sigma   weight residual
    1.528  1.507  0.021 1.39e-02 5.18e+03 2.22e+00
  ... (remaining 2665 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 3240
        1.05 -     2.10: 318
        2.10 -     3.15: 42
        3.15 -     4.20: 12
        4.20 -     5.25: 12
  Bond angle restraints: 3624
  Sorted by residual:
  angle pdb=" OG1 THR H  92 "
        pdb=" CB  THR H  92 "
        pdb=" CG2 THR H  92 "
      ideal   model   delta    sigma   weight residual
     109.30  104.05    5.25 2.00e+00 2.50e-01 6.90e+00
  angle pdb=" OG1 THR E  92 "
        pdb=" CB  THR E  92 "
        pdb=" CG2 THR E  92 "
      ideal   model   delta    sigma   weight residual
     109.30  104.05    5.25 2.00e+00 2.50e-01 6.88e+00
  angle pdb=" OG1 THR C  92 "
        pdb=" CB  THR C  92 "
        pdb=" CG2 THR C  92 "
      ideal   model   delta    sigma   weight residual
     109.30  104.06    5.24 2.00e+00 2.50e-01 6.86e+00
  angle pdb=" OG1 THR F  92 "
        pdb=" CB  THR F  92 "
        pdb=" CG2 THR F  92 "
      ideal   model   delta    sigma   weight residual
     109.30  104.08    5.22 2.00e+00 2.50e-01 6.81e+00
  angle pdb=" OG1 THR G  92 "
        pdb=" CB  THR G  92 "
        pdb=" CG2 THR G  92 "
      ideal   model   delta    sigma   weight residual
     109.30  104.08    5.22 2.00e+00 2.50e-01 6.81e+00
  ... (remaining 3619 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 1458
       16.72 -    33.43: 78
       33.43 -    50.15: 24
       50.15 -    66.86: 0
       66.86 -    83.58: 6
  Dihedral angle restraints: 1566
    sinusoidal: 528
      harmonic: 1038
  Sorted by residual:
  dihedral pdb=" CA  ASP C  51 "
           pdb=" CB  ASP C  51 "
           pdb=" CG  ASP C  51 "
           pdb=" OD1 ASP C  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.13   50.13     1      2.00e+01 2.50e-03 8.61e+00
  dihedral pdb=" CA  ASP G  51 "
           pdb=" CB  ASP G  51 "
           pdb=" CG  ASP G  51 "
           pdb=" OD1 ASP G  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.13   50.13     1      2.00e+01 2.50e-03 8.61e+00
  dihedral pdb=" CA  ASP D  51 "
           pdb=" CB  ASP D  51 "
           pdb=" CG  ASP D  51 "
           pdb=" OD1 ASP D  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.12   50.12     1      2.00e+01 2.50e-03 8.61e+00
  ... (remaining 1563 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 172
       0.029 -    0.058: 164
       0.058 -    0.087: 36
       0.087 -    0.116: 90
       0.116 -    0.145: 18
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  VAL F  49 "
            pdb=" N   VAL F  49 "
            pdb=" C   VAL F  49 "
            pdb=" CB  VAL F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  VAL H  49 "
            pdb=" N   VAL H  49 "
            pdb=" C   VAL H  49 "
            pdb=" CB  VAL H  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  VAL C  49 "
            pdb=" N   VAL C  49 "
            pdb=" C   VAL C  49 "
            pdb=" CB  VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 477 not shown)

  Planarity restraints: 456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F  50 "   -0.015 2.00e-02 2.50e+03   1.25e-02 2.33e+00
        pdb=" CG  HIS F  50 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS F  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS F  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 HIS F  50 "   -0.006 2.00e-02 2.50e+03
        pdb=" NE2 HIS F  50 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H  50 "   -0.015 2.00e-02 2.50e+03   1.25e-02 2.33e+00
        pdb=" CG  HIS H  50 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS H  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS H  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 HIS H  50 "   -0.006 2.00e-02 2.50e+03
        pdb=" NE2 HIS H  50 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  50 "   -0.015 2.00e-02 2.50e+03   1.24e-02 2.31e+00
        pdb=" CG  HIS E  50 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  50 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  50 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 453 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 156
        2.73 -     3.27: 2500
        3.27 -     3.82: 4119
        3.82 -     4.36: 4739
        4.36 -     4.90: 9658
  Nonbonded interactions: 21172
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS C  50 "
            pdb=" OD2 ASP C  51 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" ND1 HIS G  50 "
            pdb=" OD2 ASP G  51 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" ND1 HIS H  50 "
            pdb=" OD2 ASP H  51 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" ND1 HIS E  50 "
            pdb=" OD2 ASP E  51 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" ND1 HIS D  50 "
            pdb=" OD2 ASP D  51 "
     model   vdw
     2.190 3.120
  ... (remaining 21167 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 'C'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'G'
  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:             1.560
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.020
  Find NCS groups from input model:        0.030
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
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      :  0.009   0.042   2670  Z= 0.418
  Angle     :  0.743   5.253   3624  Z= 0.421
  Chirality :  0.060   0.145    480
  Planarity :  0.003   0.012    456
  Dihedral  : 13.666  83.577    906
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  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: -4.39 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR E  39 
 PHE   0.016   0.004   PHE E  94 
 HIS   0.008   0.005   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00899 ( 2670)
  covalent geometry    : angle       0.74341 ( 3624)
  hydrogen bonds       : bond        0.15295 (   32)
  hydrogen bonds       : angle       7.50545 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.096 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8442 (mttm) cc_final: 0.8156 (mttp)
REVERT: D   97 LYS cc_start: 0.8826 (mttm) cc_final: 0.8614 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0858
  time to fit residues: 2.6464
Evaluate side-chains
  24 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
C  58 ASN
C  65 ASN
E  65 ASN
D  58 ASN
F  58 ASN
G  58 ASN
G  65 ASN
H  58 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.129929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.095286 restraints weight = 3109.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.71
r_work: 0.3310 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2670  Z= 0.169
  Angle     :  0.474   4.608   3624  Z= 0.264
  Chirality :  0.053   0.141    480
  Planarity :  0.002   0.010    456
  Dihedral  :  4.860  14.919    378
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.67 (0.38), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR F  39 
 PHE   0.011   0.003   PHE E  94 
 HIS   0.006   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 2670)
  covalent geometry    : angle       0.47397 ( 3624)
  hydrogen bonds       : bond        0.01268 (   32)
  hydrogen bonds       : angle       4.41814 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.093 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8428 (mttm) cc_final: 0.8193 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1133
  time to fit residues: 2.2434
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0770
   chunk 17 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0020
   chunk 12 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.6152

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.129621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.094835 restraints weight = 3074.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.67
r_work: 0.3316 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2670  Z= 0.158
  Angle     :  0.448   3.788   3624  Z= 0.251
  Chirality :  0.052   0.142    480
  Planarity :  0.002   0.007    456
  Dihedral  :  4.726  14.403    378
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  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: -3.11 (0.41), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR F  39 
 PHE   0.010   0.002   PHE E  94 
 HIS   0.005   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 2670)
  covalent geometry    : angle       0.44810 ( 3624)
  hydrogen bonds       : bond        0.00994 (   32)
  hydrogen bonds       : angle       4.07630 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.060 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8372 (mttm) cc_final: 0.8132 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0710
  time to fit residues: 1.4168
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.129557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.094860 restraints weight = 3067.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.66
r_work: 0.3311 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2670  Z= 0.178
  Angle     :  0.456   3.448   3624  Z= 0.257
  Chirality :  0.052   0.142    480
  Planarity :  0.002   0.008    456
  Dihedral  :  4.812  14.205    378
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  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 are not related in a simple way.
  whole: -2.84 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR F  39 
 PHE   0.011   0.003   PHE E  94 
 HIS   0.005   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 2670)
  covalent geometry    : angle       0.45593 ( 3624)
  hydrogen bonds       : bond        0.01017 (   32)
  hydrogen bonds       : angle       4.08548 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.097 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8375 (mttm) cc_final: 0.8130 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1147
  time to fit residues: 2.2730
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.129979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.095522 restraints weight = 3068.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.65
r_work: 0.3315 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2670  Z= 0.167
  Angle     :  0.441   3.173   3624  Z= 0.249
  Chirality :  0.052   0.141    480
  Planarity :  0.002   0.008    456
  Dihedral  :  4.763  14.101    378
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  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 are not related in a simple way.
  whole: -2.68 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR F  39 
 PHE   0.010   0.002   PHE E  94 
 HIS   0.005   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 2670)
  covalent geometry    : angle       0.44086 ( 3624)
  hydrogen bonds       : bond        0.00946 (   32)
  hydrogen bonds       : angle       4.01848 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.058 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8382 (mttm) cc_final: 0.8141 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0782
  time to fit residues: 1.5496
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   overall best weight:    4.1588

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.128439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093692 restraints weight = 3088.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.66
r_work: 0.3286 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   2670  Z= 0.243
  Angle     :  0.501   3.298   3624  Z= 0.285
  Chirality :  0.053   0.145    480
  Planarity :  0.002   0.011    456
  Dihedral  :  5.072  14.470    378
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  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: -2.69 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR F  39 
 PHE   0.013   0.003   PHE E  94 
 HIS   0.007   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 2670)
  covalent geometry    : angle       0.50112 ( 3624)
  hydrogen bonds       : bond        0.01205 (   32)
  hydrogen bonds       : angle       4.17356 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.061 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8384 (mttm) cc_final: 0.8132 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0721
  time to fit residues: 1.4427
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3873 r_free = 0.3873 target = 0.130627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.096052 restraints weight = 3079.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.69
r_work: 0.3332 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2670  Z= 0.122
  Angle     :  0.410   2.924   3624  Z= 0.232
  Chirality :  0.051   0.138    480
  Planarity :  0.001   0.007    456
  Dihedral  :  4.637  14.251    378
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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: -2.56 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR D  39 
 PHE   0.008   0.002   PHE E  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 2670)
  covalent geometry    : angle       0.41006 ( 3624)
  hydrogen bonds       : bond        0.00790 (   32)
  hydrogen bonds       : angle       3.89013 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.061 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8401 (mttm) cc_final: 0.8153 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1044
  time to fit residues: 1.9408
Evaluate side-chains
  16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.128383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.093667 restraints weight = 3158.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.69
r_work: 0.3278 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2670  Z= 0.222
  Angle     :  0.480   3.121   3624  Z= 0.273
  Chirality :  0.053   0.142    480
  Planarity :  0.002   0.010    456
  Dihedral  :  4.998  14.587    378
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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: -2.57 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR F  39 
 PHE   0.012   0.003   PHE E  94 
 HIS   0.006   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 2670)
  covalent geometry    : angle       0.48039 ( 3624)
  hydrogen bonds       : bond        0.01114 (   32)
  hydrogen bonds       : angle       4.11301 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.104 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8386 (mttm) cc_final: 0.8137 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1184
  time to fit residues: 2.3494
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.128063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.093325 restraints weight = 3155.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.70
r_work: 0.3273 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
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      :  0.006   0.028   2670  Z= 0.246
  Angle     :  0.505   3.301   3624  Z= 0.288
  Chirality :  0.053   0.144    480
  Planarity :  0.002   0.011    456
  Dihedral  :  5.152  14.874    378
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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: -2.61 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR F  39 
 PHE   0.013   0.003   PHE E  94 
 HIS   0.007   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 2670)
  covalent geometry    : angle       0.50517 ( 3624)
  hydrogen bonds       : bond        0.01221 (   32)
  hydrogen bonds       : angle       4.18190 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.059 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8408 (mttm) cc_final: 0.8154 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0707
  time to fit residues: 1.4106
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.130233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.095634 restraints weight = 3124.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.68
r_work: 0.3329 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2670  Z= 0.129
  Angle     :  0.415   2.836   3624  Z= 0.235
  Chirality :  0.051   0.138    480
  Planarity :  0.001   0.007    456
  Dihedral  :  4.711  14.618    378
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR D  39 
 PHE   0.008   0.002   PHE E  94 
 HIS   0.004   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2670)
  covalent geometry    : angle       0.41459 ( 3624)
  hydrogen bonds       : bond        0.00841 (   32)
  hydrogen bonds       : angle       3.93866 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.062 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8409 (mttm) cc_final: 0.8163 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0757
  time to fit residues: 1.5341
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 25 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.129413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.094749 restraints weight = 3079.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.69
r_work: 0.3301 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2670  Z= 0.163
  Angle     :  0.437   2.941   3624  Z= 0.248
  Chirality :  0.051   0.139    480
  Planarity :  0.002   0.008    456
  Dihedral  :  4.818  14.338    378
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.001   TYR H  39 
 PHE   0.009   0.002   PHE E  94 
 HIS   0.005   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 2670)
  covalent geometry    : angle       0.43711 ( 3624)
  hydrogen bonds       : bond        0.00951 (   32)
  hydrogen bonds       : angle       4.02086 (   96)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 791.89 seconds
wall clock time: 14 minutes 18.02 seconds (858.02 seconds total)