Starting phenix.real_space_refine
on Wed Sep 17 04:46:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqw_45825/09_2025/9cqw_45825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqw_45825/09_2025/9cqw_45825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqw_45825/09_2025/9cqw_45825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqw_45825/09_2025/9cqw_45825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqw_45825/09_2025/9cqw_45825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqw_45825/09_2025/9cqw_45825.cif"
  }
  resolution = 2.61
  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=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  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: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.40, per 1000 atoms: 0.31
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (77.175, 72.765, 66.885, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 170.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      88.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.500A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.699A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.613A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.870A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.143A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 77 through 79
      No H-bonds generated for 'chain 'B' and resid 77 through 79'
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.962A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.709A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.590A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.849A  pdb=" N   GLY D  24 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 41
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.569A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 76
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.964A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 143

    341 hydrogen bonds defined for protein.
    975 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: 0.57

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.20 -     1.37: 1498
        1.37 -     1.54: 3041
        1.54 -     1.71: 37
        1.71 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.17e-02 7.31e+03 1.15e+01
  bond pdb=" N   VAL D  23 "
       pdb=" CA  VAL D  23 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.17e-02 7.31e+03 1.06e+01
  bond pdb=" N   PHE D  42 "
       pdb=" CA  PHE D  42 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.18e-02 7.18e+03 9.54e+00
  bond pdb=" C   PRO A   4 "
       pdb=" O   PRO A   4 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.26e-02 6.30e+03 9.24e+00
  bond pdb=" N   VAL B  67 "
       pdb=" CA  VAL B  67 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.81e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 5691
        1.26 -     2.53: 439
        2.53 -     3.79: 158
        3.79 -     5.06: 30
        5.06 -     6.32: 12
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" N   GLU B  22 "
        pdb=" CA  GLU B  22 "
        pdb=" C   GLU B  22 "
      ideal   model   delta    sigma   weight residual
     111.14  116.45   -5.31 1.08e+00 8.57e-01 2.41e+01
  angle pdb=" N   GLU D  22 "
        pdb=" CA  GLU D  22 "
        pdb=" C   GLU D  22 "
      ideal   model   delta    sigma   weight residual
     111.14  115.86   -4.72 1.08e+00 8.57e-01 1.91e+01
  angle pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
        pdb=" O   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     121.17  117.10    4.07 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" CA  VAL D  23 "
        pdb=" C   VAL D  23 "
        pdb=" O   VAL D  23 "
      ideal   model   delta    sigma   weight residual
     121.17  117.28    3.89 1.06e+00 8.90e-01 1.35e+01
  angle pdb=" CA  VAL D  20 "
        pdb=" C   VAL D  20 "
        pdb=" O   VAL D  20 "
      ideal   model   delta    sigma   weight residual
     120.95  117.24    3.71 1.04e+00 9.25e-01 1.27e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 2288
       17.87 -    35.74: 224
       35.74 -    53.60: 81
       53.60 -    71.47: 12
       71.47 -    89.34: 9
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" CA  ASP C 126 "
           pdb=" CB  ASP C 126 "
           pdb=" CG  ASP C 126 "
           pdb=" OD1 ASP C 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -90.09   60.09     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" C1A HEM C 201 "
           pdb=" C2A HEM C 201 "
           pdb=" CAA HEM C 201 "
           pdb=" CBA HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.34  -89.34     2      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" C1A HEM A 201 "
           pdb=" C2A HEM A 201 "
           pdb=" CAA HEM A 201 "
           pdb=" CBA HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.43  -87.43     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 565
       0.065 -    0.130: 104
       0.130 -    0.195: 18
       0.195 -    0.259: 3
       0.259 -    0.324: 2
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CB  VAL D 134 "
            pdb=" CA  VAL D 134 "
            pdb=" CG1 VAL D 134 "
            pdb=" CG2 VAL D 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CB  VAL D  18 "
            pdb=" CA  VAL D  18 "
            pdb=" CG1 VAL D  18 "
            pdb=" CG2 VAL D  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 123 "    0.032 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO D 124 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO D 124 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 124 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO B 124 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 124 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO B 125 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 125 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 125 "    0.022 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 83
        2.71 -     3.25: 4305
        3.25 -     3.80: 7714
        3.80 -     4.35: 9849
        4.35 -     4.90: 16056
  Nonbonded interactions: 38007
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 101 "
            pdb=" NH1 ARG D 104 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" OE1 GLU B 101 "
            pdb=" NH1 ARG B 104 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   PRO A 114 "
            pdb=" NE2 HIS B 116 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" O   PRO C 114 "
            pdb=" NE2 HIS D 116 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OE2 GLU C  30 "
            pdb=" ND1 HIS C  50 "
     model   vdw
     2.373 3.120
  ... (remaining 38002 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  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:             3.010
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.124   4614  Z= 0.376
  Angle     :  0.868   6.324   6330  Z= 0.595
  Chirality :  0.057   0.324    692
  Planarity :  0.006   0.048    790
  Dihedral  : 17.308  89.341   1562
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 15.20 %
    Favored  : 79.30 %
  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:  2.83 (0.36), residues: 558
  helix:  2.34 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  0.25 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  40 
 TYR   0.013   0.002   TYR D 130 
 PHE   0.015   0.002   PHE A  36 
 TRP   0.022   0.003   TRP B  15 
 HIS   0.006   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 4610)
  covalent geometry    : angle       0.86841 ( 6330)
  hydrogen bonds       : bond        0.12561 (  341)
  hydrogen bonds       : angle       5.21394 (  975)
  Misc. bond           : bond        0.09133 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8077 (tttt) cc_final: 0.7312 (mptm)
REVERT: A  126 ASP cc_start: 0.8067 (t70) cc_final: 0.7792 (t70)
REVERT: B   90 GLU cc_start: 0.7832 (tp30) cc_final: 0.7559 (mm-30)
REVERT: B   99 ASP cc_start: 0.7535 (t70) cc_final: 0.7269 (t70)
REVERT: C   56 LYS cc_start: 0.8043 (tttt) cc_final: 0.7277 (mptm)
REVERT: C   92 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7441 (mtt-85)
REVERT: C  126 ASP cc_start: 0.8070 (t70) cc_final: 0.7780 (t70)
REVERT: C  127 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7890 (mtmt)
REVERT: D   17 LYS cc_start: 0.8390 (mttt) cc_final: 0.7886 (mtpt)
REVERT: D   22 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6546 (mm-30)
REVERT: D   43 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6835 (mm-30)
REVERT: D   65 LYS cc_start: 0.8509 (tttm) cc_final: 0.7953 (ttmt)
REVERT: D   66 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8257 (mtmt)
REVERT: D   90 GLU cc_start: 0.7605 (tt0) cc_final: 0.7164 (mm-30)
REVERT: D  117 HIS cc_start: 0.7600 (t-170) cc_final: 0.6995 (m-70)
REVERT: D  120 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7194 (tptt)
REVERT: D  139 ASN cc_start: 0.7338 (m110) cc_final: 0.7053 (m-40)
  outliers start: 25
  outliers final: 8
  residues processed: 96
  average time/residue: 0.7463
  time to fit residues: 73.6741
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   21 ASP
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0370
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
B 139 ASN
D  19 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.146474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.123445 restraints weight = 4233.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.46
r_work: 0.3290 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4614  Z= 0.115
  Angle     :  0.551   5.262   6330  Z= 0.259
  Chirality :  0.038   0.117    692
  Planarity :  0.006   0.046    790
  Dihedral  : 12.780  89.171    637
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.20 %
    Favored  : 81.28 %
  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:  3.04 (0.36), residues: 558
  helix:  2.45 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.47 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.009   0.001   TYR D 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4610)
  covalent geometry    : angle       0.55100 ( 6330)
  hydrogen bonds       : bond        0.03440 (  341)
  hydrogen bonds       : angle       4.02653 (  975)
  Misc. bond           : bond        0.04491 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7984 (tttt) cc_final: 0.7278 (mptm)
REVERT: B   65 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7962 (mtpt)
REVERT: B   90 GLU cc_start: 0.7863 (tp30) cc_final: 0.7564 (mm-30)
REVERT: B   99 ASP cc_start: 0.7430 (t70) cc_final: 0.7132 (t70)
REVERT: B  101 GLU cc_start: 0.7960 (tp30) cc_final: 0.7685 (mm-30)
REVERT: B  132 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8296 (mtmm)
REVERT: C   56 LYS cc_start: 0.7955 (tttt) cc_final: 0.7281 (mptm)
REVERT: C   92 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7466 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7914 (mtmt)
REVERT: D   17 LYS cc_start: 0.8457 (mttt) cc_final: 0.7962 (mtpt)
REVERT: D   22 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6378 (mm-30)
REVERT: D   26 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6887 (tm-30)
REVERT: D   43 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6883 (mm-30)
REVERT: D   65 LYS cc_start: 0.8475 (tttm) cc_final: 0.7893 (ttmt)
REVERT: D   90 GLU cc_start: 0.7612 (tt0) cc_final: 0.7123 (mm-30)
REVERT: D   99 ASP cc_start: 0.7467 (t70) cc_final: 0.7164 (t70)
REVERT: D  101 GLU cc_start: 0.7972 (tp30) cc_final: 0.7719 (mm-30)
REVERT: D  117 HIS cc_start: 0.7469 (t-170) cc_final: 0.6878 (m-70)
REVERT: D  120 LYS cc_start: 0.7489 (mmtm) cc_final: 0.7218 (tptp)
  outliers start: 16
  outliers final: 8
  residues processed: 90
  average time/residue: 0.7750
  time to fit residues: 71.6351
Evaluate side-chains
  88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   21 ASP
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.141843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.118666 restraints weight = 4217.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.48
r_work: 0.3232 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.0900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   4614  Z= 0.165
  Angle     :  0.616   5.606   6330  Z= 0.292
  Chirality :  0.042   0.130    692
  Planarity :  0.006   0.050    790
  Dihedral  : 12.890  87.671    634
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.54 %
    Favored  : 81.28 %
  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:  3.04 (0.36), residues: 558
  helix:  2.27 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.39 (0.62), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.010   0.002   TYR C 140 
 PHE   0.013   0.002   PHE D 118 
 TRP   0.009   0.001   TRP C  14 
 HIS   0.005   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 4610)
  covalent geometry    : angle       0.61573 ( 6330)
  hydrogen bonds       : bond        0.04378 (  341)
  hydrogen bonds       : angle       4.08687 (  975)
  Misc. bond           : bond        0.06833 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8159 (tttt) cc_final: 0.7417 (mptm)
REVERT: A  126 ASP cc_start: 0.8150 (t70) cc_final: 0.7792 (t70)
REVERT: B   90 GLU cc_start: 0.7976 (tp30) cc_final: 0.7670 (mm-30)
REVERT: B   99 ASP cc_start: 0.7610 (t70) cc_final: 0.7285 (t70)
REVERT: C   56 LYS cc_start: 0.8105 (tttt) cc_final: 0.7416 (mptm)
REVERT: C   92 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7566 (mtt-85)
REVERT: C  126 ASP cc_start: 0.8154 (t70) cc_final: 0.7786 (t70)
REVERT: C  127 LYS cc_start: 0.8521 (mtpt) cc_final: 0.7992 (mtmt)
REVERT: D   17 LYS cc_start: 0.8631 (mttt) cc_final: 0.8094 (mtpt)
REVERT: D   43 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7022 (mm-30)
REVERT: D   65 LYS cc_start: 0.8598 (tttm) cc_final: 0.8023 (ttmt)
REVERT: D   66 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8278 (mtmm)
REVERT: D   90 GLU cc_start: 0.7764 (tt0) cc_final: 0.7161 (mm-30)
REVERT: D   95 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7601 (mttm)
REVERT: D   99 ASP cc_start: 0.7645 (t70) cc_final: 0.7319 (t70)
REVERT: D  117 HIS cc_start: 0.7591 (t-170) cc_final: 0.7012 (m-70)
REVERT: D  120 LYS cc_start: 0.7494 (mmtm) cc_final: 0.7145 (tptt)
  outliers start: 19
  outliers final: 6
  residues processed: 84
  average time/residue: 0.8283
  time to fit residues: 71.4195
Evaluate side-chains
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   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 = 0.3563 r_free = 0.3563 target = 0.142604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119655 restraints weight = 4217.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.48
r_work: 0.3245 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   4614  Z= 0.134
  Angle     :  0.571   5.331   6330  Z= 0.270
  Chirality :  0.040   0.121    692
  Planarity :  0.006   0.048    790
  Dihedral  : 11.833  86.779    627
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.42 %
    Favored  : 81.06 %
  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:  3.18 (0.36), residues: 558
  helix:  2.40 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.34 (0.62), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.007   0.001   TYR D 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.007   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4610)
  covalent geometry    : angle       0.57113 ( 6330)
  hydrogen bonds       : bond        0.03660 (  341)
  hydrogen bonds       : angle       3.95303 (  975)
  Misc. bond           : bond        0.05842 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8067 (tttt) cc_final: 0.7316 (mptm)
REVERT: A  126 ASP cc_start: 0.8045 (t70) cc_final: 0.7755 (t70)
REVERT: B   26 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7298 (mm-30)
REVERT: B   99 ASP cc_start: 0.7504 (t70) cc_final: 0.7174 (t70)
REVERT: C   56 LYS cc_start: 0.8015 (tttt) cc_final: 0.7300 (mptm)
REVERT: C   92 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7449 (mtt-85)
REVERT: C  126 ASP cc_start: 0.8046 (t70) cc_final: 0.7843 (t70)
REVERT: C  127 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7891 (mtmt)
REVERT: D   17 LYS cc_start: 0.8606 (mttt) cc_final: 0.8029 (mtpt)
REVERT: D   26 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7289 (mm-30)
REVERT: D   43 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7101 (mm-30)
REVERT: D   65 LYS cc_start: 0.8525 (tttm) cc_final: 0.7938 (ttmt)
REVERT: D   66 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8145 (mtmm)
REVERT: D   90 GLU cc_start: 0.7677 (tt0) cc_final: 0.7039 (mm-30)
REVERT: D   95 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7520 (mttm)
REVERT: D   99 ASP cc_start: 0.7543 (t70) cc_final: 0.7209 (t70)
REVERT: D  117 HIS cc_start: 0.7491 (t-170) cc_final: 0.6885 (m-70)
REVERT: D  120 LYS cc_start: 0.7488 (mmtm) cc_final: 0.7125 (tptt)
  outliers start: 16
  outliers final: 5
  residues processed: 83
  average time/residue: 0.7778
  time to fit residues: 66.3475
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   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 = 0.3560 r_free = 0.3560 target = 0.142440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.119515 restraints weight = 4226.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.49
r_work: 0.3243 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4614  Z= 0.133
  Angle     :  0.571   5.330   6330  Z= 0.269
  Chirality :  0.040   0.124    692
  Planarity :  0.006   0.048    790
  Dihedral  : 11.812  86.025    627
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.64 %
    Favored  : 81.06 %
  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 (0.35), residues: 558
  helix:  2.42 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.21 (0.59), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.007   0.001   TYR B 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.007   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4610)
  covalent geometry    : angle       0.57117 ( 6330)
  hydrogen bonds       : bond        0.03683 (  341)
  hydrogen bonds       : angle       3.94299 (  975)
  Misc. bond           : bond        0.05529 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8135 (tttt) cc_final: 0.7427 (mptm)
REVERT: A  126 ASP cc_start: 0.8112 (t70) cc_final: 0.7807 (t70)
REVERT: B   26 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7329 (mm-30)
REVERT: B   99 ASP cc_start: 0.7542 (t70) cc_final: 0.7221 (t70)
REVERT: B  132 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8390 (mtmt)
REVERT: C   56 LYS cc_start: 0.8075 (tttt) cc_final: 0.7407 (mptm)
REVERT: C   92 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7510 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8486 (mtpt) cc_final: 0.7972 (mtmt)
REVERT: D   17 LYS cc_start: 0.8654 (mttt) cc_final: 0.8066 (mtpt)
REVERT: D   22 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6742 (mp0)
REVERT: D   26 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7323 (mm-30)
REVERT: D   43 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7191 (mm-30)
REVERT: D   65 LYS cc_start: 0.8568 (tttm) cc_final: 0.7988 (ttmt)
REVERT: D   66 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8165 (mtmm)
REVERT: D   90 GLU cc_start: 0.7710 (tt0) cc_final: 0.7083 (mm-30)
REVERT: D   95 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7611 (mttm)
REVERT: D   99 ASP cc_start: 0.7584 (t70) cc_final: 0.7244 (t70)
REVERT: D  117 HIS cc_start: 0.7595 (t-170) cc_final: 0.7046 (m-70)
REVERT: D  120 LYS cc_start: 0.7531 (mmtm) cc_final: 0.7154 (tptt)
  outliers start: 15
  outliers final: 5
  residues processed: 82
  average time/residue: 0.7770
  time to fit residues: 65.5171
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.148216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.128057 restraints weight = 4285.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.36
r_work: 0.3313 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   4614  Z= 0.184
  Angle     :  0.639   5.997   6330  Z= 0.305
  Chirality :  0.044   0.132    692
  Planarity :  0.006   0.051    790
  Dihedral  : 12.216  87.206    627
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.76 %
    Favored  : 81.50 %
  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 (0.35), residues: 558
  helix:  2.14 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.20 (0.59), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 104 
 TYR   0.009   0.002   TYR C 140 
 PHE   0.014   0.002   PHE D 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 4610)
  covalent geometry    : angle       0.63910 ( 6330)
  hydrogen bonds       : bond        0.04572 (  341)
  hydrogen bonds       : angle       4.11016 (  975)
  Misc. bond           : bond        0.07334 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8068 (tttt) cc_final: 0.7329 (mptm)
REVERT: A  126 ASP cc_start: 0.8177 (t70) cc_final: 0.7851 (t70)
REVERT: B   90 GLU cc_start: 0.8009 (tp30) cc_final: 0.7796 (mm-30)
REVERT: B   95 LYS cc_start: 0.8134 (tttt) cc_final: 0.7883 (tttm)
REVERT: B   99 ASP cc_start: 0.7588 (t70) cc_final: 0.7260 (t70)
REVERT: C   56 LYS cc_start: 0.8067 (tttt) cc_final: 0.7325 (mptm)
REVERT: C   92 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7538 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8003 (mtmt)
REVERT: D   17 LYS cc_start: 0.8652 (mttt) cc_final: 0.8097 (mtpt)
REVERT: D   22 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6550 (mp0)
REVERT: D   26 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7304 (mm-30)
REVERT: D   43 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7271 (mm-30)
REVERT: D   65 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8043 (ttmt)
REVERT: D   66 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8259 (mtmm)
REVERT: D   90 GLU cc_start: 0.7661 (tt0) cc_final: 0.7067 (mm-30)
REVERT: D   95 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7643 (mttm)
REVERT: D   99 ASP cc_start: 0.7650 (t70) cc_final: 0.7289 (t70)
REVERT: D  117 HIS cc_start: 0.7565 (t-170) cc_final: 0.7010 (m-70)
REVERT: D  120 LYS cc_start: 0.7558 (mmtm) cc_final: 0.7157 (tptt)
  outliers start: 17
  outliers final: 7
  residues processed: 85
  average time/residue: 0.8012
  time to fit residues: 69.9612
Evaluate side-chains
  86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   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 = 0.3682 r_free = 0.3682 target = 0.150120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.131411 restraints weight = 4295.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.23
r_work: 0.3338 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   4614  Z= 0.136
  Angle     :  0.578   5.330   6330  Z= 0.273
  Chirality :  0.040   0.123    692
  Planarity :  0.006   0.049    790
  Dihedral  : 11.856  87.073    627
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.64 %
    Favored  : 81.06 %
  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:  3.06 (0.35), residues: 558
  helix:  2.34 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.22 (0.60), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 104 
 TYR   0.007   0.001   TYR B 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.006   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4610)
  covalent geometry    : angle       0.57811 ( 6330)
  hydrogen bonds       : bond        0.03740 (  341)
  hydrogen bonds       : angle       3.98170 (  975)
  Misc. bond           : bond        0.05664 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8091 (tttt) cc_final: 0.7469 (mptm)
REVERT: A  126 ASP cc_start: 0.8235 (t70) cc_final: 0.7916 (t70)
REVERT: B   26 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7308 (mm-30)
REVERT: B   95 LYS cc_start: 0.8150 (tttt) cc_final: 0.7929 (tttm)
REVERT: B   99 ASP cc_start: 0.7523 (t70) cc_final: 0.7238 (t70)
REVERT: C   56 LYS cc_start: 0.8117 (tttt) cc_final: 0.7462 (mptm)
REVERT: C   92 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7601 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8054 (mtmt)
REVERT: D   17 LYS cc_start: 0.8710 (mttt) cc_final: 0.8177 (mtpt)
REVERT: D   26 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7323 (mm-30)
REVERT: D   43 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7371 (mm-30)
REVERT: D   65 LYS cc_start: 0.8653 (tttm) cc_final: 0.8114 (ttmt)
REVERT: D   66 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8250 (mtmm)
REVERT: D   90 GLU cc_start: 0.7771 (tt0) cc_final: 0.7205 (mm-30)
REVERT: D   95 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7713 (mttm)
REVERT: D   99 ASP cc_start: 0.7593 (t70) cc_final: 0.7271 (t70)
REVERT: D  117 HIS cc_start: 0.7624 (t-170) cc_final: 0.7166 (m-70)
REVERT: D  120 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7295 (tptt)
  outliers start: 15
  outliers final: 7
  residues processed: 85
  average time/residue: 0.7192
  time to fit residues: 62.8954
Evaluate side-chains
  86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   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 = 0.3684 r_free = 0.3684 target = 0.150254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.130300 restraints weight = 4260.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.36
r_work: 0.3340 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   4614  Z= 0.136
  Angle     :  0.575   5.339   6330  Z= 0.271
  Chirality :  0.040   0.124    692
  Planarity :  0.006   0.049    790
  Dihedral  : 11.792  87.320    627
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.64 %
    Favored  : 80.84 %
  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:  3.10 (0.36), residues: 558
  helix:  2.37 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.21 (0.60), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 104 
 TYR   0.007   0.001   TYR B 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.006   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4610)
  covalent geometry    : angle       0.57512 ( 6330)
  hydrogen bonds       : bond        0.03718 (  341)
  hydrogen bonds       : angle       3.96341 (  975)
  Misc. bond           : bond        0.05841 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8005 (tttt) cc_final: 0.7312 (mptm)
REVERT: A  126 ASP cc_start: 0.8162 (t70) cc_final: 0.7857 (t70)
REVERT: B   26 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7226 (mm-30)
REVERT: B   95 LYS cc_start: 0.8086 (tttt) cc_final: 0.7863 (tttm)
REVERT: B   99 ASP cc_start: 0.7479 (t70) cc_final: 0.7145 (t70)
REVERT: C   56 LYS cc_start: 0.8014 (tttt) cc_final: 0.7299 (mptm)
REVERT: C   92 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7496 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8493 (mtpt) cc_final: 0.7928 (mtmt)
REVERT: D   17 LYS cc_start: 0.8644 (mttt) cc_final: 0.8056 (mtpt)
REVERT: D   22 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6594 (mp0)
REVERT: D   26 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7228 (mm-30)
REVERT: D   43 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7280 (mm-30)
REVERT: D   65 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8008 (ttmt)
REVERT: D   66 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8182 (mtmm)
REVERT: D   90 GLU cc_start: 0.7679 (tt0) cc_final: 0.7029 (mm-30)
REVERT: D   95 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7641 (mttm)
REVERT: D   99 ASP cc_start: 0.7524 (t70) cc_final: 0.7168 (t70)
REVERT: D  117 HIS cc_start: 0.7578 (t-170) cc_final: 0.7036 (m-70)
REVERT: D  120 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7266 (tptt)
  outliers start: 16
  outliers final: 7
  residues processed: 86
  average time/residue: 0.7801
  time to fit residues: 68.9061
Evaluate side-chains
  90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.151101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.130839 restraints weight = 4196.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.36
r_work: 0.3352 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4614  Z= 0.124
  Angle     :  0.559   5.296   6330  Z= 0.263
  Chirality :  0.039   0.121    692
  Planarity :  0.006   0.048    790
  Dihedral  : 11.626  87.410    627
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.08 %
    Favored  : 80.84 %
  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:  3.21 (0.36), residues: 558
  helix:  2.46 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.24 (0.60), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 104 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.009   0.001   PHE D 118 
 TRP   0.006   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4610)
  covalent geometry    : angle       0.55881 ( 6330)
  hydrogen bonds       : bond        0.03454 (  341)
  hydrogen bonds       : angle       3.90069 (  975)
  Misc. bond           : bond        0.05208 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7969 (tttt) cc_final: 0.7295 (mptm)
REVERT: B   26 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7227 (mm-30)
REVERT: B   95 LYS cc_start: 0.8025 (tttt) cc_final: 0.7406 (mttm)
REVERT: B   99 ASP cc_start: 0.7430 (t70) cc_final: 0.7089 (t70)
REVERT: C   56 LYS cc_start: 0.7989 (tttt) cc_final: 0.7277 (mptm)
REVERT: C   92 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7488 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7940 (mtmt)
REVERT: D   17 LYS cc_start: 0.8648 (mttt) cc_final: 0.8064 (mtpt)
REVERT: D   22 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6598 (mp0)
REVERT: D   26 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7239 (mm-30)
REVERT: D   43 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7284 (mm-30)
REVERT: D   65 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8001 (ttmt)
REVERT: D   66 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8177 (mtmm)
REVERT: D   90 GLU cc_start: 0.7675 (tt0) cc_final: 0.7028 (mm-30)
REVERT: D   95 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7650 (mttm)
REVERT: D   99 ASP cc_start: 0.7465 (t70) cc_final: 0.7109 (t70)
REVERT: D  117 HIS cc_start: 0.7562 (t-170) cc_final: 0.7039 (m-70)
REVERT: D  120 LYS cc_start: 0.7612 (mmtm) cc_final: 0.7260 (tptt)
  outliers start: 14
  outliers final: 4
  residues processed: 83
  average time/residue: 0.7648
  time to fit residues: 65.1675
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   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 = 0.3683 r_free = 0.3683 target = 0.150259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.131972 restraints weight = 4219.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.18
r_work: 0.3345 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   4614  Z= 0.134
  Angle     :  0.572   5.334   6330  Z= 0.270
  Chirality :  0.040   0.124    692
  Planarity :  0.006   0.048    790
  Dihedral  : 11.713  87.422    627
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.96 %
    Favored  : 80.40 %
  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:  3.13 (0.36), residues: 558
  helix:  2.35 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.34 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 104 
 TYR   0.007   0.001   TYR B 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.007   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4610)
  covalent geometry    : angle       0.57197 ( 6330)
  hydrogen bonds       : bond        0.03685 (  341)
  hydrogen bonds       : angle       3.92368 (  975)
  Misc. bond           : bond        0.05920 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8068 (tttt) cc_final: 0.7464 (mptm)
REVERT: B   26 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7307 (mm-30)
REVERT: B   99 ASP cc_start: 0.7459 (t70) cc_final: 0.7155 (t70)
REVERT: C   56 LYS cc_start: 0.8091 (tttt) cc_final: 0.7465 (mptm)
REVERT: C   92 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7596 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8057 (mtmt)
REVERT: D   17 LYS cc_start: 0.8721 (mttt) cc_final: 0.8183 (mtpt)
REVERT: D   22 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6692 (mp0)
REVERT: D   26 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7321 (mm-30)
REVERT: D   43 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7370 (mm-30)
REVERT: D   65 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8124 (ttmt)
REVERT: D   66 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8246 (mtmm)
REVERT: D   90 GLU cc_start: 0.7753 (tt0) cc_final: 0.7168 (mm-30)
REVERT: D   95 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7722 (mttm)
REVERT: D   99 ASP cc_start: 0.7503 (t70) cc_final: 0.7176 (t70)
REVERT: D  117 HIS cc_start: 0.7628 (t-170) cc_final: 0.7180 (m-70)
REVERT: D  120 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7357 (tptt)
  outliers start: 12
  outliers final: 4
  residues processed: 79
  average time/residue: 0.7300
  time to fit residues: 59.2139
Evaluate side-chains
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.158257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.140968 restraints weight = 4304.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.14
r_work: 0.3481 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   4614  Z= 0.163
  Angle     :  0.612   5.812   6330  Z= 0.291
  Chirality :  0.042   0.128    692
  Planarity :  0.006   0.049    790
  Dihedral  : 12.020  87.670    627
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.52 %
    Favored  : 80.40 %
  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:  2.92 (0.35), residues: 558
  helix:  2.19 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.34 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 104 
 TYR   0.008   0.002   TYR C 140 
 PHE   0.012   0.002   PHE D 118 
 TRP   0.007   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 4610)
  covalent geometry    : angle       0.61185 ( 6330)
  hydrogen bonds       : bond        0.04222 (  341)
  hydrogen bonds       : angle       4.01456 (  975)
  Misc. bond           : bond        0.07035 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1973.13 seconds
wall clock time: 34 minutes 22.64 seconds (2062.64 seconds total)