Starting phenix.real_space_refine
on Thu Sep 10 22:21:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v2u_64740/09_2026/9v2u_64740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v2u_64740/09_2026/9v2u_64740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v2u_64740/09_2026/9v2u_64740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v2u_64740/09_2026/9v2u_64740.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v2u_64740/09_2026/9v2u_64740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v2u_64740/09_2026/9v2u_64740.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    2788      2.51       5
     N     724      2.21       5
     O     840      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4380
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1147
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 2, 'TRANS': 152}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1553
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 191}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1680
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
  Time building chain proxies: 1.21, per 1000 atoms: 0.28
  Number of scatterers: 4380
  At special positions: 0
  Unit cell: (55.25, 66.3, 144.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     840      8.00
     N     724      7.00
     C    2788      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 145 " - pdb=" SG  CYS H 201 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 133.1 milliseconds
  

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 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:
      8 helices and 12 sheets defined
      21.0% alpha, 35.4% 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 5 through 27
    Processing helix  chain 'A' and resid 75 through 99
    Processing helix  chain 'A' and resid 115 through 145
      removed outlier: 3.741A  pdb=" N   THR A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 194
      removed outlier: 3.617A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 103
      No H-bonds generated for 'chain 'H' and resid 101 through 103'
    Processing helix  chain 'H' and resid 161 through 163
      No H-bonds generated for 'chain 'H' and resid 161 through 163'
    Processing helix  chain 'L' and resid 127 through 132
      removed outlier: 3.567A  pdb=" N   LEU L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS L 132 " --> pdb=" O   ASP L 128 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 127 through 132'
    Processing helix  chain 'L' and resid 189 through 195
      removed outlier: 3.517A  pdb=" N   HIS L 195 " --> pdb=" O   ASP L 191 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 47
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.589A  pdb=" N   VAL H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.559A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.559A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA H 104 " --> pdb=" O   TYR H 100 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 127 through 128
      removed outlier: 6.266A  pdb=" N   TYR H 181 " --> pdb=" O   ASP H 149 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 127 through 128
      removed outlier: 6.266A  pdb=" N   TYR H 181 " --> pdb=" O   ASP H 149 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 155 through 159
    Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.953A  pdb=" N   PHE L  77 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 4.065A  pdb=" N   GLU L 111 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA L  90 " --> pdb=" O   VAL L 110 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE L  54 " --> pdb=" O   TRP L  41 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   GLN L  43 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   LEU L  52 " --> pdb=" O   GLN L  43 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.606A  pdb=" N   VAL L 139 " --> pdb=" O   PHE L 124 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 159 through 160

    218 hydrogen bonds defined for protein.
    594 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: 0.63

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1377
        1.35 -     1.47: 1154
        1.47 -     1.59: 1902
        1.59 -     1.71: 0
        1.71 -     1.83: 42
  Bond restraints: 4475
  Sorted by residual:
  bond pdb=" C   ASP H  52 "
       pdb=" N   PRO H  53 "
    ideal  model  delta    sigma   weight residual
    1.336  1.327  0.009 9.80e-03 1.04e+04 8.36e-01
  bond pdb=" CB  PRO L 101 "
       pdb=" CG  PRO L 101 "
    ideal  model  delta    sigma   weight residual
    1.506  1.475  0.031 3.90e-02 6.57e+02 6.37e-01
  bond pdb=" C   LEU A  49 "
       pdb=" N   TRP A  50 "
    ideal  model  delta    sigma   weight residual
    1.331  1.321  0.011 1.40e-02 5.10e+03 6.04e-01
  bond pdb=" CA  MET H  81 "
       pdb=" CB  MET H  81 "
    ideal  model  delta    sigma   weight residual
    1.534  1.516  0.018 2.47e-02 1.64e+03 5.40e-01
  bond pdb=" CG  PRO L   8 "
       pdb=" CD  PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.512  1.493  0.019 2.70e-02 1.37e+03 5.13e-01
  ... (remaining 4470 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 5695
        1.19 -     2.39: 288
        2.39 -     3.58: 77
        3.58 -     4.77: 14
        4.77 -     5.97: 3
  Bond angle restraints: 6077
  Sorted by residual:
  angle pdb=" C   THR H  91 "
        pdb=" N   ALA H  92 "
        pdb=" CA  ALA H  92 "
      ideal   model   delta    sigma   weight residual
     122.45  117.94    4.51 1.78e+00 3.16e-01 6.42e+00
  angle pdb=" N   ILE H  51 "
        pdb=" CA  ILE H  51 "
        pdb=" C   ILE H  51 "
      ideal   model   delta    sigma   weight residual
     108.17  111.68   -3.51 1.46e+00 4.69e-01 5.77e+00
  angle pdb=" C   ASN H  35 "
        pdb=" N   TRP H  36 "
        pdb=" CA  TRP H  36 "
      ideal   model   delta    sigma   weight residual
     122.94  119.49    3.45 1.50e+00 4.44e-01 5.29e+00
  angle pdb=" CA  CYS L 140 "
        pdb=" CB  CYS L 140 "
        pdb=" SG  CYS L 140 "
      ideal   model   delta    sigma   weight residual
     114.40  119.33   -4.93 2.30e+00 1.89e-01 4.60e+00
  angle pdb=" CA  MET H  99 "
        pdb=" CB  MET H  99 "
        pdb=" CG  MET H  99 "
      ideal   model   delta    sigma   weight residual
     114.10  118.33   -4.23 2.00e+00 2.50e-01 4.46e+00
  ... (remaining 6072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 2390
       15.05 -    30.10: 180
       30.10 -    45.15: 57
       45.15 -    60.21: 7
       60.21 -    75.26: 6
  Dihedral angle restraints: 2640
    sinusoidal: 991
      harmonic: 1649
  Sorted by residual:
  dihedral pdb=" CA  MET A 191 "
           pdb=" C   MET A 191 "
           pdb=" N   MET A 192 "
           pdb=" CA  MET A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.14   30.86     1      1.00e+01 1.00e-02 1.36e+01
  dihedral pdb=" CA  LEU H 129 "
           pdb=" C   LEU H 129 "
           pdb=" N   ALA H 130 "
           pdb=" CA  ALA H 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.13  -16.87     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 2637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 409
       0.027 -    0.054: 176
       0.054 -    0.082: 64
       0.082 -    0.109: 28
       0.109 -    0.136: 17
  Chirality restraints: 694
  Sorted by residual:
  chirality pdb=" CA  CYS L 140 "
            pdb=" N   CYS L 140 "
            pdb=" C   CYS L 140 "
            pdb=" CB  CYS L 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  TYR L  55 "
            pdb=" N   TYR L  55 "
            pdb=" C   TYR L  55 "
            pdb=" CB  TYR L  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  ILE H  72 "
            pdb=" N   ILE H  72 "
            pdb=" C   ILE H  72 "
            pdb=" CB  ILE H  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 691 not shown)

  Planarity restraints: 763
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  36 "   -0.024 2.00e-02 2.50e+03   2.53e-02 1.61e+01
        pdb=" CG  TRP H  36 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  36 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  36 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  36 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  36 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  36 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  36 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  36 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "   -0.040 5.00e-02 4.00e+02   6.16e-02 6.08e+00
        pdb=" N   PRO L   8 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 171 "    0.035 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO H 172 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO H 172 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO H 172 "    0.030 5.00e-02 4.00e+02
  ... (remaining 760 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 699
        2.76 -     3.30: 4086
        3.30 -     3.83: 6746
        3.83 -     4.37: 7208
        4.37 -     4.90: 13167
  Nonbonded interactions: 31906
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP L 157 "
            pdb=" ND1 HIS L 195 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" OG1 THR L  40 "
            pdb=" OD2 ASP L  97 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   SER L  83 "
            pdb=" NE2 GLN L  85 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" OE1 GLN A  33 "
            pdb=" ND2 ASN A  45 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" O   ASN L  34 "
            pdb=" ND2 ASN L  34 "
     model   vdw
     2.352 3.120
  ... (remaining 31901 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             2.520
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.920
  Find NCS groups from input model:        0.020
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4480  Z= 0.163
  Angle     :  0.653   5.967   6087  Z= 0.363
  Chirality :  0.041   0.136    694
  Planarity :  0.005   0.062    763
  Dihedral  : 12.369  75.257   1573
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  1.20 (0.37), residues: 561
  helix:  3.23 (0.49), residues: 107
  sheet:  0.89 (0.34), residues: 236
  loop : -0.55 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  80 
 TYR   0.017   0.002   TYR A  46 
 PHE   0.026   0.002   PHE A 125 
 TRP   0.063   0.003   TRP H  36 
 HIS   0.003   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.16 ( 4475)
  covalent geometry    : angle       0.64885 /  0.36 ( 6077)
  SS BOND              : bond        0.00542 /  0.26 (    5)
  SS BOND              : angle       1.89167 /  1.00 (   10)
  hydrogen bonds       : bond        0.16121 / 11.19 (  205)
  hydrogen bonds       : angle       6.40849 /  4.45 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8248 (tp) cc_final: 0.8046 (tp)
REVERT: A  125 PHE cc_start: 0.8139 (m-80) cc_final: 0.7644 (m-80)
REVERT: A  131 CYS cc_start: 0.7243 (m) cc_final: 0.7032 (m)
REVERT: A  175 LEU cc_start: 0.8481 (mt) cc_final: 0.8150 (mt)
REVERT: A  192 MET cc_start: 0.7978 (mmp) cc_final: 0.7296 (mmp)
REVERT: H   30 THR cc_start: 0.8645 (p) cc_final: 0.8124 (t)
REVERT: H  127 PHE cc_start: 0.8069 (m-10) cc_final: 0.7838 (m-80)
REVERT: H  143 LEU cc_start: 0.7929 (mm) cc_final: 0.7726 (mm)
REVERT: L   11 LEU cc_start: 0.8472 (tp) cc_final: 0.8262 (tp)
REVERT: L   39 LEU cc_start: 0.8131 (tp) cc_final: 0.7835 (tp)
REVERT: L  146 TYR cc_start: 0.7702 (t80) cc_final: 0.7359 (t80)
REVERT: L  149 GLU cc_start: 0.8002 (tt0) cc_final: 0.7783 (tt0)
REVERT: L  167 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: L  172 GLN cc_start: 0.8556 (mt0) cc_final: 0.8276 (mm110)
REVERT: L  211 VAL cc_start: 0.8382 (p) cc_final: 0.7988 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0721
  time to fit residues: 13.0905
Evaluate side-chains
  136 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 146 ASN
H 101 HIS
L  34 ASN
L  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.116493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098431 restraints weight = 7906.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.102028 restraints weight = 3674.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104316 restraints weight = 2099.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.105775 restraints weight = 1370.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.106709 restraints weight = 1001.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4480  Z= 0.159
  Angle     :  0.666   6.768   6087  Z= 0.350
  Chirality :  0.041   0.140    694
  Planarity :  0.005   0.052    763
  Dihedral  :  4.681  17.031    612
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.34 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  1.07 (0.37), residues: 561
  helix:  3.15 (0.49), residues: 107
  sheet:  0.82 (0.34), residues: 235
  loop : -0.66 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.024   0.002   TYR H  54 
 PHE   0.027   0.002   PHE H  29 
 TRP   0.037   0.002   TRP H  36 
 HIS   0.007   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.16 ( 4475)
  covalent geometry    : angle       0.66279 /  0.35 ( 6077)
  SS BOND              : bond        0.00683 /  0.35 (    5)
  SS BOND              : angle       1.78619 /  1.00 (   10)
  hydrogen bonds       : bond        0.04450 /  2.92 (  205)
  hydrogen bonds       : angle       5.19420 /  3.62 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8129 (tp) cc_final: 0.7881 (tp)
REVERT: A  175 LEU cc_start: 0.8485 (mt) cc_final: 0.8194 (mt)
REVERT: A  192 MET cc_start: 0.7689 (mmp) cc_final: 0.7165 (mmp)
REVERT: H  127 PHE cc_start: 0.8143 (m-10) cc_final: 0.7931 (m-10)
REVERT: L   39 LEU cc_start: 0.8098 (tp) cc_final: 0.7791 (tp)
REVERT: L   95 GLN cc_start: 0.7988 (tt0) cc_final: 0.7778 (tt0)
REVERT: L  130 GLN cc_start: 0.7984 (tt0) cc_final: 0.7631 (tt0)
REVERT: L  146 TYR cc_start: 0.7780 (t80) cc_final: 0.7438 (t80)
REVERT: L  149 GLU cc_start: 0.7798 (tt0) cc_final: 0.7571 (tt0)
REVERT: L  211 VAL cc_start: 0.8411 (p) cc_final: 0.7987 (m)
  outliers start: 7
  outliers final: 7
  residues processed: 145
  average time/residue: 0.0700
  time to fit residues: 12.7213
Evaluate side-chains
  143 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  158 SER
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  180 SER
Chi-restraints excluded: chain L residue  197 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0030
   chunk 55 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0980
   chunk 51 optimal weight:    0.5980
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.2990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.119094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.100814 restraints weight = 7846.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104380 restraints weight = 3678.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.106630 restraints weight = 2110.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108099 restraints weight = 1383.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.108913 restraints weight = 1009.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   4480  Z= 0.114
  Angle     :  0.625   7.287   6087  Z= 0.320
  Chirality :  0.040   0.135    694
  Planarity :  0.004   0.051    763
  Dihedral  :  4.453  15.477    612
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.49 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  1.14 (0.36), residues: 561
  helix:  2.91 (0.48), residues: 109
  sheet:  1.14 (0.35), residues: 223
  loop : -0.73 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  80 
 TYR   0.015   0.001   TYR H  54 
 PHE   0.018   0.001   PHE L 124 
 TRP   0.027   0.001   TRP H  36 
 HIS   0.005   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 4475)
  covalent geometry    : angle       0.62325 /  0.32 ( 6077)
  SS BOND              : bond        0.00442 /  0.24 (    5)
  SS BOND              : angle       1.24773 /  0.70 (   10)
  hydrogen bonds       : bond        0.03818 /  2.47 (  205)
  hydrogen bonds       : angle       4.83100 /  3.42 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8158 (tp) cc_final: 0.7915 (tp)
REVERT: A  175 LEU cc_start: 0.8456 (mt) cc_final: 0.8141 (mt)
REVERT: A  192 MET cc_start: 0.7667 (mmp) cc_final: 0.7141 (mmp)
REVERT: A  194 ILE cc_start: 0.8810 (mm) cc_final: 0.8569 (mm)
REVERT: L   39 LEU cc_start: 0.8119 (tp) cc_final: 0.7831 (tp)
REVERT: L   42 TYR cc_start: 0.8179 (m-80) cc_final: 0.7422 (m-80)
REVERT: L   55 TYR cc_start: 0.8481 (p90) cc_final: 0.8186 (p90)
REVERT: L  130 GLN cc_start: 0.7949 (tt0) cc_final: 0.7700 (tt0)
REVERT: L  146 TYR cc_start: 0.7796 (t80) cc_final: 0.7457 (t80)
REVERT: L  161 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7099 (mp10)
REVERT: L  184 THR cc_start: 0.7891 (m) cc_final: 0.7452 (t)
REVERT: L  211 VAL cc_start: 0.8351 (p) cc_final: 0.7928 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 144
  average time/residue: 0.0706
  time to fit residues: 12.7644
Evaluate side-chains
  154 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  161 GLN
Chi-restraints excluded: chain L residue  197 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.114153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095968 restraints weight = 7861.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.099515 restraints weight = 3705.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.101728 restraints weight = 2142.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.103174 restraints weight = 1413.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.104117 restraints weight = 1036.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4480  Z= 0.240
  Angle     :  0.696   8.052   6087  Z= 0.364
  Chirality :  0.042   0.133    694
  Planarity :  0.005   0.060    763
  Dihedral  :  4.830  18.004    612
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.11 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.84 (0.36), residues: 561
  helix:  2.90 (0.49), residues: 107
  sheet:  0.80 (0.34), residues: 233
  loop : -0.90 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 148 
 TYR   0.027   0.003   TYR A  46 
 PHE   0.012   0.002   PHE H  29 
 TRP   0.032   0.002   TRP H  36 
 HIS   0.005   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00519 /  0.24 ( 4475)
  covalent geometry    : angle       0.69232 /  0.36 ( 6077)
  SS BOND              : bond        0.00935 /  0.49 (    5)
  SS BOND              : angle       1.92268 /  1.11 (   10)
  hydrogen bonds       : bond        0.04849 /  3.15 (  205)
  hydrogen bonds       : angle       5.17772 /  3.68 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8211 (tp) cc_final: 0.7948 (tp)
REVERT: A  175 LEU cc_start: 0.8491 (mt) cc_final: 0.8208 (mt)
REVERT: A  194 ILE cc_start: 0.8892 (mm) cc_final: 0.8661 (mm)
REVERT: L   39 LEU cc_start: 0.8231 (tp) cc_final: 0.7988 (tp)
REVERT: L   85 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7933 (mm-40)
REVERT: L  146 TYR cc_start: 0.7905 (t80) cc_final: 0.7645 (t80)
REVERT: L  166 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8183 (mm-40)
REVERT: L  184 THR cc_start: 0.8095 (m) cc_final: 0.7643 (t)
REVERT: L  211 VAL cc_start: 0.8395 (p) cc_final: 0.7979 (m)
  outliers start: 13
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0750
  time to fit residues: 13.5757
Evaluate side-chains
  141 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  197 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 45 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0470
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.116654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.097932 restraints weight = 7840.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101494 restraints weight = 3703.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.103734 restraints weight = 2152.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.105106 restraints weight = 1435.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106057 restraints weight = 1076.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4480  Z= 0.138
  Angle     :  0.654   9.298   6087  Z= 0.330
  Chirality :  0.041   0.143    694
  Planarity :  0.005   0.055    763
  Dihedral  :  4.613  16.638    612
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.56 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.95 (0.36), residues: 561
  helix:  2.73 (0.48), residues: 109
  sheet:  1.06 (0.35), residues: 223
  loop : -0.88 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 148 
 TYR   0.016   0.002   TYR A  46 
 PHE   0.013   0.001   PHE L 104 
 TRP   0.030   0.002   TRP H  36 
 HIS   0.003   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 4475)
  covalent geometry    : angle       0.65194 /  0.33 ( 6077)
  SS BOND              : bond        0.00581 /  0.31 (    5)
  SS BOND              : angle       1.34361 /  0.76 (   10)
  hydrogen bonds       : bond        0.04001 /  2.61 (  205)
  hydrogen bonds       : angle       4.83948 /  3.44 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8190 (tp) cc_final: 0.7951 (tp)
REVERT: A  175 LEU cc_start: 0.8478 (mt) cc_final: 0.8174 (mt)
REVERT: A  194 ILE cc_start: 0.8858 (mm) cc_final: 0.8606 (mm)
REVERT: H  110 GLN cc_start: 0.7679 (pm20) cc_final: 0.7439 (pm20)
REVERT: L  146 TYR cc_start: 0.7877 (t80) cc_final: 0.7628 (t80)
REVERT: L  184 THR cc_start: 0.8011 (m) cc_final: 0.7564 (t)
REVERT: L  211 VAL cc_start: 0.8377 (p) cc_final: 0.7964 (m)
  outliers start: 19
  outliers final: 16
  residues processed: 138
  average time/residue: 0.0751
  time to fit residues: 12.9461
Evaluate side-chains
  151 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  202 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 ASN
L  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.115988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.097405 restraints weight = 7917.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.101007 restraints weight = 3724.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.103293 restraints weight = 2145.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.104731 restraints weight = 1418.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.105661 restraints weight = 1047.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4480  Z= 0.163
  Angle     :  0.678   9.348   6087  Z= 0.342
  Chirality :  0.041   0.135    694
  Planarity :  0.005   0.055    763
  Dihedral  :  4.660  17.240    612
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 20.62 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.87 (0.36), residues: 561
  helix:  2.76 (0.48), residues: 109
  sheet:  1.05 (0.35), residues: 218
  loop : -0.99 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 148 
 TYR   0.020   0.002   TYR A  46 
 PHE   0.017   0.001   PHE L 124 
 TRP   0.032   0.002   TRP H  36 
 HIS   0.005   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 4475)
  covalent geometry    : angle       0.67554 /  0.34 ( 6077)
  SS BOND              : bond        0.00722 /  0.39 (    5)
  SS BOND              : angle       1.67176 /  0.96 (   10)
  hydrogen bonds       : bond        0.04209 /  2.72 (  205)
  hydrogen bonds       : angle       4.88895 /  3.48 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8208 (tp) cc_final: 0.7968 (tp)
REVERT: A  175 LEU cc_start: 0.8486 (mt) cc_final: 0.8199 (mt)
REVERT: A  194 ILE cc_start: 0.8779 (mm) cc_final: 0.8537 (mm)
REVERT: H   59 SER cc_start: 0.7803 (m) cc_final: 0.7132 (p)
REVERT: H  110 GLN cc_start: 0.7657 (pm20) cc_final: 0.7429 (pm20)
REVERT: L  130 GLN cc_start: 0.8273 (tt0) cc_final: 0.7886 (tt0)
REVERT: L  146 TYR cc_start: 0.7862 (t80) cc_final: 0.7594 (t80)
REVERT: L  167 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7246 (mt-10)
REVERT: L  184 THR cc_start: 0.8048 (m) cc_final: 0.7612 (t)
REVERT: L  211 VAL cc_start: 0.8403 (p) cc_final: 0.7993 (m)
  outliers start: 18
  outliers final: 16
  residues processed: 145
  average time/residue: 0.0699
  time to fit residues: 12.6528
Evaluate side-chains
  151 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  202 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    0.0170
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0770
   chunk 25 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.3776

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.114645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.095804 restraints weight = 7870.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.099433 restraints weight = 3725.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101670 restraints weight = 2154.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103190 restraints weight = 1435.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.104178 restraints weight = 1053.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4480  Z= 0.120
  Angle     :  0.667   9.239   6087  Z= 0.331
  Chirality :  0.041   0.133    694
  Planarity :  0.004   0.051    763
  Dihedral  :  4.531  16.025    612
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.06 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.97 (0.36), residues: 561
  helix:  2.75 (0.48), residues: 109
  sheet:  1.12 (0.35), residues: 219
  loop : -0.89 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 148 
 TYR   0.012   0.001   TYR A  46 
 PHE   0.024   0.001   PHE L 124 
 TRP   0.030   0.001   TRP H  36 
 HIS   0.005   0.001   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 4475)
  covalent geometry    : angle       0.66516 /  0.33 ( 6077)
  SS BOND              : bond        0.00550 /  0.29 (    5)
  SS BOND              : angle       1.30938 /  0.74 (   10)
  hydrogen bonds       : bond        0.03703 /  2.39 (  205)
  hydrogen bonds       : angle       4.67133 /  3.33 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8240 (tp) cc_final: 0.8005 (tp)
REVERT: A  175 LEU cc_start: 0.8493 (mt) cc_final: 0.8164 (mt)
REVERT: A  194 ILE cc_start: 0.8685 (mm) cc_final: 0.8440 (mm)
REVERT: L   95 GLN cc_start: 0.7941 (tt0) cc_final: 0.7732 (tt0)
REVERT: L  130 GLN cc_start: 0.8258 (tt0) cc_final: 0.7833 (tt0)
REVERT: L  146 TYR cc_start: 0.7850 (t80) cc_final: 0.7557 (t80)
REVERT: L  184 THR cc_start: 0.7989 (m) cc_final: 0.7568 (t)
REVERT: L  211 VAL cc_start: 0.8329 (p) cc_final: 0.7907 (m)
  outliers start: 16
  outliers final: 16
  residues processed: 144
  average time/residue: 0.0658
  time to fit residues: 11.8912
Evaluate side-chains
  148 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  202 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 101 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.117177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.098785 restraints weight = 7820.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.102352 restraints weight = 3706.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104565 restraints weight = 2143.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.105970 restraints weight = 1424.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.106800 restraints weight = 1052.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4480  Z= 0.162
  Angle     :  0.692  11.522   6087  Z= 0.346
  Chirality :  0.041   0.135    694
  Planarity :  0.005   0.066    763
  Dihedral  :  4.610  18.828    612
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 21.44 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.90 (0.37), residues: 561
  helix:  2.76 (0.48), residues: 109
  sheet:  0.92 (0.35), residues: 228
  loop : -0.87 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 148 
 TYR   0.020   0.002   TYR A  46 
 PHE   0.017   0.001   PHE L 124 
 TRP   0.036   0.002   TRP H  36 
 HIS   0.017   0.003   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 4475)
  covalent geometry    : angle       0.68896 /  0.34 ( 6077)
  SS BOND              : bond        0.00735 /  0.39 (    5)
  SS BOND              : angle       1.64749 /  0.94 (   10)
  hydrogen bonds       : bond        0.04091 /  2.63 (  205)
  hydrogen bonds       : angle       4.80050 /  3.42 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8232 (tp) cc_final: 0.7991 (tp)
REVERT: A  175 LEU cc_start: 0.8475 (mt) cc_final: 0.8197 (mt)
REVERT: A  194 ILE cc_start: 0.8746 (mm) cc_final: 0.8511 (mm)
REVERT: L  146 TYR cc_start: 0.7885 (t80) cc_final: 0.7640 (t80)
REVERT: L  184 THR cc_start: 0.8030 (m) cc_final: 0.7604 (t)
REVERT: L  211 VAL cc_start: 0.8369 (p) cc_final: 0.7962 (m)
  outliers start: 21
  outliers final: 18
  residues processed: 143
  average time/residue: 0.0682
  time to fit residues: 12.1221
Evaluate side-chains
  147 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  101 HIS
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  202 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0050
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.8198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.116915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098356 restraints weight = 7890.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101898 restraints weight = 3763.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.104165 restraints weight = 2194.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105552 restraints weight = 1454.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.106482 restraints weight = 1080.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4480  Z= 0.172
  Angle     :  0.708  11.229   6087  Z= 0.354
  Chirality :  0.041   0.135    694
  Planarity :  0.005   0.064    763
  Dihedral  :  4.705  19.702    612
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.06 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.82 (0.37), residues: 561
  helix:  2.72 (0.48), residues: 109
  sheet:  0.85 (0.35), residues: 228
  loop : -0.89 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 148 
 TYR   0.021   0.002   TYR A  46 
 PHE   0.019   0.001   PHE L 124 
 TRP   0.040   0.002   TRP H  36 
 HIS   0.022   0.003   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.17 ( 4475)
  covalent geometry    : angle       0.70547 /  0.35 ( 6077)
  SS BOND              : bond        0.00772 /  0.41 (    5)
  SS BOND              : angle       1.72805 /  0.99 (   10)
  hydrogen bonds       : bond        0.04216 /  2.72 (  205)
  hydrogen bonds       : angle       4.85706 /  3.46 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8234 (tp) cc_final: 0.7994 (tp)
REVERT: A  175 LEU cc_start: 0.8495 (mt) cc_final: 0.8216 (mt)
REVERT: A  194 ILE cc_start: 0.8753 (mm) cc_final: 0.8519 (mm)
REVERT: H   60 TYR cc_start: 0.8282 (m-80) cc_final: 0.7904 (m-80)
REVERT: L  184 THR cc_start: 0.8052 (m) cc_final: 0.7619 (t)
REVERT: L  211 VAL cc_start: 0.8366 (p) cc_final: 0.7960 (m)
  outliers start: 19
  outliers final: 18
  residues processed: 139
  average time/residue: 0.0721
  time to fit residues: 12.5654
Evaluate side-chains
  147 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  158 SER
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 46 optimal weight:    0.0040
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 110 GLN
L  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.099128 restraints weight = 7859.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.102714 restraints weight = 3742.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.105007 restraints weight = 2174.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106385 restraints weight = 1436.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.107390 restraints weight = 1067.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4480  Z= 0.135
  Angle     :  0.696  10.445   6087  Z= 0.344
  Chirality :  0.041   0.135    694
  Planarity :  0.005   0.061    763
  Dihedral  :  4.622  20.266    612
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 21.86 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.89 (0.36), residues: 561
  helix:  2.77 (0.49), residues: 109
  sheet:  1.01 (0.35), residues: 218
  loop : -0.92 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 148 
 TYR   0.015   0.002   TYR A  46 
 PHE   0.019   0.001   PHE L 124 
 TRP   0.040   0.002   TRP H  36 
 HIS   0.017   0.003   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 4475)
  covalent geometry    : angle       0.69385 /  0.34 ( 6077)
  SS BOND              : bond        0.00660 /  0.35 (    5)
  SS BOND              : angle       1.52913 /  0.87 (   10)
  hydrogen bonds       : bond        0.03862 /  2.49 (  205)
  hydrogen bonds       : angle       4.72750 /  3.36 (  594)

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

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

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1122 Ramachandran restraints generated.
    561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8226 (tp) cc_final: 0.7983 (tp)
REVERT: A  175 LEU cc_start: 0.8491 (mt) cc_final: 0.8207 (mt)
REVERT: A  194 ILE cc_start: 0.8670 (mm) cc_final: 0.8434 (mm)
REVERT: H    6 GLN cc_start: 0.7266 (mt0) cc_final: 0.6950 (mt0)
REVERT: H   60 TYR cc_start: 0.8207 (m-80) cc_final: 0.7744 (m-80)
REVERT: L  184 THR cc_start: 0.8008 (m) cc_final: 0.7579 (t)
REVERT: L  211 VAL cc_start: 0.8371 (p) cc_final: 0.7953 (m)
  outliers start: 19
  outliers final: 17
  residues processed: 142
  average time/residue: 0.0716
  time to fit residues: 12.7452
Evaluate side-chains
  152 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  216 VAL
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   56 TRP
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  132 LYS
Chi-restraints excluded: chain L residue  140 CYS
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 53 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0670
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.118141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.099399 restraints weight = 7830.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.102969 restraints weight = 3751.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.105278 restraints weight = 2195.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.106657 restraints weight = 1460.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.107660 restraints weight = 1095.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4480  Z= 0.145
  Angle     :  0.701   9.701   6087  Z= 0.350
  Chirality :  0.041   0.138    694
  Planarity :  0.005   0.066    763
  Dihedral  :  4.635  20.649    612
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.65 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 20.83 %
    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:  0.87 (0.37), residues: 561
  helix:  2.73 (0.49), residues: 109
  sheet:  0.86 (0.35), residues: 228
  loop : -0.83 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 148 
 TYR   0.016   0.002   TYR A  46 
 PHE   0.038   0.002   PHE L 124 
 TRP   0.041   0.002   TRP H  36 
 HIS   0.013   0.002   HIS H 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 4475)
  covalent geometry    : angle       0.69897 /  0.35 ( 6077)
  SS BOND              : bond        0.00647 /  0.35 (    5)
  SS BOND              : angle       1.61274 /  0.92 (   10)
  hydrogen bonds       : bond        0.03870 /  2.48 (  205)
  hydrogen bonds       : angle       4.76079 /  3.38 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1005.71 seconds
wall clock time: 17 minutes 58.38 seconds (1078.38 seconds total)