Starting phenix.real_space_refine
on Wed Sep 17 14:07:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cvt_45966/09_2025/9cvt_45966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cvt_45966/09_2025/9cvt_45966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cvt_45966/09_2025/9cvt_45966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cvt_45966/09_2025/9cvt_45966.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cvt_45966/09_2025/9cvt_45966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cvt_45966/09_2025/9cvt_45966.map"
  }
  resolution = 4.41
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     182      5.49       5
     S      32      5.16       5
     C    5046      2.51       5
     N    1608      2.21       5
     O    2029      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8897
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1213
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 2, 'TRANS': 148}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1308
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 3, 'TRANS': 160}
    Chain: "C"
      Number of atoms: 1337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1337
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1308
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 5, 'TRANS': 162}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1851
          Classifications: {'DNA': 91}
          Link IDs: {'rna3p': 90}
    Chain: "J"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1880
          Classifications: {'DNA': 91}
          Link IDs: {'rna3p': 90}
  Time building chain proxies: 2.25, per 1000 atoms: 0.25
  Number of scatterers: 8897
  At special positions: 0
  Unit cell: (83.905, 114.46, 115.915, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P     182     15.00
     O    2029      8.00
     N    1608      7.00
     C    5046      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 103 " - pdb=" SG  CYS B 103 " distance=2.04

  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: 0.84
  Conformation dependent library (CDL) restraints added in 216.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1254

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      72.7% alpha, 0.3% beta
      89 base pairs and 143 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 15
    Processing helix  chain 'A' and resid 23 through 48
    Processing helix  chain 'A' and resid 54 through 63
      removed outlier: 3.966A  pdb=" N   PHE A  58 " --> pdb=" O   ARG A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 83
      removed outlier: 3.758A  pdb=" N   LYS A  71 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 3.847A  pdb=" N   ASN A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 136
    Processing helix  chain 'A' and resid 142 through 153
    Processing helix  chain 'A' and resid 153 through 161
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 22 through 48
      removed outlier: 3.575A  pdb=" N   LEU B  26 " --> pdb=" O   THR B  22 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU B  27 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 64
      removed outlier: 3.546A  pdb=" N   PHE B  58 " --> pdb=" O   ARG B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
      removed outlier: 4.329A  pdb=" N   LYS B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 100
      removed outlier: 3.931A  pdb=" N   THR B  94 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 136
      removed outlier: 3.694A  pdb=" N   VAL B 111 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 3.574A  pdb=" N   HIS B 157 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 20
    Processing helix  chain 'C' and resid 28 through 39
    Processing helix  chain 'C' and resid 48 through 74
      removed outlier: 3.667A  pdb=" N   ILE C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 132 through 136
      removed outlier: 4.071A  pdb=" N   MET C 136 " --> pdb=" O   ARG C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 158
    Processing helix  chain 'C' and resid 166 through 195
    Processing helix  chain 'C' and resid 201 through 213
    Processing helix  chain 'D' and resid 28 through 40
      removed outlier: 3.672A  pdb=" N   THR D  32 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 75
      removed outlier: 3.541A  pdb=" N   ILE D  52 " --> pdb=" O   THR D  48 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA D  74 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 91
      removed outlier: 3.668A  pdb=" N   MET D  91 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 137
      removed outlier: 4.368A  pdb=" N   LYS D 137 " --> pdb=" O   ARG D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 160
      removed outlier: 4.294A  pdb=" N   PHE D 148 " --> pdb=" O   PRO D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 195
    Processing helix  chain 'D' and resid 201 through 212
      removed outlier: 3.725A  pdb=" N   GLU D 212 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 78 through 79
      removed outlier: 3.639A  pdb=" N   ILE D  79 " --> pdb=" O   HIS D 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    335 hydrogen bonds defined for protein.
    990 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      228 hydrogen bonds
      456 hydrogen bond angles
      0 basepair planarities
      89 basepair parallelities
      143 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1617
        1.33 -     1.45: 2952
        1.45 -     1.57: 4430
        1.57 -     1.70: 362
        1.70 -     1.82: 56
  Bond restraints: 9417
  Sorted by residual:
  bond pdb=" N   CYS A 103 "
       pdb=" CA  CYS A 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 6.04e+00
  bond pdb=" N   THR C  32 "
       pdb=" CA  THR C  32 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.19e-02 7.06e+03 4.43e+00
  bond pdb=" P    DT I -39 "
       pdb=" OP2  DT I -39 "
    ideal  model  delta    sigma   weight residual
    1.480  1.520 -0.040 2.00e-02 2.50e+03 3.96e+00
  bond pdb=" N   CYS B 103 "
       pdb=" CA  CYS B 103 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.030 1.50e-02 4.44e+03 3.92e+00
  bond pdb=" P    DT I -39 "
       pdb=" OP1  DT I -39 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.42e+00
  ... (remaining 9412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 13085
        2.04 -     4.09: 335
        4.09 -     6.13: 34
        6.13 -     8.18: 7
        8.18 -    10.22: 3
  Bond angle restraints: 13464
  Sorted by residual:
  angle pdb=" C   LEU A  97 "
        pdb=" N   MET A  98 "
        pdb=" CA  MET A  98 "
      ideal   model   delta    sigma   weight residual
     120.68  112.41    8.27 1.70e+00 3.46e-01 2.36e+01
  angle pdb=" N   GLN C 174 "
        pdb=" CA  GLN C 174 "
        pdb=" CB  GLN C 174 "
      ideal   model   delta    sigma   weight residual
     110.28  115.97   -5.69 1.55e+00 4.16e-01 1.35e+01
  angle pdb=" N   CYS B 103 "
        pdb=" CA  CYS B 103 "
        pdb=" C   CYS B 103 "
      ideal   model   delta    sigma   weight residual
     110.06  105.14    4.92 1.43e+00 4.89e-01 1.18e+01
  angle pdb=" CA  CYS B 103 "
        pdb=" C   CYS B 103 "
        pdb=" O   CYS B 103 "
      ideal   model   delta    sigma   weight residual
     121.78  118.01    3.77 1.12e+00 7.97e-01 1.13e+01
  angle pdb=" C3'  DT I -39 "
        pdb=" O3'  DT I -39 "
        pdb=" P    DC I -38 "
      ideal   model   delta    sigma   weight residual
     120.20  125.12   -4.92 1.50e+00 4.44e-01 1.07e+01
  ... (remaining 13459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.20: 4018
       29.20 -    58.41: 1100
       58.41 -    87.61: 116
       87.61 -   116.81: 7
      116.81 -   146.01: 5
  Dihedral angle restraints: 5246
    sinusoidal: 3337
      harmonic: 1909
  Sorted by residual:
  dihedral pdb=" CB  CYS A 103 "
           pdb=" SG  CYS A 103 "
           pdb=" SG  CYS B 103 "
           pdb=" CB  CYS B 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.15  -83.15     1      1.00e+01 1.00e-02 8.45e+01
  dihedral pdb=" C4'  DC I   4 "
           pdb=" C3'  DC I   4 "
           pdb=" O3'  DC I   4 "
           pdb=" P    DC I   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.99  146.01     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" C4'  DC J  37 "
           pdb=" C3'  DC J  37 "
           pdb=" O3'  DC J  37 "
           pdb=" P    DG J  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.06  144.94     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 5243 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1539
       0.110 -    0.220: 21
       0.220 -    0.330: 0
       0.330 -    0.440: 0
       0.440 -    0.550: 1
  Chirality restraints: 1561
  Sorted by residual:
  chirality pdb=" P    DT I -39 "
            pdb=" OP1  DT I -39 "
            pdb=" OP2  DT I -39 "
            pdb=" O5'  DT I -39 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.90   -0.55 2.00e-01 2.50e+01 7.57e+00
  chirality pdb=" CA  CYS B 103 "
            pdb=" N   CYS B 103 "
            pdb=" C   CYS B 103 "
            pdb=" CB  CYS B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.97e-01
  chirality pdb=" CA  GLN C 174 "
            pdb=" N   GLN C 174 "
            pdb=" C   GLN C 174 "
            pdb=" CB  GLN C 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.29e-01
  ... (remaining 1558 not shown)

  Planarity restraints: 1049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 143 "   -0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO D 144 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 144 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 144 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  15 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO B  16 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 193 "   -0.012 2.00e-02 2.50e+03   1.05e-02 2.21e+00
        pdb=" CG  TYR D 193 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 193 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 193 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 193 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 193 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 193 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D 193 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1046 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1104
        2.74 -     3.28: 9379
        3.28 -     3.82: 18007
        3.82 -     4.36: 19333
        4.36 -     4.90: 27144
  Nonbonded interactions: 74967
  Sorted by model distance:
  nonbonded pdb=" N   GLN D 135 "
            pdb=" OE1 GLN D 135 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   TYR B 120 "
            pdb=" NE2 GLN B 124 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ILE D 191 "
            pdb=" OG  SER D 194 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" N   LEU B 156 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OE2 GLU B  24 "
            pdb=" OG  SER B  25 "
     model   vdw
     2.242 3.040
  ... (remaining 74962 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 9 through 15 or resid 22 through 165))
}
ncs_group {
  reference = (chain 'C' and resid 15 through 212)
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.090
  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:          0.380
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.820
  Find NCS groups from input model:        0.100
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
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      :  0.005   0.042   9418  Z= 0.213
  Angle     :  0.734  10.222  13466  Z= 0.422
  Chirality :  0.041   0.550   1561
  Planarity :  0.004   0.043   1049
  Dihedral  : 28.597 146.014   3989
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.77 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.33), residues: 641
  helix:  1.41 (0.25), residues: 437
  sheet:  None (None), residues: 0
  loop : -1.63 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 149 
 TYR   0.024   0.002   TYR D 193 
 PHE   0.023   0.002   PHE B 160 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9417)
  covalent geometry    : angle       0.73447 (13464)
  SS BOND              : bond        0.00586 (    1)
  SS BOND              : angle       0.30687 (    2)
  hydrogen bonds       : bond        0.10808 (  563)
  hydrogen bonds       : angle       4.27635 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9176 (tt) cc_final: 0.8922 (tt)
REVERT: B   31 ASN cc_start: 0.9370 (m110) cc_final: 0.9142 (m110)
REVERT: B  120 TYR cc_start: 0.8982 (t80) cc_final: 0.8750 (t80)
REVERT: B  126 MET cc_start: 0.7816 (ppp) cc_final: 0.7432 (ppp)
REVERT: B  159 MET cc_start: 0.8286 (ptp) cc_final: 0.7896 (ptm)
REVERT: C   79 ILE cc_start: 0.8728 (pt) cc_final: 0.8358 (pt)
REVERT: D   65 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: D   69 LEU cc_start: 0.9100 (mt) cc_final: 0.8793 (mt)
REVERT: D   89 GLU cc_start: 0.9229 (pp20) cc_final: 0.8972 (pp20)
REVERT: D  189 LEU cc_start: 0.9628 (tt) cc_final: 0.8745 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0874
  time to fit residues: 19.9928
Evaluate side-chains
  122 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
B 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.058856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.043076 restraints weight = 55021.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.044483 restraints weight = 31154.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.045445 restraints weight = 21384.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.046097 restraints weight = 16631.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.046337 restraints weight = 14100.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9418  Z= 0.162
  Angle     :  0.642   7.024  13466  Z= 0.376
  Chirality :  0.037   0.176   1561
  Planarity :  0.004   0.046   1049
  Dihedral  : 32.564 144.729   2656
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.84 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  4.53 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.34), residues: 641
  helix:  1.53 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.60 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 199 
 TYR   0.012   0.001   TYR D 193 
 PHE   0.012   0.001   PHE D  96 
 TRP   0.005   0.001   TRP B  60 
 HIS   0.004   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9417)
  covalent geometry    : angle       0.64194 (13464)
  SS BOND              : bond        0.00491 (    1)
  SS BOND              : angle       0.91063 (    2)
  hydrogen bonds       : bond        0.04149 (  563)
  hydrogen bonds       : angle       3.32666 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ILE cc_start: 0.7318 (mt) cc_final: 0.7098 (mt)
REVERT: A   46 ILE cc_start: 0.9131 (tt) cc_final: 0.8847 (tt)
REVERT: A   48 ILE cc_start: 0.9318 (tp) cc_final: 0.9107 (tp)
REVERT: A  120 TYR cc_start: 0.9061 (t80) cc_final: 0.8847 (t80)
REVERT: B   28 THR cc_start: 0.9729 (p) cc_final: 0.9515 (p)
REVERT: B   31 ASN cc_start: 0.9397 (m110) cc_final: 0.9125 (m110)
REVERT: B  120 TYR cc_start: 0.8931 (t80) cc_final: 0.8625 (t80)
REVERT: B  126 MET cc_start: 0.7710 (ppp) cc_final: 0.7271 (ppp)
REVERT: C   79 ILE cc_start: 0.8735 (pt) cc_final: 0.8449 (pt)
REVERT: C  171 ASP cc_start: 0.8045 (t70) cc_final: 0.7785 (t70)
REVERT: C  174 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8998 (pm20)
REVERT: C  178 GLU cc_start: 0.8066 (pp20) cc_final: 0.7716 (pp20)
REVERT: D   65 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: D   69 LEU cc_start: 0.9101 (mt) cc_final: 0.8700 (mt)
REVERT: D   96 PHE cc_start: 0.8893 (m-80) cc_final: 0.8567 (m-80)
REVERT: D  210 MET cc_start: 0.8807 (tpt) cc_final: 0.8438 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0929
  time to fit residues: 21.6854
Evaluate side-chains
  123 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0040
   chunk 42 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
** A  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  72 HIS
A 101 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.058069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.042244 restraints weight = 54941.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.043589 restraints weight = 31335.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.044538 restraints weight = 21649.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.045190 restraints weight = 16936.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.045630 restraints weight = 14366.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9418  Z= 0.172
  Angle     :  0.633   7.586  13466  Z= 0.371
  Chirality :  0.036   0.139   1561
  Planarity :  0.004   0.047   1049
  Dihedral  : 32.513 145.699   2656
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.52 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.34), residues: 641
  helix:  1.58 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.55 (0.44), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  13 
 TYR   0.016   0.001   TYR D 193 
 PHE   0.012   0.001   PHE D 148 
 TRP   0.004   0.001   TRP A  60 
 HIS   0.004   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9417)
  covalent geometry    : angle       0.63346 (13464)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       0.70247 (    2)
  hydrogen bonds       : bond        0.04076 (  563)
  hydrogen bonds       : angle       3.27951 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9143 (tt) cc_final: 0.8825 (tt)
REVERT: A   48 ILE cc_start: 0.9319 (tp) cc_final: 0.9105 (tp)
REVERT: A   75 ASP cc_start: 0.9386 (t0) cc_final: 0.9147 (m-30)
REVERT: A  120 TYR cc_start: 0.9098 (t80) cc_final: 0.8691 (t80)
REVERT: B   28 THR cc_start: 0.9729 (p) cc_final: 0.9507 (p)
REVERT: B   31 ASN cc_start: 0.9432 (m110) cc_final: 0.9165 (m110)
REVERT: B  120 TYR cc_start: 0.8957 (t80) cc_final: 0.8685 (t80)
REVERT: B  126 MET cc_start: 0.7751 (ppp) cc_final: 0.7316 (ppp)
REVERT: C   79 ILE cc_start: 0.8754 (pt) cc_final: 0.8485 (pt)
REVERT: D   65 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: D   69 LEU cc_start: 0.9120 (mt) cc_final: 0.8716 (mt)
REVERT: D  143 ILE cc_start: 0.8868 (tp) cc_final: 0.8462 (tp)
REVERT: D  186 GLU cc_start: 0.8922 (pt0) cc_final: 0.8714 (pt0)
REVERT: D  210 MET cc_start: 0.8848 (tpt) cc_final: 0.8454 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0931
  time to fit residues: 21.4656
Evaluate side-chains
  115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0570
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.7502

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A 101 ASN
B  45 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.058182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.042145 restraints weight = 55196.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.043533 restraints weight = 31328.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.044498 restraints weight = 21527.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.045164 restraints weight = 16762.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.045591 restraints weight = 14166.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9418  Z= 0.162
  Angle     :  0.627   7.052  13466  Z= 0.366
  Chirality :  0.036   0.192   1561
  Planarity :  0.004   0.046   1049
  Dihedral  : 32.405 145.084   2656
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.37 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  5.23 %
    Favored  : 94.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.34), residues: 641
  helix:  1.62 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.62 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  13 
 TYR   0.018   0.001   TYR D 193 
 PHE   0.012   0.001   PHE D 148 
 TRP   0.004   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9417)
  covalent geometry    : angle       0.62658 (13464)
  SS BOND              : bond        0.00613 (    1)
  SS BOND              : angle       1.10430 (    2)
  hydrogen bonds       : bond        0.03762 (  563)
  hydrogen bonds       : angle       3.16232 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.9300 (tp) cc_final: 0.9078 (tp)
REVERT: A  120 TYR cc_start: 0.9098 (t80) cc_final: 0.8834 (t80)
REVERT: B   28 THR cc_start: 0.9715 (p) cc_final: 0.9503 (p)
REVERT: B   31 ASN cc_start: 0.9451 (m110) cc_final: 0.9160 (m-40)
REVERT: B   43 GLN cc_start: 0.9658 (mm-40) cc_final: 0.9410 (mm-40)
REVERT: B  126 MET cc_start: 0.7756 (ppp) cc_final: 0.7313 (ppp)
REVERT: C   79 ILE cc_start: 0.8757 (pt) cc_final: 0.8543 (pt)
REVERT: D   65 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8351 (tm-30)
REVERT: D   69 LEU cc_start: 0.9109 (mt) cc_final: 0.8682 (mt)
REVERT: D  165 ILE cc_start: 0.9407 (pt) cc_final: 0.9206 (mm)
REVERT: D  189 LEU cc_start: 0.9632 (tt) cc_final: 0.9422 (tt)
REVERT: D  210 MET cc_start: 0.8822 (tpt) cc_final: 0.8476 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0950
  time to fit residues: 21.9234
Evaluate side-chains
  116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 13 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  43 GLN
A  72 HIS
A 124 GLN
B  45 ASN
B  74 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.055025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.039589 restraints weight = 57029.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.040851 restraints weight = 32628.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.041755 restraints weight = 22670.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.042349 restraints weight = 17758.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.042722 restraints weight = 15151.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9418  Z= 0.280
  Angle     :  0.720   8.644  13466  Z= 0.420
  Chirality :  0.039   0.155   1561
  Planarity :  0.005   0.050   1049
  Dihedral  : 32.433 147.339   2656
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.40 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.96 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.33), residues: 641
  helix:  1.30 (0.24), residues: 447
  sheet:  None (None), residues: 0
  loop : -1.70 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 149 
 TYR   0.018   0.002   TYR D 193 
 PHE   0.034   0.002   PHE D 148 
 TRP   0.007   0.001   TRP A  60 
 HIS   0.005   0.001   HIS C 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 9417)
  covalent geometry    : angle       0.71946 (13464)
  SS BOND              : bond        0.00369 (    1)
  SS BOND              : angle       1.19778 (    2)
  hydrogen bonds       : bond        0.05939 (  563)
  hydrogen bonds       : angle       3.77516 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ASN cc_start: 0.9470 (m110) cc_final: 0.9269 (m-40)
REVERT: A   46 ILE cc_start: 0.9291 (tp) cc_final: 0.9084 (tp)
REVERT: A   60 TRP cc_start: 0.8813 (m100) cc_final: 0.8581 (m100)
REVERT: A  120 TYR cc_start: 0.9158 (t80) cc_final: 0.8843 (t80)
REVERT: B   28 THR cc_start: 0.9721 (p) cc_final: 0.9516 (p)
REVERT: B   31 ASN cc_start: 0.9508 (m110) cc_final: 0.9219 (m-40)
REVERT: B  120 TYR cc_start: 0.9094 (t80) cc_final: 0.8764 (t80)
REVERT: B  126 MET cc_start: 0.7893 (ppp) cc_final: 0.7441 (ppp)
REVERT: C   71 MET cc_start: 0.9356 (tmm) cc_final: 0.9120 (tmm)
REVERT: C   79 ILE cc_start: 0.8831 (pt) cc_final: 0.8602 (pt)
REVERT: C  174 GLN cc_start: 0.9161 (pm20) cc_final: 0.8739 (pm20)
REVERT: D   33 GLN cc_start: 0.9159 (mp10) cc_final: 0.8903 (mp10)
REVERT: D   65 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8372 (tm-30)
REVERT: D   69 LEU cc_start: 0.9154 (mt) cc_final: 0.8775 (mt)
REVERT: D   76 ARG cc_start: 0.8766 (ttp-110) cc_final: 0.8448 (ttp-110)
REVERT: D  143 ILE cc_start: 0.9011 (tp) cc_final: 0.8625 (tp)
REVERT: D  210 MET cc_start: 0.8885 (tpt) cc_final: 0.8465 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 162
  average time/residue: 0.0917
  time to fit residues: 20.8251
Evaluate side-chains
  115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.056885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.041234 restraints weight = 55491.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.042594 restraints weight = 31152.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.043539 restraints weight = 21324.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.044178 restraints weight = 16533.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.044568 restraints weight = 13975.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9418  Z= 0.170
  Angle     :  0.660   7.266  13466  Z= 0.381
  Chirality :  0.037   0.142   1561
  Planarity :  0.004   0.044   1049
  Dihedral  : 32.381 144.998   2656
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.99 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.79 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.34), residues: 641
  helix:  1.52 (0.24), residues: 449
  sheet:  None (None), residues: 0
  loop : -1.80 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  13 
 TYR   0.019   0.002   TYR D 193 
 PHE   0.014   0.001   PHE D 148 
 TRP   0.003   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9417)
  covalent geometry    : angle       0.66006 (13464)
  SS BOND              : bond        0.00380 (    1)
  SS BOND              : angle       1.00764 (    2)
  hydrogen bonds       : bond        0.04136 (  563)
  hydrogen bonds       : angle       3.30650 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.9602 (mt) cc_final: 0.9360 (pp)
REVERT: A  120 TYR cc_start: 0.9168 (t80) cc_final: 0.8906 (t80)
REVERT: B   28 THR cc_start: 0.9722 (p) cc_final: 0.9476 (p)
REVERT: B   31 ASN cc_start: 0.9519 (m110) cc_final: 0.9245 (m110)
REVERT: B   99 ARG cc_start: 0.9166 (mmt180) cc_final: 0.8853 (mmt180)
REVERT: B  120 TYR cc_start: 0.9086 (t80) cc_final: 0.8709 (t80)
REVERT: B  126 MET cc_start: 0.7826 (ppp) cc_final: 0.7379 (ppp)
REVERT: C   71 MET cc_start: 0.9361 (tmm) cc_final: 0.9083 (tmm)
REVERT: C   79 ILE cc_start: 0.8809 (pt) cc_final: 0.8608 (pt)
REVERT: C  178 GLU cc_start: 0.8176 (pp20) cc_final: 0.7790 (pp20)
REVERT: D   65 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: D   69 LEU cc_start: 0.9106 (mt) cc_final: 0.8693 (mt)
REVERT: D  143 ILE cc_start: 0.8880 (tp) cc_final: 0.8578 (tp)
REVERT: D  147 ARG cc_start: 0.9410 (mmm-85) cc_final: 0.8748 (mmm-85)
REVERT: D  189 LEU cc_start: 0.9640 (tt) cc_final: 0.9426 (tt)
REVERT: D  210 MET cc_start: 0.8807 (tpt) cc_final: 0.8383 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0898
  time to fit residues: 20.7312
Evaluate side-chains
  123 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0870
   chunk 6 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    2.4164

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.056635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.041082 restraints weight = 55748.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.042458 restraints weight = 31220.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.043410 restraints weight = 21301.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.044059 restraints weight = 16475.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.044507 restraints weight = 13858.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9418  Z= 0.183
  Angle     :  0.662   6.950  13466  Z= 0.385
  Chirality :  0.038   0.155   1561
  Planarity :  0.004   0.044   1049
  Dihedral  : 32.318 145.659   2656
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.40 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.34), residues: 641
  helix:  1.49 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.69 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  13 
 TYR   0.019   0.002   TYR D 193 
 PHE   0.019   0.002   PHE A  76 
 TRP   0.005   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 9417)
  covalent geometry    : angle       0.66160 (13464)
  SS BOND              : bond        0.00357 (    1)
  SS BOND              : angle       0.94669 (    2)
  hydrogen bonds       : bond        0.04354 (  563)
  hydrogen bonds       : angle       3.35099 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9299 (tp) cc_final: 0.8949 (tt)
REVERT: A   76 PHE cc_start: 0.8813 (m-80) cc_final: 0.8568 (m-10)
REVERT: A  120 TYR cc_start: 0.9252 (t80) cc_final: 0.8783 (t80)
REVERT: B   28 THR cc_start: 0.9720 (p) cc_final: 0.9479 (p)
REVERT: B   31 ASN cc_start: 0.9530 (m110) cc_final: 0.9243 (m110)
REVERT: B   99 ARG cc_start: 0.9171 (mmt180) cc_final: 0.8839 (mmt180)
REVERT: B  120 TYR cc_start: 0.9087 (t80) cc_final: 0.8722 (t80)
REVERT: B  126 MET cc_start: 0.7857 (ppp) cc_final: 0.7405 (ppp)
REVERT: C   79 ILE cc_start: 0.8829 (pt) cc_final: 0.8583 (pt)
REVERT: C  178 GLU cc_start: 0.8188 (pp20) cc_final: 0.7826 (pp20)
REVERT: D   65 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: D   69 LEU cc_start: 0.9085 (mt) cc_final: 0.8667 (mt)
REVERT: D  143 ILE cc_start: 0.8878 (tp) cc_final: 0.8633 (tp)
REVERT: D  210 MET cc_start: 0.8814 (tpt) cc_final: 0.8410 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0933
  time to fit residues: 21.5030
Evaluate side-chains
  118 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 101 ASN
A 157 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.056827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.041101 restraints weight = 55898.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.042473 restraints weight = 31463.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.043417 restraints weight = 21592.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.044059 restraints weight = 16788.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.044456 restraints weight = 14200.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9418  Z= 0.170
  Angle     :  0.658   6.855  13466  Z= 0.380
  Chirality :  0.037   0.155   1561
  Planarity :  0.004   0.047   1049
  Dihedral  : 32.262 145.054   2656
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.62 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.34), residues: 641
  helix:  1.45 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.69 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  13 
 TYR   0.024   0.003   TYR D 193 
 PHE   0.018   0.001   PHE D 148 
 TRP   0.004   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9417)
  covalent geometry    : angle       0.65774 (13464)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       0.93490 (    2)
  hydrogen bonds       : bond        0.04065 (  563)
  hydrogen bonds       : angle       3.29881 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9298 (tp) cc_final: 0.8932 (tt)
REVERT: B   28 THR cc_start: 0.9721 (p) cc_final: 0.9483 (p)
REVERT: B   31 ASN cc_start: 0.9531 (m110) cc_final: 0.9240 (m110)
REVERT: B   89 PHE cc_start: 0.8831 (m-80) cc_final: 0.8303 (m-10)
REVERT: B  120 TYR cc_start: 0.9070 (t80) cc_final: 0.8740 (t80)
REVERT: B  126 MET cc_start: 0.7845 (ppp) cc_final: 0.7393 (ppp)
REVERT: C   79 ILE cc_start: 0.8828 (pt) cc_final: 0.8594 (pt)
REVERT: C  178 GLU cc_start: 0.8197 (pp20) cc_final: 0.7833 (pp20)
REVERT: D   65 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8302 (tm-30)
REVERT: D   69 LEU cc_start: 0.9073 (mt) cc_final: 0.8667 (mt)
REVERT: D  189 LEU cc_start: 0.9579 (tt) cc_final: 0.9344 (tt)
REVERT: D  210 MET cc_start: 0.8794 (tpt) cc_final: 0.8469 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0937
  time to fit residues: 20.9963
Evaluate side-chains
  119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 7 optimal weight:    0.1980
   chunk 54 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    2.6388

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
A 157 HIS
B 124 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.056350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.040916 restraints weight = 55540.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.042277 restraints weight = 31586.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.043208 restraints weight = 21730.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.043815 restraints weight = 16889.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.044267 restraints weight = 14297.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9418  Z= 0.188
  Angle     :  0.673   7.928  13466  Z= 0.391
  Chirality :  0.038   0.151   1561
  Planarity :  0.004   0.047   1049
  Dihedral  : 32.216 145.618   2656
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.93 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.34), residues: 641
  helix:  1.41 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.82 (0.44), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  13 
 TYR   0.025   0.002   TYR D 193 
 PHE   0.024   0.002   PHE D 148 
 TRP   0.006   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9417)
  covalent geometry    : angle       0.67300 (13464)
  SS BOND              : bond        0.00368 (    1)
  SS BOND              : angle       0.86600 (    2)
  hydrogen bonds       : bond        0.04383 (  563)
  hydrogen bonds       : angle       3.48389 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 TYR cc_start: 0.9136 (t80) cc_final: 0.8839 (t80)
REVERT: B   28 THR cc_start: 0.9729 (p) cc_final: 0.9506 (p)
REVERT: B   31 ASN cc_start: 0.9534 (m110) cc_final: 0.9253 (m110)
REVERT: B  120 TYR cc_start: 0.9147 (t80) cc_final: 0.8780 (t80)
REVERT: B  126 MET cc_start: 0.7913 (ppp) cc_final: 0.7466 (ppp)
REVERT: C  178 GLU cc_start: 0.8218 (pp20) cc_final: 0.7853 (pp20)
REVERT: D   65 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8347 (tm-30)
REVERT: D   69 LEU cc_start: 0.9070 (mt) cc_final: 0.8697 (mt)
REVERT: D  189 LEU cc_start: 0.9620 (tt) cc_final: 0.9368 (tt)
REVERT: D  210 MET cc_start: 0.8808 (tpt) cc_final: 0.8491 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1013
  time to fit residues: 20.9119
Evaluate side-chains
  117 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 3 optimal weight:    0.2980
   chunk 33 optimal weight:    4.9990
   overall best weight:    4.0588

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 157 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.055257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.039927 restraints weight = 56516.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.041261 restraints weight = 31808.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.042196 restraints weight = 21814.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.042824 restraints weight = 16858.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.043182 restraints weight = 14222.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9418  Z= 0.233
  Angle     :  0.709   8.876  13466  Z= 0.410
  Chirality :  0.039   0.155   1561
  Planarity :  0.005   0.057   1049
  Dihedral  : 32.211 146.279   2656
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.24 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.33), residues: 641
  helix:  1.31 (0.24), residues: 449
  sheet:  None (None), residues: 0
  loop : -2.04 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C  53 
 TYR   0.024   0.002   TYR D 193 
 PHE   0.029   0.002   PHE D 148 
 TRP   0.007   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 9417)
  covalent geometry    : angle       0.70904 (13464)
  SS BOND              : bond        0.00396 (    1)
  SS BOND              : angle       1.10071 (    2)
  hydrogen bonds       : bond        0.05026 (  563)
  hydrogen bonds       : angle       3.66026 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.8887 (m100) cc_final: 0.8655 (m100)
REVERT: A  120 TYR cc_start: 0.9212 (t80) cc_final: 0.8951 (t80)
REVERT: B   31 ASN cc_start: 0.9548 (m110) cc_final: 0.9255 (m-40)
REVERT: B  120 TYR cc_start: 0.9169 (t80) cc_final: 0.8791 (t80)
REVERT: B  126 MET cc_start: 0.7946 (ppp) cc_final: 0.7506 (ppp)
REVERT: C   79 ILE cc_start: 0.8700 (pt) cc_final: 0.8474 (pt)
REVERT: D   33 GLN cc_start: 0.8967 (mp10) cc_final: 0.8754 (mp10)
REVERT: D   65 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: D   69 LEU cc_start: 0.9112 (mt) cc_final: 0.8782 (mt)
REVERT: D  189 LEU cc_start: 0.9646 (tt) cc_final: 0.9421 (tt)
REVERT: D  210 MET cc_start: 0.8828 (tpt) cc_final: 0.8517 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0953
  time to fit residues: 19.6589
Evaluate side-chains
  111 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.0670
   chunk 30 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    1.5124

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
A 157 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.056830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.041387 restraints weight = 54477.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.042752 restraints weight = 30633.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.043706 restraints weight = 20921.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.044357 restraints weight = 16178.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.044766 restraints weight = 13599.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9418  Z= 0.164
  Angle     :  0.680   8.505  13466  Z= 0.388
  Chirality :  0.038   0.148   1561
  Planarity :  0.005   0.083   1049
  Dihedral  : 32.147 144.788   2656
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.30 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.52 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.34), residues: 641
  helix:  1.40 (0.25), residues: 451
  sheet:  None (None), residues: 0
  loop : -2.01 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 149 
 TYR   0.023   0.002   TYR D 193 
 PHE   0.016   0.001   PHE D 148 
 TRP   0.004   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9417)
  covalent geometry    : angle       0.67991 (13464)
  SS BOND              : bond        0.00383 (    1)
  SS BOND              : angle       0.99164 (    2)
  hydrogen bonds       : bond        0.04082 (  563)
  hydrogen bonds       : angle       3.36714 ( 1446)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2286.85 seconds
wall clock time: 40 minutes 1.10 seconds (2401.10 seconds total)