Starting phenix.real_space_refine
on Sat May  2 08:27:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21di_67586/05_2026/21di_67586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21di_67586/05_2026/21di_67586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/21di_67586/05_2026/21di_67586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21di_67586/05_2026/21di_67586.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/21di_67586/05_2026/21di_67586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21di_67586/05_2026/21di_67586.cif"
  }
  resolution = 3.5
  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=   0.052
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       9      5.16       5
     C    2331      2.51       5
     N     666      2.21       5
     O     747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3753
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "E"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "B"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "C"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "F"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "H"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "I"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
  Time building chain proxies: 1.23, per 1000 atoms: 0.33
  Number of scatterers: 3753
  At special positions: 0
  Unit cell: (77.04, 75.97, 64.2, 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       9     16.00
     O     747      8.00
     N     666      7.00
     C    2331      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 144.3 milliseconds
  

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 1 sheets defined
      69.8% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'E' and resid 65 through 84
    Processing helix  chain 'E' and resid 85 through 101
    Processing helix  chain 'A' and resid 65 through 84
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'B' and resid 65 through 84
    Processing helix  chain 'B' and resid 85 through 101
    Processing helix  chain 'C' and resid 65 through 84
    Processing helix  chain 'C' and resid 85 through 101
    Processing helix  chain 'D' and resid 65 through 84
    Processing helix  chain 'D' and resid 85 through 101
    Processing helix  chain 'F' and resid 65 through 84
    Processing helix  chain 'F' and resid 85 through 101
    Processing helix  chain 'G' and resid 65 through 84
    Processing helix  chain 'G' and resid 85 through 101
    Processing helix  chain 'H' and resid 65 through 84
    Processing helix  chain 'H' and resid 85 through 101
    Processing helix  chain 'I' and resid 65 through 84
    Processing helix  chain 'I' and resid 85 through 101
    Processing sheet with id=AA1, first strand: chain 'E' and resid 109 through 112
      removed outlier: 3.523A  pdb=" N   VAL G 110 " --> pdb=" O   THR F 107 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   VAL E 110 " --> pdb=" O   ASN I 109 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   ASN I 111 " --> pdb=" O   VAL E 110 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ILE E 112 " --> pdb=" O   ASN I 111 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    852 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: 0.60

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1322
        1.34 -     1.46: 305
        1.46 -     1.57: 2144
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3789
  Sorted by residual:
  bond pdb=" CB  ILE D  86 "
       pdb=" CG2 ILE D  86 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.02e-01
  bond pdb=" CB  ILE H  86 "
       pdb=" CG2 ILE H  86 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.08e-01
  bond pdb=" CB  GLU F  99 "
       pdb=" CG  GLU F  99 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.14e-01
  bond pdb=" CB  PHE G 103 "
       pdb=" CG  PHE G 103 "
    ideal  model  delta    sigma   weight residual
    1.502  1.485  0.017 2.30e-02 1.89e+03 5.15e-01
  bond pdb=" CB  ASN G  76 "
       pdb=" CG  ASN G  76 "
    ideal  model  delta    sigma   weight residual
    1.516  1.498  0.018 2.50e-02 1.60e+03 4.96e-01
  ... (remaining 3784 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 4677
        0.92 -     1.84: 303
        1.84 -     2.76: 88
        2.76 -     3.68: 30
        3.68 -     4.60: 14
  Bond angle restraints: 5112
  Sorted by residual:
  angle pdb=" N   PHE E 103 "
        pdb=" CA  PHE E 103 "
        pdb=" C   PHE E 103 "
      ideal   model   delta    sigma   weight residual
     111.92  109.38    2.54 1.34e+00 5.57e-01 3.60e+00
  angle pdb=" N   PHE H 103 "
        pdb=" CA  PHE H 103 "
        pdb=" C   PHE H 103 "
      ideal   model   delta    sigma   weight residual
     111.92  109.45    2.47 1.34e+00 5.57e-01 3.39e+00
  angle pdb=" N   MET D 102 "
        pdb=" CA  MET D 102 "
        pdb=" C   MET D 102 "
      ideal   model   delta    sigma   weight residual
     109.31  106.84    2.47 1.42e+00 4.96e-01 3.03e+00
  angle pdb=" N   PHE C 103 "
        pdb=" CA  PHE C 103 "
        pdb=" C   PHE C 103 "
      ideal   model   delta    sigma   weight residual
     111.92  109.65    2.27 1.34e+00 5.57e-01 2.87e+00
  angle pdb=" N   PHE F 103 "
        pdb=" CA  PHE F 103 "
        pdb=" C   PHE F 103 "
      ideal   model   delta    sigma   weight residual
     111.92  109.66    2.26 1.34e+00 5.57e-01 2.85e+00
  ... (remaining 5107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 2082
       17.93 -    35.86: 197
       35.86 -    53.79: 20
       53.79 -    71.73: 22
       71.73 -    89.66: 10
  Dihedral angle restraints: 2331
    sinusoidal: 963
      harmonic: 1368
  Sorted by residual:
  dihedral pdb=" CA  MET G 102 "
           pdb=" C   MET G 102 "
           pdb=" N   PHE G 103 "
           pdb=" CA  PHE G 103 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.74  -22.26     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  MET E 102 "
           pdb=" C   MET E 102 "
           pdb=" N   PHE E 103 "
           pdb=" CA  PHE E 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.79  -22.21     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  MET I 102 "
           pdb=" C   MET I 102 "
           pdb=" N   PHE I 103 "
           pdb=" CA  PHE I 103 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.15  -21.85     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 2328 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 317
       0.023 -    0.046: 102
       0.046 -    0.069: 99
       0.069 -    0.091: 39
       0.091 -    0.114: 37
  Chirality restraints: 594
  Sorted by residual:
  chirality pdb=" CA  VAL E 110 "
            pdb=" N   VAL E 110 "
            pdb=" C   VAL E 110 "
            pdb=" CB  VAL E 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.26e-01
  chirality pdb=" CA  VAL B 110 "
            pdb=" N   VAL B 110 "
            pdb=" C   VAL B 110 "
            pdb=" CB  VAL B 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.17e-01
  chirality pdb=" CA  VAL I 110 "
            pdb=" N   VAL I 110 "
            pdb=" C   VAL I 110 "
            pdb=" CB  VAL I 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.16e-01
  ... (remaining 591 not shown)

  Planarity restraints: 675
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 106 "   -0.096 9.50e-02 1.11e+02   4.31e-02 1.28e+00
        pdb=" NE  ARG C 106 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 106 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 106 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 106 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU I  99 "   -0.006 2.00e-02 2.50e+03   1.13e-02 1.28e+00
        pdb=" CD  GLU I  99 "    0.020 2.00e-02 2.50e+03
        pdb=" OE1 GLU I  99 "   -0.007 2.00e-02 2.50e+03
        pdb=" OE2 GLU I  99 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 106 "    0.093 9.50e-02 1.11e+02   4.17e-02 1.27e+00
        pdb=" NE  ARG B 106 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 106 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 106 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 106 "    0.001 2.00e-02 2.50e+03
  ... (remaining 672 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 375
        2.74 -     3.28: 3939
        3.28 -     3.82: 6351
        3.82 -     4.36: 7327
        4.36 -     4.90: 12865
  Nonbonded interactions: 30857
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG E  66 "
            pdb=" OE2 GLU E  99 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NH2 ARG C  66 "
            pdb=" OE2 GLU C  99 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OG  SER H  65 "
            pdb=" OE1 GLU H  67 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" ND2 ASN F  76 "
            pdb=" OD1 ASN G  90 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG  SER C  65 "
            pdb=" OE1 GLU C  67 "
     model   vdw
     2.257 3.040
  ... (remaining 30852 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'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.970
  Find NCS groups from input model:        0.070
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
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   0.030   3789  Z= 0.147
  Angle     :  0.617   4.595   5112  Z= 0.317
  Chirality :  0.043   0.114    594
  Planarity :  0.005   0.043    675
  Dihedral  : 15.948  89.657   1431
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 23.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.41), residues: 459
  helix:  3.29 (0.27), residues: 324
  sheet:  None (None), residues: 0
  loop : -3.61 (0.42), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG D 106 
 PHE   0.011   0.002   PHE C 103 
 TRP   0.001   0.000   TRP D  68 
 HIS   0.001   0.000   HIS H 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3789)
  covalent geometry    : angle       0.61660 ( 5112)
  hydrogen bonds       : bond        0.14926 (  289)
  hydrogen bonds       : angle       6.40739 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: G   86 ILE cc_start: 0.8900 (mm) cc_final: 0.8592 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0736
  time to fit residues: 10.5844
Evaluate side-chains
  100 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B  90 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 = 0.4033 r_free = 0.4033 target = 0.190083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.172614 restraints weight = 4982.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.177389 restraints weight = 2738.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.180748 restraints weight = 1705.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.183053 restraints weight = 1136.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.184477 restraints weight = 794.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3789  Z= 0.132
  Angle     :  0.519   4.429   5112  Z= 0.276
  Chirality :  0.041   0.124    594
  Planarity :  0.005   0.035    675
  Dihedral  :  5.195  18.643    495
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.98 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.40), residues: 459
  helix:  3.46 (0.27), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.72 (0.38), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  66 
 PHE   0.009   0.003   PHE H 103 
 TRP   0.003   0.000   TRP F  68 
 HIS   0.000   0.000   HIS H 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3789)
  covalent geometry    : angle       0.51865 ( 5112)
  hydrogen bonds       : bond        0.03584 (  289)
  hydrogen bonds       : angle       4.44593 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   86 ILE cc_start: 0.8739 (mm) cc_final: 0.8233 (mm)
REVERT: C   90 ASN cc_start: 0.7869 (m-40) cc_final: 0.7604 (m-40)
REVERT: D   86 ILE cc_start: 0.8762 (mm) cc_final: 0.8532 (mm)
REVERT: G   86 ILE cc_start: 0.8661 (mm) cc_final: 0.8115 (mm)
REVERT: I   67 GLU cc_start: 0.8154 (mp0) cc_final: 0.7563 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 120
  average time/residue: 0.0855
  time to fit residues: 12.3185
Evaluate side-chains
  103 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain I residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 13 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 109 ASN
** I  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.184372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.163244 restraints weight = 4821.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.168158 restraints weight = 2851.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.171632 restraints weight = 1899.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.174123 restraints weight = 1358.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.176035 restraints weight = 1022.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3789  Z= 0.126
  Angle     :  0.519   4.378   5112  Z= 0.273
  Chirality :  0.041   0.122    594
  Planarity :  0.005   0.051    675
  Dihedral  :  4.891  18.343    495
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.63 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.58 (0.39), residues: 459
  helix:  3.42 (0.26), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.50 (0.36), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 106 
 PHE   0.015   0.003   PHE C 103 
 TRP   0.002   0.000   TRP I  68 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3789)
  covalent geometry    : angle       0.51852 ( 5112)
  hydrogen bonds       : bond        0.03338 (  289)
  hydrogen bonds       : angle       4.23757 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   86 ILE cc_start: 0.8697 (mm) cc_final: 0.8390 (mm)
REVERT: A  108 GLU cc_start: 0.7458 (tp30) cc_final: 0.6614 (tp30)
REVERT: C   86 ILE cc_start: 0.8737 (mm) cc_final: 0.8398 (mm)
REVERT: C   90 ASN cc_start: 0.7704 (m-40) cc_final: 0.7494 (m-40)
REVERT: C   93 LEU cc_start: 0.8682 (mm) cc_final: 0.8137 (mm)
REVERT: D  106 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.7614 (mpt180)
REVERT: F   93 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8097 (mm)
REVERT: F  102 MET cc_start: 0.6167 (mtm) cc_final: 0.5964 (mtm)
REVERT: F  104 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7807 (p)
REVERT: H   67 GLU cc_start: 0.8214 (mp0) cc_final: 0.7799 (mp0)
REVERT: H  100 LEU cc_start: 0.9017 (mm) cc_final: 0.8788 (mm)
  outliers start: 14
  outliers final: 4
  residues processed: 114
  average time/residue: 0.0653
  time to fit residues: 9.3824
Evaluate side-chains
  107 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Chi-restraints excluded: chain I residue  107 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 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 = 0.3939 r_free = 0.3939 target = 0.179381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.159041 restraints weight = 4817.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.163594 restraints weight = 2903.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.166829 restraints weight = 1962.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.169223 restraints weight = 1421.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.171024 restraints weight = 1079.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3789  Z= 0.172
  Angle     :  0.552   4.965   5112  Z= 0.290
  Chirality :  0.045   0.249    594
  Planarity :  0.005   0.046    675
  Dihedral  :  4.633  17.019    495
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.84 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.38), residues: 459
  helix:  3.27 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.51 (0.35), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  66 
 PHE   0.011   0.003   PHE C 103 
 TRP   0.003   0.000   TRP F  68 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 3789)
  covalent geometry    : angle       0.55177 ( 5112)
  hydrogen bonds       : bond        0.03691 (  289)
  hydrogen bonds       : angle       4.16450 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: C   86 ILE cc_start: 0.8787 (mm) cc_final: 0.8545 (mm)
REVERT: C   93 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8009 (mm)
REVERT: C  106 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7681 (mpt180)
REVERT: D  106 ARG cc_start: 0.8500 (mmt-90) cc_final: 0.8129 (mpt180)
REVERT: F   93 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8203 (mm)
REVERT: F  102 MET cc_start: 0.6246 (mtm) cc_final: 0.5978 (mtm)
REVERT: G   86 ILE cc_start: 0.8749 (mm) cc_final: 0.8539 (mm)
REVERT: H   67 GLU cc_start: 0.8110 (mp0) cc_final: 0.7701 (mp0)
REVERT: H  100 LEU cc_start: 0.8959 (mm) cc_final: 0.8739 (mm)
  outliers start: 14
  outliers final: 5
  residues processed: 113
  average time/residue: 0.0599
  time to fit residues: 8.7047
Evaluate side-chains
  110 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  106 ARG
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** F  90 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 = 0.3960 r_free = 0.3960 target = 0.181507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.160702 restraints weight = 4857.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.165461 restraints weight = 2889.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.168802 restraints weight = 1940.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.171287 restraints weight = 1398.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.173095 restraints weight = 1057.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3789  Z= 0.131
  Angle     :  0.504   4.337   5112  Z= 0.267
  Chirality :  0.042   0.122    594
  Planarity :  0.005   0.042    675
  Dihedral  :  4.639  17.664    495
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.05 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.38), residues: 459
  helix:  3.41 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.35 (0.36), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  66 
 PHE   0.010   0.002   PHE C 103 
 TRP   0.002   0.000   TRP F  68 
 HIS   0.000   0.000   HIS H 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3789)
  covalent geometry    : angle       0.50436 ( 5112)
  hydrogen bonds       : bond        0.03290 (  289)
  hydrogen bonds       : angle       4.08529 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.8110 (mp0) cc_final: 0.7616 (mp0)
REVERT: C   67 GLU cc_start: 0.8131 (mp0) cc_final: 0.7491 (pm20)
REVERT: C   86 ILE cc_start: 0.8790 (mm) cc_final: 0.8433 (mm)
REVERT: C   90 ASN cc_start: 0.7703 (m-40) cc_final: 0.7456 (m-40)
REVERT: C   93 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8065 (mm)
REVERT: D  106 ARG cc_start: 0.8412 (mmt-90) cc_final: 0.8006 (mpt180)
REVERT: F   93 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8147 (mm)
REVERT: F  102 MET cc_start: 0.6185 (mtm) cc_final: 0.5916 (mtm)
REVERT: G   86 ILE cc_start: 0.8721 (mm) cc_final: 0.8470 (mm)
REVERT: H   67 GLU cc_start: 0.8091 (mp0) cc_final: 0.7684 (mp0)
  outliers start: 14
  outliers final: 5
  residues processed: 109
  average time/residue: 0.0514
  time to fit residues: 7.4914
Evaluate side-chains
  107 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.181912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.161540 restraints weight = 4873.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.166281 restraints weight = 2854.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.169635 restraints weight = 1890.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.172042 restraints weight = 1351.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.173884 restraints weight = 1015.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3789  Z= 0.136
  Angle     :  0.519   4.955   5112  Z= 0.271
  Chirality :  0.043   0.237    594
  Planarity :  0.005   0.043    675
  Dihedral  :  4.586  18.055    495
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.46 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.38), residues: 459
  helix:  3.43 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.27 (0.37), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 106 
 PHE   0.015   0.002   PHE E 103 
 TRP   0.002   0.000   TRP F  68 
 HIS   0.000   0.000   HIS I 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3789)
  covalent geometry    : angle       0.51889 ( 5112)
  hydrogen bonds       : bond        0.03306 (  289)
  hydrogen bonds       : angle       4.03023 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   86 ILE cc_start: 0.8787 (mm) cc_final: 0.8424 (mm)
REVERT: C   90 ASN cc_start: 0.7702 (m-40) cc_final: 0.7453 (m-40)
REVERT: C   93 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8081 (mm)
REVERT: D  106 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.7817 (mpt180)
REVERT: F   93 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8141 (mm)
REVERT: F  102 MET cc_start: 0.6221 (mtm) cc_final: 0.5971 (mtm)
REVERT: H   67 GLU cc_start: 0.8086 (mp0) cc_final: 0.7695 (mp0)
  outliers start: 11
  outliers final: 3
  residues processed: 108
  average time/residue: 0.0586
  time to fit residues: 8.1435
Evaluate side-chains
  106 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0670
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 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 = 0.3958 r_free = 0.3958 target = 0.181919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.161479 restraints weight = 4885.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.166226 restraints weight = 2851.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.169527 restraints weight = 1887.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.171987 restraints weight = 1353.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.173871 restraints weight = 1015.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3789  Z= 0.133
  Angle     :  0.527   6.727   5112  Z= 0.274
  Chirality :  0.043   0.198    594
  Planarity :  0.005   0.044    675
  Dihedral  :  4.665  18.285    495
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.95 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.38), residues: 459
  helix:  3.45 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.24 (0.37), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 106 
 PHE   0.011   0.002   PHE E 103 
 TRP   0.002   0.000   TRP F  68 
 HIS   0.000   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3789)
  covalent geometry    : angle       0.52713 ( 5112)
  hydrogen bonds       : bond        0.03265 (  289)
  hydrogen bonds       : angle       4.02276 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 ASN cc_start: 0.7884 (m110) cc_final: 0.7572 (m110)
REVERT: C   90 ASN cc_start: 0.7741 (m-40) cc_final: 0.7502 (m-40)
REVERT: C   93 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8049 (mm)
REVERT: D  106 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.7891 (mpt180)
REVERT: F   93 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8106 (mm)
REVERT: F  102 MET cc_start: 0.6178 (mtm) cc_final: 0.5947 (mtm)
REVERT: G   86 ILE cc_start: 0.8765 (mm) cc_final: 0.8556 (mm)
REVERT: H   67 GLU cc_start: 0.8122 (mp0) cc_final: 0.7723 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 104
  average time/residue: 0.0460
  time to fit residues: 6.6866
Evaluate side-chains
  108 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  112 ILE
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Chi-restraints excluded: chain I residue  104 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 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 = 0.3952 r_free = 0.3952 target = 0.181733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.161062 restraints weight = 4840.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.165870 restraints weight = 2825.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.169303 restraints weight = 1874.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.171801 restraints weight = 1340.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.173632 restraints weight = 1004.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3789  Z= 0.130
  Angle     :  0.525   6.560   5112  Z= 0.273
  Chirality :  0.042   0.166    594
  Planarity :  0.005   0.039    675
  Dihedral  :  4.632  18.366    495
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.43 %
    Favored  : 72.95 %
  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 are not related in a simple way.
  whole:  2.76 (0.38), residues: 459
  helix:  3.48 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.19 (0.37), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  66 
 PHE   0.009   0.002   PHE D 103 
 TRP   0.002   0.000   TRP F  68 
 HIS   0.000   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3789)
  covalent geometry    : angle       0.52516 ( 5112)
  hydrogen bonds       : bond        0.03218 (  289)
  hydrogen bonds       : angle       4.00130 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 ASN cc_start: 0.7770 (m110) cc_final: 0.7463 (m110)
REVERT: C   86 ILE cc_start: 0.8729 (mm) cc_final: 0.8373 (mm)
REVERT: C   90 ASN cc_start: 0.7711 (m-40) cc_final: 0.7458 (m-40)
REVERT: C   93 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8009 (mm)
REVERT: C  106 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7713 (mpt180)
REVERT: D  106 ARG cc_start: 0.8181 (mmt-90) cc_final: 0.7950 (mpt180)
REVERT: F   93 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8065 (mm)
REVERT: F  102 MET cc_start: 0.6200 (mtm) cc_final: 0.5937 (mtm)
REVERT: G   86 ILE cc_start: 0.8758 (mm) cc_final: 0.8525 (mm)
REVERT: H   67 GLU cc_start: 0.8184 (mp0) cc_final: 0.7716 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0523
  time to fit residues: 7.5248
Evaluate side-chains
  111 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  106 ARG
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  112 ILE
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Chi-restraints excluded: chain I residue  104 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 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 = 0.3942 r_free = 0.3942 target = 0.180572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.160431 restraints weight = 4832.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.165146 restraints weight = 2818.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.168494 restraints weight = 1864.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.170847 restraints weight = 1333.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.172727 restraints weight = 1003.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3789  Z= 0.158
  Angle     :  0.573   7.004   5112  Z= 0.297
  Chirality :  0.044   0.194    594
  Planarity :  0.005   0.037    675
  Dihedral  :  4.658  18.583    495
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 24.40 %
    Favored  : 72.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.38), residues: 459
  helix:  3.43 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.29 (0.36), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  66 
 PHE   0.010   0.003   PHE D 103 
 TRP   0.001   0.000   TRP G  68 
 HIS   0.000   0.000   HIS I 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3789)
  covalent geometry    : angle       0.57291 ( 5112)
  hydrogen bonds       : bond        0.03478 (  289)
  hydrogen bonds       : angle       4.05691 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   67 GLU cc_start: 0.8172 (mp0) cc_final: 0.7921 (mp0)
REVERT: C   86 ILE cc_start: 0.8751 (mm) cc_final: 0.8394 (mm)
REVERT: C   90 ASN cc_start: 0.7668 (m-40) cc_final: 0.7408 (m-40)
REVERT: C   93 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8044 (mm)
REVERT: D  106 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7849 (mpt180)
REVERT: F   93 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8139 (mm)
REVERT: F  102 MET cc_start: 0.6269 (mtm) cc_final: 0.6028 (mtm)
REVERT: G   86 ILE cc_start: 0.8792 (mm) cc_final: 0.8550 (mm)
REVERT: H   67 GLU cc_start: 0.8198 (mp0) cc_final: 0.7730 (mp0)
REVERT: H  100 LEU cc_start: 0.9224 (mm) cc_final: 0.9008 (mt)
  outliers start: 12
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0522
  time to fit residues: 7.4628
Evaluate side-chains
  110 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  112 ILE
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Chi-restraints excluded: chain I residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 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 = 0.3956 r_free = 0.3956 target = 0.181639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.160134 restraints weight = 4913.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.164953 restraints weight = 2950.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.168378 restraints weight = 1990.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.170877 restraints weight = 1447.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.172727 restraints weight = 1104.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3789  Z= 0.153
  Angle     :  0.586   7.129   5112  Z= 0.303
  Chirality :  0.044   0.171    594
  Planarity :  0.005   0.039    675
  Dihedral  :  4.668  19.041    495
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.15 %
    Favored  : 72.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.38), residues: 459
  helix:  3.41 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.22 (0.36), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 106 
 PHE   0.010   0.003   PHE D 103 
 TRP   0.001   0.000   TRP A  68 
 HIS   0.000   0.000   HIS I 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3789)
  covalent geometry    : angle       0.58580 ( 5112)
  hydrogen bonds       : bond        0.03454 (  289)
  hydrogen bonds       : angle       4.07728 (  852)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   67 GLU cc_start: 0.8172 (mp0) cc_final: 0.7965 (mp0)
REVERT: C   86 ILE cc_start: 0.8766 (mm) cc_final: 0.8405 (mm)
REVERT: C   90 ASN cc_start: 0.7681 (m-40) cc_final: 0.7425 (m-40)
REVERT: C   93 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8033 (mm)
REVERT: F   93 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8097 (mm)
REVERT: F  102 MET cc_start: 0.6112 (mtm) cc_final: 0.5857 (mtm)
REVERT: G   86 ILE cc_start: 0.8791 (mm) cc_final: 0.8545 (mm)
REVERT: H   67 GLU cc_start: 0.8188 (mp0) cc_final: 0.7724 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 106
  average time/residue: 0.0534
  time to fit residues: 7.4661
Evaluate side-chains
  109 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  112 ILE
Chi-restraints excluded: chain F residue   93 LEU
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  104 VAL
Chi-restraints excluded: chain I residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** E  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 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 = 0.3932 r_free = 0.3932 target = 0.179533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.158533 restraints weight = 4775.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.163250 restraints weight = 2876.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.166287 restraints weight = 1940.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.168942 restraints weight = 1425.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.170804 restraints weight = 1084.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3789  Z= 0.139
  Angle     :  0.576   8.938   5112  Z= 0.296
  Chirality :  0.043   0.157    594
  Planarity :  0.005   0.043    675
  Dihedral  :  4.723  19.911    495
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.64 %
    Favored  : 72.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.74 (0.38), residues: 459
  helix:  3.43 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.11 (0.37), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 106 
 PHE   0.009   0.002   PHE D 103 
 TRP   0.001   0.000   TRP A  68 
 HIS   0.000   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3789)
  covalent geometry    : angle       0.57634 ( 5112)
  hydrogen bonds       : bond        0.03311 (  289)
  hydrogen bonds       : angle       4.08659 (  852)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 770.17 seconds
wall clock time: 14 minutes 5.02 seconds (845.02 seconds total)