Starting phenix.real_space_refine
on Tue Aug  4 23:11:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jfq_61436/08_2026/9jfq_61436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jfq_61436/08_2026/9jfq_61436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jfq_61436/08_2026/9jfq_61436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jfq_61436/08_2026/9jfq_61436.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jfq_61436/08_2026/9jfq_61436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jfq_61436/08_2026/9jfq_61436.map"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.041
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     165      5.49       5
     S      19      5.16       5
     C    3980      2.51       5
     N    1356      2.21       5
     O    1761      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7281
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3787
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 27, 'TRANS': 450}
    Chain: "C"
      Number of atoms: 447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 447
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "F"
      Number of atoms: 2236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 2236
          Classifications: {'RNA': 104}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 56, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 9, 'rna3p': 94}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 811
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
  Time building chain proxies: 1.82, per 1000 atoms: 0.25
  Number of scatterers: 7281
  At special positions: 0
  Unit cell: (108.25, 97.425, 113.662, 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      19     16.00
     P     165     15.00
     O    1761      8.00
     N    1356      7.00
     C    3980      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: 0.61
  Conformation dependent library (CDL) restraints added in 378.9 milliseconds
  

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  910

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 5 sheets defined
      39.5% alpha, 7.1% beta
      55 base pairs and 100 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 51
    Processing helix  chain 'A' and resid 77 through 88
      removed outlier: 3.599A  pdb=" N   ARG A  81 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.577A  pdb=" N   ILE A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 117
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 191 through 199
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.657A  pdb=" N   ASP A 276 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
    Processing helix  chain 'A' and resid 299 through 319
      removed outlier: 3.698A  pdb=" N   ASP A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 374
      removed outlier: 3.507A  pdb=" N   GLY A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 399
    Processing helix  chain 'A' and resid 402 through 414
      removed outlier: 4.006A  pdb=" N   PHE A 406 " --> pdb=" O   ALA A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 446
      removed outlier: 3.972A  pdb=" N   ASN A 446 " --> pdb=" O   ALA A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 481
      removed outlier: 3.636A  pdb=" N   ASN A 466 " --> pdb=" O   ASN A 462 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13
      removed outlier: 3.700A  pdb=" N   ASN A   8 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20
      removed outlier: 3.753A  pdb=" N   MET A  19 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   THR A 206 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A 145 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 250
      removed outlier: 6.182A  pdb=" N   GLU A 248 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LEU A 377 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253
      removed outlier: 3.727A  pdb=" N   ALA A 260 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)

    144 hydrogen bonds defined for protein.
    414 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      137 hydrogen bonds
      258 hydrogen bond angles
      0 basepair planarities
      55 basepair parallelities
      100 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 0.83 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: 1482
        1.33 -     1.45: 2619
        1.45 -     1.58: 3324
        1.58 -     1.70: 325
        1.70 -     1.82: 30
  Bond restraints: 7780
  Sorted by residual:
  bond pdb=" C1'  DT G  19 "
       pdb=" N1   DT G  19 "
    ideal  model  delta    sigma   weight residual
    1.468  1.520 -0.052 1.40e-02 5.10e+03 1.40e+01
  bond pdb=" C3'  DA G  28 "
       pdb=" C2'  DA G  28 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  bond pdb=" C3'  DG G  25 "
       pdb=" C2'  DG G  25 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.79e+00
  bond pdb=" C1'  DC C  14 "
       pdb=" N1   DC C  14 "
    ideal  model  delta    sigma   weight residual
    1.468  1.507 -0.039 1.40e-02 5.10e+03 7.72e+00
  bond pdb=" C3'  DC C  11 "
       pdb=" C2'  DC C  11 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.63e+00
  ... (remaining 7775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 10443
        1.56 -     3.12: 783
        3.12 -     4.68: 51
        4.68 -     6.24: 8
        6.24 -     7.80: 5
  Bond angle restraints: 11290
  Sorted by residual:
  angle pdb=" N   ILE A 259 "
        pdb=" CA  ILE A 259 "
        pdb=" C   ILE A 259 "
      ideal   model   delta    sigma   weight residual
     113.71  105.91    7.80 9.50e-01 1.11e+00 6.73e+01
  angle pdb=" N1    C F  20 "
        pdb=" C2    C F  20 "
        pdb=" O2    C F  20 "
      ideal   model   delta    sigma   weight residual
     118.90  121.54   -2.64 6.00e-01 2.78e+00 1.93e+01
  angle pdb=" O2    C F  20 "
        pdb=" C2    C F  20 "
        pdb=" N3    C F  20 "
      ideal   model   delta    sigma   weight residual
     121.90  118.86    3.04 7.00e-01 2.04e+00 1.89e+01
  angle pdb=" O4'  DT G   9 "
        pdb=" C4'  DT G   9 "
        pdb=" C3'  DT G   9 "
      ideal   model   delta    sigma   weight residual
     106.00  103.40    2.60 6.00e-01 2.78e+00 1.88e+01
  angle pdb=" N3   DT C  20 "
        pdb=" C4   DT C  20 "
        pdb=" O4   DT C  20 "
      ideal   model   delta    sigma   weight residual
     119.90  122.48   -2.58 6.00e-01 2.78e+00 1.84e+01
  ... (remaining 11285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.29: 4021
       34.29 -    68.59: 594
       68.59 -   102.88: 49
      102.88 -   137.18: 7
      137.18 -   171.47: 3
  Dihedral angle restraints: 4674
    sinusoidal: 3273
      harmonic: 1401
  Sorted by residual:
  dihedral pdb=" C5'   G F  77 "
           pdb=" C4'   G F  77 "
           pdb=" C3'   G F  77 "
           pdb=" O3'   G F  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  103.49   43.51     1      8.00e+00 1.56e-02 4.12e+01
  dihedral pdb=" O4'   G F  77 "
           pdb=" C4'   G F  77 "
           pdb=" C3'   G F  77 "
           pdb=" C2'   G F  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -12.48   36.48     1      8.00e+00 1.56e-02 2.94e+01
  dihedral pdb=" CA  SER A 142 "
           pdb=" C   SER A 142 "
           pdb=" N   PHE A 143 "
           pdb=" CA  PHE A 143 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.94   26.06     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 4671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 995
       0.052 -    0.105: 200
       0.105 -    0.157: 123
       0.157 -    0.209: 7
       0.209 -    0.261: 4
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" C3'   U F  23 "
            pdb=" C4'   U F  23 "
            pdb=" O3'   U F  23 "
            pdb=" C2'   U F  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.48   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" C3'   G F  77 "
            pdb=" C4'   G F  77 "
            pdb=" O3'   G F  77 "
            pdb=" C2'   G F  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.52   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" C1'   C F  20 "
            pdb=" O4'   C F  20 "
            pdb=" C2'   C F  20 "
            pdb=" N1    C F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.26    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1326 not shown)

  Planarity restraints: 845
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 173 "    0.025 2.00e-02 2.50e+03   1.15e-02 3.63e+00
        pdb=" N9    A F 173 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8    A F 173 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A F 173 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A F 173 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A F 173 "    0.007 2.00e-02 2.50e+03
        pdb=" N6    A F 173 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A F 173 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A F 173 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A F 173 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    A F 173 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F  20 "    0.019 2.00e-02 2.50e+03   1.15e-02 2.99e+00
        pdb=" N1    C F  20 "   -0.027 2.00e-02 2.50e+03
        pdb=" C2    C F  20 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    C F  20 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C F  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    C F  20 "    0.005 2.00e-02 2.50e+03
        pdb=" N4    C F  20 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C F  20 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C F  20 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 326 "   -0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO A 327 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 842 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 415
        2.70 -     3.25: 7062
        3.25 -     3.80: 13621
        3.80 -     4.35: 16700
        4.35 -     4.90: 24092
  Nonbonded interactions: 61890
  Sorted by model distance:
  nonbonded pdb=" O2'   A F 137 "
            pdb=" O4'   A F 138 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O2'   A F 131 "
            pdb=" OP2   U F 132 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NE2 GLN A  32 "
            pdb=" O   LYS A 168 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" NZ  LYS A 174 "
            pdb=" OP2   G F 160 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" O2   DT C  15 "
            pdb=" N2    G F 176 "
     model   vdw
     2.223 2.496
  ... (remaining 61885 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.660
  Find NCS groups from input model:        0.030
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5912
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      :  0.004   0.074   7780  Z= 0.355
  Angle     :  0.807   7.795  11290  Z= 0.656
  Chirality :  0.055   0.261   1329
  Planarity :  0.005   0.043    845
  Dihedral  : 25.409 171.470   3764
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.99 %
    Favored  : 98.77 %
  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: -1.62 (0.38), residues: 476
  helix: -0.04 (0.38), residues: 184
  sheet: -3.46 (0.58), residues: 60
  loop : -1.16 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 176 
 TYR   0.024   0.002   TYR A 364 
 PHE   0.024   0.002   PHE A 143 
 TRP   0.013   0.002   TRP A  69 
 HIS   0.008   0.002   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.35 ( 7780)
  covalent geometry    : angle       0.80655 /  0.66 (11290)
  hydrogen bonds       : bond        0.13532 /  8.24 (  281)
  hydrogen bonds       : angle       5.56350 /  4.00 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7123 (ttp80)
  outliers start: 1
  outliers final: 1
  residues processed: 59
  average time/residue: 0.1238
  time to fit residues: 9.3261
Evaluate side-chains
  47 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:   50.0000
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   overall best weight:    4.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 ASN
A 392 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.210574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.167900 restraints weight = 12766.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.168132 restraints weight = 12468.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.169419 restraints weight = 10923.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.169863 restraints weight = 7169.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.170524 restraints weight = 6624.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.121   7780  Z= 0.435
  Angle     :  1.043  11.869  11290  Z= 0.544
  Chirality :  0.065   0.448   1329
  Planarity :  0.008   0.068    845
  Dihedral  : 27.580 150.934   2805
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 25.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  :  9.88 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -2.62 (0.36), residues: 476
  helix: -0.74 (0.36), residues: 191
  sheet: -3.85 (0.63), residues: 48
  loop : -2.10 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 354 
 TYR   0.061   0.005   TYR A 412 
 PHE   0.059   0.005   PHE A 143 
 TRP   0.017   0.004   TRP A 114 
 HIS   0.021   0.005   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00945 /  0.43 ( 7780)
  covalent geometry    : angle       1.04254 /  0.54 (11290)
  hydrogen bonds       : bond        0.11093 /  7.16 (  281)
  hydrogen bonds       : angle       5.19698 /  3.67 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   49 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.6189 (t-90)
REVERT: A  152 ILE cc_start: 0.5895 (mt) cc_final: 0.5466 (mt)
REVERT: A  223 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7669 (m-10)
REVERT: A  354 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7171 (ttp80)
  outliers start: 17
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1185
  time to fit residues: 8.7461
Evaluate side-chains
  53 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  392 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:   50.0000
   chunk 48 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
A 392 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.216771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.174888 restraints weight = 12542.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.176486 restraints weight = 11711.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.177863 restraints weight = 9084.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178181 restraints weight = 6055.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.178914 restraints weight = 5728.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7780  Z= 0.199
  Angle     :  0.732  10.882  11290  Z= 0.400
  Chirality :  0.050   0.369   1329
  Planarity :  0.006   0.043    845
  Dihedral  : 27.473 145.685   2805
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 12.59 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -2.04 (0.37), residues: 476
  helix: -0.24 (0.37), residues: 181
  sheet: -3.80 (0.60), residues: 48
  loop : -1.67 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 393 
 TYR   0.032   0.003   TYR A 412 
 PHE   0.025   0.002   PHE A 143 
 TRP   0.013   0.002   TRP A 235 
 HIS   0.022   0.003   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.20 ( 7780)
  covalent geometry    : angle       0.73153 /  0.40 (11290)
  hydrogen bonds       : bond        0.07931 /  5.16 (  281)
  hydrogen bonds       : angle       4.55472 /  3.26 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 6
  residues processed: 50
  average time/residue: 0.1051
  time to fit residues: 6.9709
Evaluate side-chains
  46 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  392 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    8.9990
   chunk 56 optimal weight:   30.0000
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    5.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 159 GLN
A 204 ASN
A 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.218247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.186025 restraints weight = 13306.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.187658 restraints weight = 26026.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.188909 restraints weight = 15029.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.189011 restraints weight = 11081.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.189623 restraints weight = 10287.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6162
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.126   7780  Z= 0.487
  Angle     :  1.130  14.231  11290  Z= 0.586
  Chirality :  0.070   0.452   1329
  Planarity :  0.009   0.071    845
  Dihedral  : 27.700 140.138   2805
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 33.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.03 %
    Favored  : 86.97 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 14.32 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.35), residues: 476
  helix: -1.24 (0.34), residues: 192
  sheet: -4.37 (0.64), residues: 43
  loop : -2.33 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 176 
 TYR   0.048   0.005   TYR A 412 
 PHE   0.058   0.005   PHE A 143 
 TRP   0.018   0.004   TRP A  80 
 HIS   0.011   0.004   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01053 /  0.49 ( 7780)
  covalent geometry    : angle       1.12981 /  0.59 (11290)
  hydrogen bonds       : bond        0.12500 /  8.07 (  281)
  hydrogen bonds       : angle       5.54046 /  3.89 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6457 (t-90)
REVERT: A  152 ILE cc_start: 0.5584 (mt) cc_final: 0.5160 (mt)
REVERT: A  173 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6182 (mt)
REVERT: A  176 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (tpt90)
REVERT: A  286 ARG cc_start: 0.7523 (ptt90) cc_final: 0.6819 (ptt-90)
  outliers start: 22
  outliers final: 14
  residues processed: 58
  average time/residue: 0.1013
  time to fit residues: 7.8743
Evaluate side-chains
  56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  176 ARG
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  361 ASP
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  419 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 56 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.217153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.183536 restraints weight = 13152.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.184958 restraints weight = 25072.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.186331 restraints weight = 14794.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.186525 restraints weight = 10618.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.187160 restraints weight = 9783.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.135   7780  Z= 0.500
  Angle     :  1.149  13.714  11290  Z= 0.595
  Chirality :  0.071   0.437   1329
  Planarity :  0.009   0.080    845
  Dihedral  : 27.732 141.303   2801
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 35.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.87 %
    Favored  : 86.13 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 17.53 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.44 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.64 (0.34), residues: 476
  helix: -1.66 (0.33), residues: 191
  sheet: -4.44 (0.61), residues: 43
  loop : -2.66 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG A 176 
 TYR   0.043   0.005   TYR A 412 
 PHE   0.063   0.004   PHE A 143 
 TRP   0.020   0.004   TRP A 235 
 HIS   0.009   0.003   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01094 /  0.50 ( 7780)
  covalent geometry    : angle       1.14866 /  0.60 (11290)
  hydrogen bonds       : bond        0.12562 /  8.07 (  281)
  hydrogen bonds       : angle       5.70316 /  3.96 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 46
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5370 (t80)
REVERT: A  173 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6092 (mt)
REVERT: A  286 ARG cc_start: 0.7701 (ptt90) cc_final: 0.7276 (ptt-90)
  outliers start: 26
  outliers final: 16
  residues processed: 63
  average time/residue: 0.0932
  time to fit residues: 7.9686
Evaluate side-chains
  59 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  361 ASP
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  419 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.225756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.194707 restraints weight = 13257.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.196580 restraints weight = 23071.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.197650 restraints weight = 14724.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.197482 restraints weight = 10514.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.198235 restraints weight = 9514.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.4607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5986
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7780  Z= 0.210
  Angle     :  0.782  10.034  11290  Z= 0.421
  Chirality :  0.051   0.332   1329
  Planarity :  0.006   0.060    845
  Dihedral  : 27.414 139.908   2801
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.23 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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 (0.36), residues: 476
  helix: -0.88 (0.35), residues: 187
  sheet: -4.15 (0.64), residues: 43
  loop : -2.03 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 300 
 TYR   0.027   0.003   TYR A 412 
 PHE   0.025   0.003   PHE A 406 
 TRP   0.020   0.002   TRP A 235 
 HIS   0.014   0.002   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.21 ( 7780)
  covalent geometry    : angle       0.78154 /  0.42 (11290)
  hydrogen bonds       : bond        0.08478 /  5.44 (  281)
  hydrogen bonds       : angle       4.78226 /  3.38 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.5597 (OUTLIER) cc_final: 0.5248 (t80)
REVERT: A  286 ARG cc_start: 0.7673 (ptt90) cc_final: 0.7101 (ptt-90)
  outliers start: 12
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0940
  time to fit residues: 6.5435
Evaluate side-chains
  48 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  412 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 56 optimal weight:   30.0000
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.228597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.195532 restraints weight = 13286.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.195853 restraints weight = 21321.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.197492 restraints weight = 17347.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.199325 restraints weight = 10855.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.199532 restraints weight = 9094.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.4611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5976
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7780  Z= 0.166
  Angle     :  0.705   9.755  11290  Z= 0.380
  Chirality :  0.047   0.322   1329
  Planarity :  0.006   0.058    845
  Dihedral  : 27.214 140.089   2801
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.47 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.37), residues: 476
  helix: -0.47 (0.37), residues: 187
  sheet: -3.92 (0.67), residues: 43
  loop : -1.91 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 393 
 TYR   0.021   0.002   TYR A 412 
 PHE   0.025   0.002   PHE A 406 
 TRP   0.013   0.002   TRP A 235 
 HIS   0.020   0.003   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.17 ( 7780)
  covalent geometry    : angle       0.70462 /  0.38 (11290)
  hydrogen bonds       : bond        0.07395 /  4.86 (  281)
  hydrogen bonds       : angle       4.47292 /  3.16 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.5408 (OUTLIER) cc_final: 0.4826 (t80)
REVERT: A  286 ARG cc_start: 0.7674 (ptt90) cc_final: 0.7179 (ptt-90)
  outliers start: 10
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0852
  time to fit residues: 6.4268
Evaluate side-chains
  50 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:   50.0000
   chunk 11 optimal weight:    0.0050
   chunk 9 optimal weight:    0.5980
   chunk 48 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 40 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   overall best weight:    1.6198

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.226921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.195620 restraints weight = 13303.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.199241 restraints weight = 20900.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.198319 restraints weight = 9651.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.198431 restraints weight = 8979.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.198568 restraints weight = 8521.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.4610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5973
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7780  Z= 0.199
  Angle     :  0.722  10.319  11290  Z= 0.387
  Chirality :  0.048   0.324   1329
  Planarity :  0.006   0.053    845
  Dihedral  : 27.177 140.890   2801
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.21 %
    Favored  : 73.58 %
  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: -2.28 (0.37), residues: 476
  helix: -0.41 (0.37), residues: 187
  sheet: -4.03 (0.65), residues: 43
  loop : -1.91 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 393 
 TYR   0.029   0.003   TYR A 412 
 PHE   0.029   0.002   PHE A 143 
 TRP   0.010   0.002   TRP A 235 
 HIS   0.019   0.003   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.20 ( 7780)
  covalent geometry    : angle       0.72229 /  0.39 (11290)
  hydrogen bonds       : bond        0.07616 /  5.00 (  281)
  hydrogen bonds       : angle       4.38854 /  3.12 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5178 (t80)
REVERT: A   49 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.6018 (t-90)
REVERT: A  252 LEU cc_start: 0.4334 (OUTLIER) cc_final: 0.4016 (tp)
REVERT: A  286 ARG cc_start: 0.7622 (ptt90) cc_final: 0.7401 (ptt90)
  outliers start: 13
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0896
  time to fit residues: 6.7049
Evaluate side-chains
  54 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  412 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0040
   chunk 51 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0970
   chunk 55 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.5992

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.229433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.196811 restraints weight = 13028.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.198149 restraints weight = 22053.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.199992 restraints weight = 17254.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.200410 restraints weight = 10741.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.201103 restraints weight = 9636.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.4647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7780  Z= 0.142
  Angle     :  0.691  16.228  11290  Z= 0.367
  Chirality :  0.045   0.329   1329
  Planarity :  0.005   0.046    845
  Dihedral  : 27.099 141.521   2801
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 23.95 %
    Favored  : 73.83 %
  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: -2.15 (0.37), residues: 476
  helix: -0.35 (0.37), residues: 187
  sheet: -3.85 (0.66), residues: 43
  loop : -1.82 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 132 
 TYR   0.019   0.002   TYR A 342 
 PHE   0.016   0.002   PHE A  37 
 TRP   0.014   0.002   TRP A  69 
 HIS   0.021   0.003   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.14 ( 7780)
  covalent geometry    : angle       0.69070 /  0.37 (11290)
  hydrogen bonds       : bond        0.06843 /  4.53 (  281)
  hydrogen bonds       : angle       4.19549 /  2.98 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.5175 (OUTLIER) cc_final: 0.4487 (t80)
REVERT: A  252 LEU cc_start: 0.4357 (OUTLIER) cc_final: 0.3815 (tp)
REVERT: A  286 ARG cc_start: 0.7563 (ptt90) cc_final: 0.7354 (ptt90)
  outliers start: 9
  outliers final: 7
  residues processed: 53
  average time/residue: 0.0910
  time to fit residues: 6.5579
Evaluate side-chains
  53 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  447 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 48 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 20 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.226934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.190228 restraints weight = 12728.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.191854 restraints weight = 17823.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.194115 restraints weight = 12246.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.193968 restraints weight = 8723.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.194839 restraints weight = 8077.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5930
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7780  Z= 0.141
  Angle     :  0.668  14.499  11290  Z= 0.356
  Chirality :  0.044   0.331   1329
  Planarity :  0.005   0.043    845
  Dihedral  : 27.025 142.476   2801
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 24.20 %
    Favored  : 73.09 %
  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: -2.08 (0.38), residues: 476
  helix: -0.32 (0.36), residues: 190
  sheet: -3.98 (0.58), residues: 50
  loop : -1.62 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 349 
 TYR   0.022   0.002   TYR A 342 
 PHE   0.017   0.002   PHE A 143 
 TRP   0.011   0.002   TRP A  69 
 HIS   0.003   0.001   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 ( 7780)
  covalent geometry    : angle       0.66792 /  0.36 (11290)
  hydrogen bonds       : bond        0.06604 /  4.40 (  281)
  hydrogen bonds       : angle       4.06066 /  2.89 (  672)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.5469 (OUTLIER) cc_final: 0.4828 (t80)
REVERT: A  286 ARG cc_start: 0.7777 (ptt90) cc_final: 0.7506 (ptt90)
  outliers start: 11
  outliers final: 8
  residues processed: 52
  average time/residue: 0.0951
  time to fit residues: 6.7410
Evaluate side-chains
  51 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  447 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 392 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.223936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.186595 restraints weight = 12754.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.186421 restraints weight = 15874.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.187860 restraints weight = 12446.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.190042 restraints weight = 8547.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.190118 restraints weight = 7568.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.4439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7780  Z= 0.194
  Angle     :  0.706  14.975  11290  Z= 0.375
  Chirality :  0.047   0.331   1329
  Planarity :  0.006   0.049    845
  Dihedral  : 27.049 142.857   2801
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.44 %
    Favored  : 72.59 %
  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: -2.25 (0.37), residues: 476
  helix: -0.36 (0.36), residues: 190
  sheet: -4.27 (0.55), residues: 50
  loop : -1.77 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 393 
 TYR   0.029   0.003   TYR A 412 
 PHE   0.031   0.002   PHE A 143 
 TRP   0.034   0.003   TRP A 235 
 HIS   0.014   0.003   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.19 ( 7780)
  covalent geometry    : angle       0.70566 /  0.38 (11290)
  hydrogen bonds       : bond        0.07181 /  4.72 (  281)
  hydrogen bonds       : angle       4.15842 /  2.95 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1161.47 seconds
wall clock time: 20 minutes 55.10 seconds (1255.10 seconds total)