Starting phenix.real_space_refine
on Tue Feb  3 22:00:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jfq_61436/02_2026/9jfq_61436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jfq_61436/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jfq_61436/02_2026/9jfq_61436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jfq_61436/02_2026/9jfq_61436.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jfq_61436/02_2026/9jfq_61436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jfq_61436/02_2026/9jfq_61436.cif"
  }
  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-2.0-5952/lib/python3.9/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: 1.95, per 1000 atoms: 0.27
  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: 0.77
  Conformation dependent library (CDL) restraints added in 167.6 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: 1.42
  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: 1.43

  Time building geometry restraints manager: 0.98 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=" CG1 ILE A 356 "
       pdb=" CD1 ILE A 356 "
    ideal  model  delta    sigma   weight residual
    1.513  1.439  0.074 3.90e-02 6.57e+02 3.62e+00
  bond pdb=" O3'   U F  23 "
       pdb=" P     G F  24 "
    ideal  model  delta    sigma   weight residual
    1.607  1.630 -0.023 1.50e-02 4.44e+03 2.40e+00
  bond pdb=" N   ARG A 300 "
       pdb=" CA  ARG A 300 "
    ideal  model  delta    sigma   weight residual
    1.459  1.442  0.017 1.19e-02 7.06e+03 2.13e+00
  bond pdb=" O5'   C F  17 "
       pdb=" C5'   C F  17 "
    ideal  model  delta    sigma   weight residual
    1.420  1.439 -0.019 1.50e-02 4.44e+03 1.67e+00
  bond pdb=" C   PHE A 299 "
       pdb=" N   ARG A 300 "
    ideal  model  delta    sigma   weight residual
    1.334  1.318  0.016 1.27e-02 6.20e+03 1.60e+00
  ... (remaining 7775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 10879
        1.56 -     3.12: 354
        3.12 -     4.68: 44
        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=" C4'   U F  23 "
        pdb=" C3'   U F  23 "
        pdb=" O3'   U F  23 "
      ideal   model   delta    sigma   weight residual
     109.40  116.05   -6.65 1.50e+00 4.44e-01 1.96e+01
  angle pdb=" N   ARG A 300 "
        pdb=" CA  ARG A 300 "
        pdb=" C   ARG A 300 "
      ideal   model   delta    sigma   weight residual
     111.07  106.79    4.28 1.07e+00 8.73e-01 1.60e+01
  angle pdb=" O3'   C F  76 "
        pdb=" C3'   C F  76 "
        pdb=" C2'   C F  76 "
      ideal   model   delta    sigma   weight residual
     109.50  115.21   -5.71 1.50e+00 4.44e-01 1.45e+01
  angle pdb=" C   LYS A 411 "
        pdb=" N   TYR A 412 "
        pdb=" CA  TYR A 412 "
      ideal   model   delta    sigma   weight residual
     122.06  115.11    6.95 1.86e+00 2.89e-01 1.40e+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: 1136
       0.052 -    0.105: 156
       0.105 -    0.157: 28
       0.157 -    0.209: 6
       0.209 -    0.261: 3
  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=" P     A F  78 "
            pdb=" OP1   A F  78 "
            pdb=" OP2   A F  78 "
            pdb=" O5'   A F  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.62   -0.21 2.00e-01 2.50e+01 1.11e+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:             1.600
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.330
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5826
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= 0.166
  Angle     :  0.649   7.795  11290  Z= 0.368
  Chirality :  0.040   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
  covalent geometry    : bond        0.00352 ( 7780)
  covalent geometry    : angle       0.64899 (11290)
  hydrogen bonds       : bond        0.13532 (  281)
  hydrogen bonds       : angle       5.56350 (  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  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  354 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7122 (ttp80)
  outliers start: 1
  outliers final: 1
  residues processed: 59
  average time/residue: 0.1003
  time to fit residues: 7.4046
Evaluate side-chains
  46 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:   20.0000
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4864 r_free = 0.4864 target = 0.221086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.190850 restraints weight = 13144.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.193258 restraints weight = 25233.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.193396 restraints weight = 12472.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.193448 restraints weight = 10098.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.193752 restraints weight = 9417.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.4560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5979
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.106   7780  Z= 0.428
  Angle     :  0.993  10.158  11290  Z= 0.513
  Chirality :  0.053   0.338   1329
  Planarity :  0.008   0.093    845
  Dihedral  : 27.764 154.792   2805
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 25.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.18 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 11.60 %
    Favored  : 85.19 %
  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 (0.35), residues: 476
  helix: -0.69 (0.35), residues: 191
  sheet: -4.28 (0.63), residues: 43
  loop : -2.11 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 176 
 TYR   0.055   0.005   TYR A 412 
 PHE   0.049   0.004   PHE A 143 
 TRP   0.012   0.003   TRP A 235 
 HIS   0.020   0.004   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00945 ( 7780)
  covalent geometry    : angle       0.99265 (11290)
  hydrogen bonds       : bond        0.09826 (  281)
  hydrogen bonds       : angle       5.07862 (  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
  62 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   49 HIS cc_start: 0.6765 (OUTLIER) cc_final: 0.6211 (t-90)
REVERT: A  286 ARG cc_start: 0.7551 (ptt90) cc_final: 0.7173 (ptt90)
  outliers start: 13
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1018
  time to fit residues: 7.5432
Evaluate side-chains
  51 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
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   91 ILE
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  254 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 42 optimal weight:   30.0000
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.229159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.198233 restraints weight = 13115.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.197144 restraints weight = 18938.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.198747 restraints weight = 14847.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.198853 restraints weight = 10207.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.199079 restraints weight = 11343.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.4636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5800
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7780  Z= 0.163
  Angle     :  0.665   9.644  11290  Z= 0.355
  Chirality :  0.039   0.230   1329
  Planarity :  0.005   0.043    845
  Dihedral  : 27.298 169.911   2801
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.33 %
    Favored  : 83.70 %
  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: -1.92 (0.37), residues: 476
  helix: -0.17 (0.37), residues: 187
  sheet: -4.03 (0.65), residues: 37
  loop : -1.69 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 132 
 TYR   0.020   0.002   TYR A 412 
 PHE   0.017   0.002   PHE A 143 
 TRP   0.010   0.002   TRP A 235 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7780)
  covalent geometry    : angle       0.66486 (11290)
  hydrogen bonds       : bond        0.06261 (  281)
  hydrogen bonds       : angle       4.16580 (  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
  62 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  286 ARG cc_start: 0.7638 (ptt90) cc_final: 0.7238 (ptt90)
  outliers start: 12
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0771
  time to fit residues: 5.7089
Evaluate side-chains
  49 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4886 r_free = 0.4886 target = 0.223577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.190167 restraints weight = 13319.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.192668 restraints weight = 23516.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.193643 restraints weight = 14401.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.193973 restraints weight = 10419.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.195831 restraints weight = 9889.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5971
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.078   7780  Z= 0.332
  Angle     :  0.850  10.944  11290  Z= 0.442
  Chirality :  0.048   0.273   1329
  Planarity :  0.007   0.064    845
  Dihedral  : 27.525 155.948   2801
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 20.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.34 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 15.56 %
    Favored  : 79.75 %
  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: -2.20 (0.37), residues: 476
  helix: -0.53 (0.36), residues: 196
  sheet: -4.02 (0.68), residues: 43
  loop : -1.71 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 176 
 TYR   0.042   0.004   TYR A 412 
 PHE   0.041   0.003   PHE A 143 
 TRP   0.011   0.003   TRP A 235 
 HIS   0.018   0.003   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 ( 7780)
  covalent geometry    : angle       0.84979 (11290)
  hydrogen bonds       : bond        0.08369 (  281)
  hydrogen bonds       : angle       4.48398 (  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
  63 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.5794 (OUTLIER) cc_final: 0.5451 (t80)
REVERT: A   49 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.5811 (t-90)
REVERT: A  173 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6165 (mp)
REVERT: A  286 ARG cc_start: 0.7704 (ptt90) cc_final: 0.7349 (ptt90)
  outliers start: 19
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0974
  time to fit residues: 7.3013
Evaluate side-chains
  54 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
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  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  361 ASP
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  398 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4826 r_free = 0.4826 target = 0.222280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.184879 restraints weight = 12733.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.184466 restraints weight = 17401.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.186486 restraints weight = 12786.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.186975 restraints weight = 8529.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.187773 restraints weight = 7947.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6010
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   7780  Z= 0.226
  Angle     :  0.731   9.913  11290  Z= 0.386
  Chirality :  0.043   0.239   1329
  Planarity :  0.006   0.048    845
  Dihedral  : 27.404 157.025   2801
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 17.28 %
    Favored  : 78.52 %
  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: -1.91 (0.38), residues: 476
  helix: -0.28 (0.37), residues: 190
  sheet: -3.75 (0.71), residues: 43
  loop : -1.56 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 163 
 TYR   0.029   0.003   TYR A 412 
 PHE   0.029   0.002   PHE A 143 
 TRP   0.011   0.002   TRP A 235 
 HIS   0.028   0.004   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 7780)
  covalent geometry    : angle       0.73061 (11290)
  hydrogen bonds       : bond        0.06963 (  281)
  hydrogen bonds       : angle       4.18786 (  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
  60 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5515 (t-90)
REVERT: A  286 ARG cc_start: 0.7946 (ptt90) cc_final: 0.7629 (ptt90)
  outliers start: 17
  outliers final: 9
  residues processed: 54
  average time/residue: 0.0928
  time to fit residues: 6.5986
Evaluate side-chains
  49 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
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  169 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  361 ASP
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  412 TYR
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:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 47 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 46 optimal weight:    9.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4820 r_free = 0.4820 target = 0.221467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.182660 restraints weight = 12778.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.184433 restraints weight = 18986.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.185762 restraints weight = 13323.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.187879 restraints weight = 8933.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.188083 restraints weight = 7722.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6019
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   7780  Z= 0.241
  Angle     :  0.748  10.533  11290  Z= 0.393
  Chirality :  0.044   0.245   1329
  Planarity :  0.006   0.043    845
  Dihedral  : 27.387 157.124   2801
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 19.01 %
    Favored  : 76.30 %
  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: -1.88 (0.38), residues: 476
  helix: -0.18 (0.37), residues: 184
  sheet: -3.73 (0.71), residues: 43
  loop : -1.58 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 393 
 TYR   0.033   0.003   TYR A 412 
 PHE   0.032   0.003   PHE A 143 
 TRP   0.010   0.002   TRP A 235 
 HIS   0.031   0.004   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 7780)
  covalent geometry    : angle       0.74838 (11290)
  hydrogen bonds       : bond        0.07160 (  281)
  hydrogen bonds       : angle       4.17287 (  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
  65 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.5432 (t80)
REVERT: A   49 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5547 (t-90)
REVERT: A  286 ARG cc_start: 0.7971 (ptt90) cc_final: 0.7678 (ptt90)
REVERT: A  354 ARG cc_start: 0.7147 (ttp-170) cc_final: 0.6521 (ttp80)
  outliers start: 19
  outliers final: 11
  residues processed: 56
  average time/residue: 0.0806
  time to fit residues: 6.0567
Evaluate side-chains
  56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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  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  191 THR
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  412 TYR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 392 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.228014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.190884 restraints weight = 12880.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.190311 restraints weight = 15333.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.192246 restraints weight = 11896.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.192660 restraints weight = 8770.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.193428 restraints weight = 8901.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5879
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7780  Z= 0.151
  Angle     :  0.647   9.786  11290  Z= 0.342
  Chirality :  0.039   0.223   1329
  Planarity :  0.005   0.043    845
  Dihedral  : 27.125 178.712   2801
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.22 %
    Favored  : 75.56 %
  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: -1.54 (0.39), residues: 476
  helix:  0.12 (0.38), residues: 185
  sheet: -3.47 (0.75), residues: 43
  loop : -1.42 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 393 
 TYR   0.019   0.002   TYR A 364 
 PHE   0.016   0.002   PHE A 143 
 TRP   0.010   0.001   TRP A  69 
 HIS   0.043   0.004   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7780)
  covalent geometry    : angle       0.64709 (11290)
  hydrogen bonds       : bond        0.05821 (  281)
  hydrogen bonds       : angle       3.79201 (  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
  56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 ARG cc_start: 0.7866 (ptt90) cc_final: 0.7598 (ptt90)
  outliers start: 9
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0981
  time to fit residues: 6.7621
Evaluate side-chains
  51 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  447 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:   30.0000
   chunk 11 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0070
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0170
   chunk 54 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 40 optimal weight:    0.5980
   chunk 44 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8238

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.227483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.189240 restraints weight = 12845.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.189648 restraints weight = 15968.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.191333 restraints weight = 12519.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.193341 restraints weight = 8527.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.193543 restraints weight = 7354.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5891
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7780  Z= 0.154
  Angle     :  0.648   9.795  11290  Z= 0.340
  Chirality :  0.039   0.221   1329
  Planarity :  0.005   0.041    845
  Dihedral  : 27.105 178.521   2801
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  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 : 0.00 %

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: -1.51 (0.39), residues: 476
  helix:  0.17 (0.37), residues: 191
  sheet: -3.48 (0.75), residues: 43
  loop : -1.46 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 360 
 TYR   0.026   0.002   TYR A 364 
 PHE   0.020   0.002   PHE A 143 
 TRP   0.018   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7780)
  covalent geometry    : angle       0.64781 (11290)
  hydrogen bonds       : bond        0.05752 (  281)
  hydrogen bonds       : angle       3.72981 (  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
  56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.5377 (OUTLIER) cc_final: 0.4840 (t80)
REVERT: A   49 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5425 (t-90)
REVERT: A  286 ARG cc_start: 0.7921 (ptt90) cc_final: 0.7610 (ptt90)
  outliers start: 12
  outliers final: 8
  residues processed: 52
  average time/residue: 0.0930
  time to fit residues: 6.4197
Evaluate side-chains
  51 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  107 LEU
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  447 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 30 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 5 optimal weight:    0.4980
   chunk 55 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 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 = 0.4828 r_free = 0.4828 target = 0.222305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.185912 restraints weight = 12663.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.186558 restraints weight = 16327.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.187585 restraints weight = 14242.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.187977 restraints weight = 8988.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.188507 restraints weight = 8080.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6000
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   7780  Z= 0.249
  Angle     :  0.751   9.884  11290  Z= 0.393
  Chirality :  0.044   0.246   1329
  Planarity :  0.006   0.042    845
  Dihedral  : 27.273 172.124   2801
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.74 %
    Favored  : 76.30 %
  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: -1.84 (0.38), residues: 476
  helix: -0.02 (0.38), residues: 186
  sheet: -3.97 (0.63), residues: 50
  loop : -1.52 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 393 
 TYR   0.034   0.003   TYR A 412 
 PHE   0.034   0.002   PHE A 143 
 TRP   0.015   0.002   TRP A 235 
 HIS   0.005   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 7780)
  covalent geometry    : angle       0.75135 (11290)
  hydrogen bonds       : bond        0.07108 (  281)
  hydrogen bonds       : angle       4.09101 (  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
  53 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.5268 (t80)
REVERT: A   49 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5512 (t-90)
REVERT: A  286 ARG cc_start: 0.7855 (ptt90) cc_final: 0.7596 (ptt90)
  outliers start: 12
  outliers final: 9
  residues processed: 49
  average time/residue: 0.0943
  time to fit residues: 6.2279
Evaluate side-chains
  51 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  107 LEU
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  398 LEU
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  417 ILE
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:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.227904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.193482 restraints weight = 12772.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.194178 restraints weight = 16135.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.196082 restraints weight = 11555.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.195985 restraints weight = 8132.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.196672 restraints weight = 7749.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5788
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7780  Z= 0.152
  Angle     :  0.665  12.682  11290  Z= 0.345
  Chirality :  0.040   0.240   1329
  Planarity :  0.005   0.041    845
  Dihedral  : 27.074 176.313   2801
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.72 %
    Favored  : 74.57 %
  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: -1.58 (0.39), residues: 476
  helix:  0.11 (0.38), residues: 187
  sheet: -3.56 (0.74), residues: 43
  loop : -1.47 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 360 
 TYR   0.031   0.002   TYR A 364 
 PHE   0.022   0.002   PHE A 406 
 TRP   0.018   0.002   TRP A 235 
 HIS   0.002   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7780)
  covalent geometry    : angle       0.66507 (11290)
  hydrogen bonds       : bond        0.05694 (  281)
  hydrogen bonds       : angle       3.87775 (  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
  52 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   49 HIS cc_start: 0.6164 (OUTLIER) cc_final: 0.5273 (t-90)
REVERT: A  164 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6241 (tp)
REVERT: A  286 ARG cc_start: 0.7884 (ptt90) cc_final: 0.7594 (ptt90)
REVERT: A  346 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6287 (tp40)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0904
  time to fit residues: 5.6403
Evaluate side-chains
  49 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
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  164 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  412 TYR
Chi-restraints excluded: chain A residue  417 ILE
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:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.227025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.189478 restraints weight = 12816.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.188620 restraints weight = 16907.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.191409 restraints weight = 12740.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.191959 restraints weight = 8262.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.192863 restraints weight = 7893.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.141   7780  Z= 0.218
  Angle     :  0.979  59.197  11290  Z= 0.553
  Chirality :  0.041   0.315   1329
  Planarity :  0.005   0.041    845
  Dihedral  : 27.071 176.677   2801
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 23.46 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.22 %
  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: -1.63 (0.39), residues: 476
  helix:  0.03 (0.38), residues: 187
  sheet: -3.55 (0.74), residues: 43
  loop : -1.47 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 360 
 TYR   0.027   0.003   TYR A 364 
 PHE   0.023   0.002   PHE A 143 
 TRP   0.014   0.002   TRP A 235 
 HIS   0.003   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 7780)
  covalent geometry    : angle       0.97937 (11290)
  hydrogen bonds       : bond        0.05770 (  281)
  hydrogen bonds       : angle       3.91778 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1035.84 seconds
wall clock time: 18 minutes 38.71 seconds (1118.71 seconds total)