Starting phenix.real_space_refine
on Fri Aug 22 15:16:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y56_38930/08_2025/8y56_38930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y56_38930/08_2025/8y56_38930.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y56_38930/08_2025/8y56_38930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y56_38930/08_2025/8y56_38930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y56_38930/08_2025/8y56_38930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y56_38930/08_2025/8y56_38930.cif"
  }
  resolution = 2.83
  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=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      28      5.16       5
     Na      1      4.78       5
     C    3252      2.51       5
     N     718      2.21       5
     O     796      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4796
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 4601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4601
          Classifications: {'peptide': 586}
          Link IDs: {'PTRANS': 22, 'TRANS': 563}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 195
          Unusual residues: {' NA': 1, 'CLR': 5, 'DKB': 1}
          Classifications: {'undetermined': 7, 'water': 5}
          Link IDs: {None: 11}
  Time building chain proxies: 1.29, per 1000 atoms: 0.27
  Number of scatterers: 4796
  At special positions: 0
  Unit cell: (72.54, 63.24, 96.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      28     16.00
     P       1     15.00
     Na      1     11.00
     O     796      8.00
     N     718      7.00
     C    3252      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: 0.36
  Conformation dependent library (CDL) restraints added in 197.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1096

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      88.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'R' and resid 38 through 40
      No H-bonds generated for 'chain 'R' and resid 38 through 40'
    Processing helix  chain 'R' and resid 41 through 62
    Processing helix  chain 'R' and resid 66 through 80
      removed outlier: 3.575A  pdb=" N   PHE R  76 " --> pdb=" O   GLY R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 80 through 92
      removed outlier: 3.828A  pdb=" N   VAL R  92 " --> pdb=" O   LYS R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 98
      removed outlier: 3.505A  pdb=" N   ASN R  97 " --> pdb=" O   ASN R  94 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL R  98 " --> pdb=" O   PHE R  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 94 through 98'
    Processing helix  chain 'R' and resid 99 through 124
      removed outlier: 4.035A  pdb=" N   LEU R 103 " --> pdb=" O   ASP R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 128
      No H-bonds generated for 'chain 'R' and resid 126 through 128'
    Processing helix  chain 'R' and resid 129 through 143
      removed outlier: 3.746A  pdb=" N   LYS R 133 " --> pdb=" O   SER R 129 " (cutoff:3.500A)
      Proline residue:  R 138  - end of helix
    Processing helix  chain 'R' and resid 149 through 158
      removed outlier: 3.889A  pdb=" N   ILE R 153 " --> pdb=" O   LEU R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 164 through 196
      removed outlier: 4.041A  pdb=" N   TYR R 168 " --> pdb=" O   GLU R 164 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ILE R 169 " --> pdb=" O   TYR R 165 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   TYR R 170 " --> pdb=" O   LEU R 166 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU R 171 " --> pdb=" O   GLN R 167 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA R 173 " --> pdb=" O   ILE R 169 " (cutoff:3.500A)
      Proline residue:  R 174  - end of helix
      Proline residue:  R 182  - end of helix
    Processing helix  chain 'R' and resid 197 through 201
    Processing helix  chain 'R' and resid 202 through 217
      removed outlier: 3.725A  pdb=" N   VAL R 214 " --> pdb=" O   GLY R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 233
      removed outlier: 3.540A  pdb=" N   PHE R 221 " --> pdb=" O   ASN R 217 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL R 223 " --> pdb=" O   ILE R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 250
    Processing helix  chain 'R' and resid 251 through 264
      removed outlier: 3.590A  pdb=" N   SER R 255 " --> pdb=" O   SER R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 288
    Processing helix  chain 'R' and resid 288 through 302
      removed outlier: 3.562A  pdb=" N   LEU R 300 " --> pdb=" O   GLU R 296 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 322
    Processing helix  chain 'R' and resid 326 through 337
      removed outlier: 4.290A  pdb=" N   ALA R 330 " --> pdb=" O   ALA R 326 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE R 331 " --> pdb=" O   PRO R 327 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 339 through 367
      removed outlier: 3.996A  pdb=" N   ALA R 355 " --> pdb=" O   THR R 351 " (cutoff:3.500A)
      Proline residue:  R 356  - end of helix
      removed outlier: 3.620A  pdb=" N   THR R 366 " --> pdb=" O   ALA R 362 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 370
      No H-bonds generated for 'chain 'R' and resid 368 through 370'
    Processing helix  chain 'R' and resid 371 through 404
      removed outlier: 3.551A  pdb=" N   VAL R 389 " --> pdb=" O   ASP R 385 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER R 404 " --> pdb=" O   ILE R 400 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 408
    Processing helix  chain 'R' and resid 409 through 436
      removed outlier: 3.687A  pdb=" N   LEU R 414 " --> pdb=" O   LEU R 410 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE R 434 " --> pdb=" O   MET R 430 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 439 through 474
      removed outlier: 3.515A  pdb=" N   LEU R 445 " --> pdb=" O   VAL R 441 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER R 453 " --> pdb=" O   LEU R 449 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLY R 462 " --> pdb=" O   TYR R 458 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 480 through 502
      Proline residue:  R 492  - end of helix
    Processing helix  chain 'R' and resid 517 through 546
      removed outlier: 3.882A  pdb=" N   MET R 521 " --> pdb=" O   GLY R 517 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 654 through 682
    Processing helix  chain 'R' and resid 688 through 711
      removed outlier: 3.564A  pdb=" N   PHE R 701 " --> pdb=" O   ALA R 697 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   GLY R 704 " --> pdb=" O   ASN R 700 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   PHE R 705 " --> pdb=" O   PHE R 701 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ILE R 710 " --> pdb=" O   ILE R 706 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 719 through 724

    355 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.69

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 691
        1.30 -     1.42: 1249
        1.42 -     1.55: 2920
        1.55 -     1.68: 10
        1.68 -     1.81: 45
  Bond restraints: 4915
  Sorted by residual:
  bond pdb=" C39 DKB R 907 "
       pdb=" C40 DKB R 907 "
    ideal  model  delta    sigma   weight residual
    1.526  1.294  0.232 2.00e-02 2.50e+03 1.35e+02
  bond pdb=" CA  GLY R 704 "
       pdb=" C   GLY R 704 "
    ideal  model  delta    sigma   weight residual
    1.516  1.448  0.068 1.12e-02 7.97e+03 3.74e+01
  bond pdb=" CA  ARG R 295 "
       pdb=" C   ARG R 295 "
    ideal  model  delta    sigma   weight residual
    1.522  1.448  0.074 1.37e-02 5.33e+03 2.91e+01
  bond pdb=" CA  PHE R 708 "
       pdb=" CB  PHE R 708 "
    ideal  model  delta    sigma   weight residual
    1.531  1.448  0.083 1.56e-02 4.11e+03 2.82e+01
  bond pdb=" C   ARG R 295 "
       pdb=" O   ARG R 295 "
    ideal  model  delta    sigma   weight residual
    1.236  1.170  0.066 1.32e-02 5.74e+03 2.50e+01
  ... (remaining 4910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 6552
        2.14 -     4.28: 118
        4.28 -     6.42: 21
        6.42 -     8.57: 3
        8.57 -    10.71: 2
  Bond angle restraints: 6696
  Sorted by residual:
  angle pdb=" C   PHE R 705 "
        pdb=" N   ILE R 706 "
        pdb=" CA  ILE R 706 "
      ideal   model   delta    sigma   weight residual
     120.46  112.31    8.15 1.37e+00 5.33e-01 3.54e+01
  angle pdb=" N   ILE R 706 "
        pdb=" CA  ILE R 706 "
        pdb=" CB  ILE R 706 "
      ideal   model   delta    sigma   weight residual
     110.54  118.51   -7.97 1.36e+00 5.41e-01 3.43e+01
  angle pdb=" CA  ILE R 706 "
        pdb=" C   ILE R 706 "
        pdb=" N   SER R 707 "
      ideal   model   delta    sigma   weight residual
     117.15  122.15   -5.00 1.14e+00 7.69e-01 1.93e+01
  angle pdb=" N   PHE R 705 "
        pdb=" CA  PHE R 705 "
        pdb=" C   PHE R 705 "
      ideal   model   delta    sigma   weight residual
     111.36  106.61    4.75 1.09e+00 8.42e-01 1.90e+01
  angle pdb=" N   ILE R 706 "
        pdb=" CA  ILE R 706 "
        pdb=" C   ILE R 706 "
      ideal   model   delta    sigma   weight residual
     110.62  114.88   -4.26 1.02e+00 9.61e-01 1.74e+01
  ... (remaining 6691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.00: 3049
       35.00 -    70.00: 74
       70.00 -   105.01: 11
      105.01 -   140.01: 1
      140.01 -   175.01: 1
  Dihedral angle restraints: 3136
    sinusoidal: 1436
      harmonic: 1700
  Sorted by residual:
  dihedral pdb=" C12 DKB R 907 "
           pdb=" C13 DKB R 907 "
           pdb=" C14 DKB R 907 "
           pdb=" C15 DKB R 907 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -75.25   99.76 -175.01     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" N   ILE R 706 "
           pdb=" C   ILE R 706 "
           pdb=" CA  ILE R 706 "
           pdb=" CB  ILE R 706 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  134.81  -11.41     0      2.50e+00 1.60e-01 2.08e+01
  dihedral pdb=" C   PHE R 708 "
           pdb=" N   PHE R 708 "
           pdb=" CA  PHE R 708 "
           pdb=" CB  PHE R 708 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.80  -10.80     0      2.50e+00 1.60e-01 1.86e+01
  ... (remaining 3133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 717
       0.064 -    0.128: 84
       0.128 -    0.191: 4
       0.191 -    0.255: 3
       0.255 -    0.319: 1
  Chirality restraints: 809
  Sorted by residual:
  chirality pdb=" C13 CLR R 904 "
            pdb=" C12 CLR R 904 "
            pdb=" C14 CLR R 904 "
            pdb=" C17 CLR R 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.61   -0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CA  ILE R 706 "
            pdb=" N   ILE R 706 "
            pdb=" C   ILE R 706 "
            pdb=" CB  ILE R 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.19    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" C10 CLR R 904 "
            pdb=" C1  CLR R 904 "
            pdb=" C5  CLR R 904 "
            pdb=" C9  CLR R 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.63   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 806 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 708 "    0.026 2.00e-02 2.50e+03   2.02e-02 7.15e+00
        pdb=" CG  PHE R 708 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 708 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 708 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 708 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 708 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 708 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 294 "   -0.010 2.00e-02 2.50e+03   1.93e-02 3.74e+00
        pdb=" C   CYS R 294 "    0.033 2.00e-02 2.50e+03
        pdb=" O   CYS R 294 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG R 295 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 705 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   PHE R 705 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE R 705 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ILE R 706 "    0.010 2.00e-02 2.50e+03
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1268
        2.80 -     3.33: 5075
        3.33 -     3.85: 7916
        3.85 -     4.38: 9963
        4.38 -     4.90: 16443
  Nonbonded interactions: 40665
  Sorted by model distance:
  nonbonded pdb=" O   LEU R  85 "
            pdb=" ND2 ASN R  89 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   SER R 390 "
            pdb=" OG  SER R 393 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG  SER R 144 "
            pdb=" OD1 ASP R 146 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   PHE R 384 "
            pdb=" OG  SER R 387 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" NZ  LYS R 133 "
            pdb=" OE2 GLU R 339 "
     model   vdw
     2.355 3.120
  ... (remaining 40660 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.050
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
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      :  0.006   0.232   4915  Z= 0.365
  Angle     :  0.727  10.706   6696  Z= 0.396
  Chirality :  0.044   0.319    809
  Planarity :  0.004   0.042    776
  Dihedral  : 15.556 175.010   2040
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  0.78 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.36 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.34), residues: 582
  helix:  1.04 (0.24), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.34 (0.52), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 295 
 TYR   0.010   0.001   TYR R 451 
 PHE   0.046   0.001   PHE R 708 
 TRP   0.008   0.001   TRP R 100 
 HIS   0.002   0.001   HIS R 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 4915)
  covalent geometry    : angle       0.72728 ( 6696)
  hydrogen bonds       : bond        0.24913 (  355)
  hydrogen bonds       : angle       7.25724 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.183 
Fit side-chains
REVERT: R  236 LYS cc_start: 0.7437 (mppt) cc_final: 0.7193 (mppt)
REVERT: R  529 PHE cc_start: 0.8051 (t80) cc_final: 0.7821 (t80)
  outliers start: 5
  outliers final: 1
  residues processed: 94
  average time/residue: 0.4887
  time to fit residues: 47.9722
Evaluate side-chains
  72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 337 ASN
R 544 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.153371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122179 restraints weight = 5393.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.93
r_work: 0.3313 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4915  Z= 0.175
  Angle     :  0.642   8.009   6696  Z= 0.319
  Chirality :  0.044   0.147    809
  Planarity :  0.005   0.046    776
  Dihedral  : 14.118 173.577    997
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.61 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.35), residues: 582
  helix:  1.77 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -1.04 (0.56), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 687 
 TYR   0.022   0.002   TYR R 451 
 PHE   0.030   0.002   PHE R 231 
 TRP   0.005   0.001   TRP R 396 
 HIS   0.003   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4915)
  covalent geometry    : angle       0.64162 ( 6696)
  hydrogen bonds       : bond        0.05418 (  355)
  hydrogen bonds       : angle       4.44149 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.186 
Fit side-chains
REVERT: R  120 LEU cc_start: 0.7952 (mt) cc_final: 0.7741 (mt)
REVERT: R  143 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8144 (mt0)
REVERT: R  276 PHE cc_start: 0.6339 (t80) cc_final: 0.6071 (m-10)
REVERT: R  301 LEU cc_start: 0.7669 (mm) cc_final: 0.7360 (mm)
REVERT: R  413 MET cc_start: 0.6752 (ttm) cc_final: 0.6417 (ttm)
REVERT: R  678 TRP cc_start: 0.6740 (t60) cc_final: 0.6010 (t60)
  outliers start: 11
  outliers final: 3
  residues processed: 79
  average time/residue: 0.4762
  time to fit residues: 39.4016
Evaluate side-chains
  75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  705 PHE
Chi-restraints excluded: chain R residue  713 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 GLN
R 506 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.153951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123127 restraints weight = 5328.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.89
r_work: 0.3396 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4915  Z= 0.153
  Angle     :  0.567   8.745   6696  Z= 0.283
  Chirality :  0.042   0.144    809
  Planarity :  0.005   0.046    776
  Dihedral  : 13.148 164.199    997
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 10.78 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.35), residues: 582
  helix:  1.92 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -0.95 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 235 
 TYR   0.019   0.001   TYR R 451 
 PHE   0.024   0.002   PHE R 221 
 TRP   0.004   0.001   TRP R 193 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4915)
  covalent geometry    : angle       0.56694 ( 6696)
  hydrogen bonds       : bond        0.04844 (  355)
  hydrogen bonds       : angle       4.17101 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8026 (mt) cc_final: 0.7803 (mt)
REVERT: R  143 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8124 (mt0)
REVERT: R  236 LYS cc_start: 0.7128 (mppt) cc_final: 0.6783 (mppt)
REVERT: R  276 PHE cc_start: 0.6445 (t80) cc_final: 0.6027 (m-10)
REVERT: R  280 ILE cc_start: 0.7948 (mt) cc_final: 0.7730 (mp)
REVERT: R  301 LEU cc_start: 0.7787 (mm) cc_final: 0.7509 (mm)
REVERT: R  303 LYS cc_start: 0.6752 (pptt) cc_final: 0.6540 (mmmt)
REVERT: R  381 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7233 (t0)
REVERT: R  678 TRP cc_start: 0.6685 (t60) cc_final: 0.6051 (t60)
  outliers start: 17
  outliers final: 5
  residues processed: 84
  average time/residue: 0.4884
  time to fit residues: 42.8550
Evaluate side-chains
  74 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 SER
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  381 ASN
Chi-restraints excluded: chain R residue  472 LYS
Chi-restraints excluded: chain R residue  713 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0670
   chunk 45 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.153823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.122990 restraints weight = 5324.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.88
r_work: 0.3391 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4915  Z= 0.146
  Angle     :  0.549   9.423   6696  Z= 0.275
  Chirality :  0.041   0.145    809
  Planarity :  0.005   0.047    776
  Dihedral  : 12.509 152.786    997
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.12 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.35), residues: 582
  helix:  2.06 (0.24), residues: 458
  sheet:  None (None), residues: 0
  loop : -1.03 (0.54), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 235 
 TYR   0.019   0.001   TYR R 451 
 PHE   0.022   0.001   PHE R 221 
 TRP   0.004   0.001   TRP R 193 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4915)
  covalent geometry    : angle       0.54854 ( 6696)
  hydrogen bonds       : bond        0.04500 (  355)
  hydrogen bonds       : angle       4.03304 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8068 (mt) cc_final: 0.7845 (mt)
REVERT: R  143 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8174 (mt0)
REVERT: R  276 PHE cc_start: 0.6401 (t80) cc_final: 0.6026 (m-10)
REVERT: R  280 ILE cc_start: 0.7930 (mt) cc_final: 0.7713 (mp)
REVERT: R  381 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7181 (t0)
REVERT: R  413 MET cc_start: 0.6769 (ttm) cc_final: 0.6425 (ttm)
REVERT: R  678 TRP cc_start: 0.6650 (t60) cc_final: 0.6022 (t60)
  outliers start: 14
  outliers final: 5
  residues processed: 76
  average time/residue: 0.4699
  time to fit residues: 37.3165
Evaluate side-chains
  69 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Chi-restraints excluded: chain R residue  472 LYS
Chi-restraints excluded: chain R residue  713 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.153928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.122827 restraints weight = 5401.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.90
r_work: 0.3331 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
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   0.035   4915  Z= 0.145
  Angle     :  0.567   9.585   6696  Z= 0.281
  Chirality :  0.041   0.145    809
  Planarity :  0.005   0.047    776
  Dihedral  : 11.927 140.444    997
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.31 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.35), residues: 582
  helix:  2.01 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -1.18 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 235 
 TYR   0.018   0.001   TYR R 451 
 PHE   0.022   0.001   PHE R 221 
 TRP   0.005   0.001   TRP R 193 
 HIS   0.003   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4915)
  covalent geometry    : angle       0.56691 ( 6696)
  hydrogen bonds       : bond        0.04345 (  355)
  hydrogen bonds       : angle       3.97169 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8126 (mt) cc_final: 0.7888 (mt)
REVERT: R  234 ASP cc_start: 0.6048 (t70) cc_final: 0.5736 (t70)
REVERT: R  235 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6430 (mtm-85)
REVERT: R  236 LYS cc_start: 0.7178 (mppt) cc_final: 0.6841 (mppt)
REVERT: R  246 ASP cc_start: 0.6821 (m-30) cc_final: 0.6350 (m-30)
REVERT: R  276 PHE cc_start: 0.6501 (t80) cc_final: 0.6098 (m-10)
REVERT: R  280 ILE cc_start: 0.7962 (mt) cc_final: 0.7746 (mp)
REVERT: R  381 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7055 (t0)
REVERT: R  413 MET cc_start: 0.6811 (ttm) cc_final: 0.6460 (ttm)
REVERT: R  511 ASP cc_start: 0.7647 (t0) cc_final: 0.7415 (t0)
REVERT: R  678 TRP cc_start: 0.6722 (t60) cc_final: 0.6153 (t60)
  outliers start: 16
  outliers final: 5
  residues processed: 86
  average time/residue: 0.4353
  time to fit residues: 39.3237
Evaluate side-chains
  74 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 SER
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 47 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0040
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.155353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.124075 restraints weight = 5445.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.92
r_work: 0.3372 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
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      :  0.003   0.033   4915  Z= 0.131
  Angle     :  0.564  10.541   6696  Z= 0.275
  Chirality :  0.041   0.144    809
  Planarity :  0.004   0.047    776
  Dihedral  : 11.295 127.879    997
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.90 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.35), residues: 582
  helix:  2.12 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -1.15 (0.56), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 235 
 TYR   0.016   0.001   TYR R 451 
 PHE   0.021   0.001   PHE R 221 
 TRP   0.004   0.001   TRP R 363 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4915)
  covalent geometry    : angle       0.56370 ( 6696)
  hydrogen bonds       : bond        0.04135 (  355)
  hydrogen bonds       : angle       3.91255 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.140 
Fit side-chains
REVERT: R  120 LEU cc_start: 0.8161 (mt) cc_final: 0.7918 (mt)
REVERT: R  235 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6593 (mtm-85)
REVERT: R  276 PHE cc_start: 0.6531 (t80) cc_final: 0.6091 (m-10)
REVERT: R  280 ILE cc_start: 0.7938 (mt) cc_final: 0.7733 (mp)
REVERT: R  381 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7178 (t0)
REVERT: R  385 ASP cc_start: 0.8209 (p0) cc_final: 0.7926 (m-30)
REVERT: R  413 MET cc_start: 0.6781 (ttm) cc_final: 0.6431 (ttm)
REVERT: R  511 ASP cc_start: 0.7659 (t0) cc_final: 0.7441 (t0)
REVERT: R  678 TRP cc_start: 0.6697 (t60) cc_final: 0.6100 (t60)
  outliers start: 14
  outliers final: 4
  residues processed: 88
  average time/residue: 0.4880
  time to fit residues: 45.0016
Evaluate side-chains
  72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 SER
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.153918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.122544 restraints weight = 5408.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.91
r_work: 0.3336 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4915  Z= 0.153
  Angle     :  0.593  10.939   6696  Z= 0.289
  Chirality :  0.042   0.145    809
  Planarity :  0.005   0.047    776
  Dihedral  : 10.896 125.991    994
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.88 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.35), residues: 582
  helix:  2.07 (0.24), residues: 463
  sheet:  None (None), residues: 0
  loop : -1.23 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 235 
 TYR   0.014   0.001   TYR R 451 
 PHE   0.023   0.001   PHE R 221 
 TRP   0.004   0.001   TRP R 363 
 HIS   0.003   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4915)
  covalent geometry    : angle       0.59346 ( 6696)
  hydrogen bonds       : bond        0.04323 (  355)
  hydrogen bonds       : angle       3.93834 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8185 (mt) cc_final: 0.7954 (mt)
REVERT: R  234 ASP cc_start: 0.6211 (t70) cc_final: 0.5816 (t70)
REVERT: R  235 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6553 (mtm-85)
REVERT: R  236 LYS cc_start: 0.7202 (mtmm) cc_final: 0.6825 (mppt)
REVERT: R  276 PHE cc_start: 0.6536 (t80) cc_final: 0.6072 (m-10)
REVERT: R  280 ILE cc_start: 0.7922 (mt) cc_final: 0.7717 (mp)
REVERT: R  381 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7186 (t0)
REVERT: R  385 ASP cc_start: 0.8271 (p0) cc_final: 0.7986 (m-30)
REVERT: R  413 MET cc_start: 0.6804 (ttm) cc_final: 0.6422 (ttm)
REVERT: R  511 ASP cc_start: 0.7665 (t0) cc_final: 0.7447 (t0)
REVERT: R  678 TRP cc_start: 0.6709 (t60) cc_final: 0.6113 (t60)
  outliers start: 11
  outliers final: 5
  residues processed: 78
  average time/residue: 0.3989
  time to fit residues: 32.8413
Evaluate side-chains
  72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 SER
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.154518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.123063 restraints weight = 5433.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.92
r_work: 0.3341 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4915  Z= 0.151
  Angle     :  0.591  11.494   6696  Z= 0.286
  Chirality :  0.042   0.145    809
  Planarity :  0.004   0.047    776
  Dihedral  : 10.722 121.667    994
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.88 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.35), residues: 582
  helix:  2.11 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.30 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 235 
 TYR   0.014   0.001   TYR R 451 
 PHE   0.023   0.001   PHE R 221 
 TRP   0.004   0.001   TRP R 363 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4915)
  covalent geometry    : angle       0.59123 ( 6696)
  hydrogen bonds       : bond        0.04317 (  355)
  hydrogen bonds       : angle       3.94113 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8181 (mt) cc_final: 0.7967 (mt)
REVERT: R  235 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6609 (mtm-85)
REVERT: R  236 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6920 (mppt)
REVERT: R  276 PHE cc_start: 0.6572 (t80) cc_final: 0.6085 (m-10)
REVERT: R  280 ILE cc_start: 0.7944 (mt) cc_final: 0.7737 (mp)
REVERT: R  381 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7412 (t0)
REVERT: R  385 ASP cc_start: 0.8287 (p0) cc_final: 0.7982 (m-30)
REVERT: R  413 MET cc_start: 0.6705 (ttm) cc_final: 0.6322 (ttm)
REVERT: R  529 PHE cc_start: 0.7806 (t80) cc_final: 0.7587 (t80)
REVERT: R  678 TRP cc_start: 0.6710 (t60) cc_final: 0.6133 (t60)
  outliers start: 10
  outliers final: 6
  residues processed: 73
  average time/residue: 0.4534
  time to fit residues: 34.8592
Evaluate side-chains
  69 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 SER
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Chi-restraints excluded: chain R residue  472 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0040
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.155494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124267 restraints weight = 5369.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.90
r_work: 0.3350 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4915  Z= 0.137
  Angle     :  0.581  11.840   6696  Z= 0.280
  Chirality :  0.042   0.146    809
  Planarity :  0.004   0.047    776
  Dihedral  : 10.528 120.071    994
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.27 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.35), residues: 582
  helix:  2.17 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.24 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 235 
 TYR   0.013   0.001   TYR R 451 
 PHE   0.022   0.001   PHE R 221 
 TRP   0.004   0.001   TRP R 363 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4915)
  covalent geometry    : angle       0.58116 ( 6696)
  hydrogen bonds       : bond        0.04165 (  355)
  hydrogen bonds       : angle       3.89303 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.188 
Fit side-chains
REVERT: R   41 ARG cc_start: 0.7655 (mtm180) cc_final: 0.6868 (mtm180)
REVERT: R  120 LEU cc_start: 0.8161 (mt) cc_final: 0.7930 (mt)
REVERT: R  215 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7475 (mm)
REVERT: R  234 ASP cc_start: 0.6277 (t70) cc_final: 0.5860 (t70)
REVERT: R  235 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6513 (mtm-85)
REVERT: R  236 LYS cc_start: 0.7211 (mtmm) cc_final: 0.6960 (mppt)
REVERT: R  246 ASP cc_start: 0.6669 (m-30) cc_final: 0.6270 (m-30)
REVERT: R  276 PHE cc_start: 0.6555 (t80) cc_final: 0.6068 (m-10)
REVERT: R  280 ILE cc_start: 0.7939 (mt) cc_final: 0.7730 (mp)
REVERT: R  381 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7131 (t0)
REVERT: R  385 ASP cc_start: 0.8295 (p0) cc_final: 0.8015 (m-30)
REVERT: R  413 MET cc_start: 0.6675 (ttm) cc_final: 0.6297 (ttm)
REVERT: R  511 ASP cc_start: 0.7699 (t0) cc_final: 0.7467 (t0)
REVERT: R  678 TRP cc_start: 0.6685 (t60) cc_final: 0.6092 (t60)
  outliers start: 9
  outliers final: 5
  residues processed: 80
  average time/residue: 0.4380
  time to fit residues: 36.8790
Evaluate side-chains
  74 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Chi-restraints excluded: chain R residue  472 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0970
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.155670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124255 restraints weight = 5375.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.91
r_work: 0.3335 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4915  Z= 0.142
  Angle     :  0.593  11.981   6696  Z= 0.288
  Chirality :  0.042   0.145    809
  Planarity :  0.005   0.047    776
  Dihedral  : 10.417 119.039    994
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.25 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.35), residues: 582
  helix:  2.15 (0.24), residues: 462
  sheet:  None (None), residues: 0
  loop : -1.25 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 235 
 TYR   0.014   0.001   TYR R 451 
 PHE   0.024   0.001   PHE R 529 
 TRP   0.004   0.001   TRP R 363 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4915)
  covalent geometry    : angle       0.59346 ( 6696)
  hydrogen bonds       : bond        0.04181 (  355)
  hydrogen bonds       : angle       3.90514 ( 1056)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8165 (mt) cc_final: 0.7933 (mt)
REVERT: R  215 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7462 (mm)
REVERT: R  234 ASP cc_start: 0.6253 (t70) cc_final: 0.5829 (t70)
REVERT: R  235 ARG cc_start: 0.7076 (mtm-85) cc_final: 0.6435 (mtm-85)
REVERT: R  236 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6993 (mppt)
REVERT: R  246 ASP cc_start: 0.6642 (m-30) cc_final: 0.6242 (m-30)
REVERT: R  276 PHE cc_start: 0.6555 (t80) cc_final: 0.6059 (m-10)
REVERT: R  280 ILE cc_start: 0.7920 (mt) cc_final: 0.7712 (mp)
REVERT: R  381 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7091 (t0)
REVERT: R  385 ASP cc_start: 0.8288 (p0) cc_final: 0.7989 (m-30)
REVERT: R  413 MET cc_start: 0.6666 (ttm) cc_final: 0.6302 (ttm)
REVERT: R  511 ASP cc_start: 0.7662 (t0) cc_final: 0.7434 (t0)
REVERT: R  678 TRP cc_start: 0.6658 (t60) cc_final: 0.6066 (t60)
REVERT: R  713 LEU cc_start: 0.7134 (mt) cc_final: 0.6887 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 81
  average time/residue: 0.4472
  time to fit residues: 38.0605
Evaluate side-chains
  79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 SER
Chi-restraints excluded: chain R residue  143 GLN
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  295 ARG
Chi-restraints excluded: chain R residue  339 GLU
Chi-restraints excluded: chain R residue  381 ASN
Chi-restraints excluded: chain R residue  472 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.122925 restraints weight = 5382.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.91
r_work: 0.3340 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4915  Z= 0.159
  Angle     :  0.595  12.183   6696  Z= 0.293
  Chirality :  0.042   0.149    809
  Planarity :  0.005   0.047    776
  Dihedral  : 10.380 118.960    994
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.45 %
    Favored  : 80.59 %
  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 aren not related in a simple way.
  whole:  2.17 (0.35), residues: 582
  helix:  2.06 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -1.12 (0.55), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 235 
 TYR   0.015   0.001   TYR R 451 
 PHE   0.023   0.002   PHE R 221 
 TRP   0.005   0.001   TRP R 100 
 HIS   0.002   0.001   HIS R 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4915)
  covalent geometry    : angle       0.59500 ( 6696)
  hydrogen bonds       : bond        0.04355 (  355)
  hydrogen bonds       : angle       3.94525 ( 1056)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.97 seconds
wall clock time: 29 minutes 50.20 seconds (1790.20 seconds total)