Starting phenix.real_space_refine
on Fri Aug 22 20:20:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k9i_36987/08_2025/8k9i_36987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k9i_36987/08_2025/8k9i_36987.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k9i_36987/08_2025/8k9i_36987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k9i_36987/08_2025/8k9i_36987.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k9i_36987/08_2025/8k9i_36987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k9i_36987/08_2025/8k9i_36987.map"
  }
  resolution = 4.2
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    4850      2.51       5
     N    1340      2.21       5
     O    1410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 7657
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 5712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 694, 5712
          Classifications: {'peptide': 694}
          Link IDs: {'PTRANS': 15, 'TRANS': 678}
          Chain breaks: 10
    Chain: "K"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 873
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 5
    Chain: "L"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 749
          Classifications: {'peptide': 95}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 92}
          Chain breaks: 6
    Chain: "R"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 323
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 1, 'TRANS': 37}
          Chain breaks: 4
  Time building chain proxies: 2.00, per 1000 atoms: 0.26
  Number of scatterers: 7657
  At special positions: 0
  Unit cell: (94.415, 88.668, 169.947, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1410      8.00
     N    1340      7.00
     C    4850      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: 0.64
  Conformation dependent library (CDL) restraints added in 362.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1802

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      67.7% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'C' and resid 26 through 46
    Processing helix  chain 'C' and resid 53 through 67
    Processing helix  chain 'C' and resid 69 through 88
    Processing helix  chain 'C' and resid 89 through 95
    Processing helix  chain 'C' and resid 100 through 121
    Processing helix  chain 'C' and resid 123 through 129
      removed outlier: 3.791A  pdb=" N   ASP C 127 " --> pdb=" O   LEU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 134
    Processing helix  chain 'C' and resid 138 through 151
    Processing helix  chain 'C' and resid 156 through 175
    Processing helix  chain 'C' and resid 179 through 195
    Processing helix  chain 'C' and resid 198 through 203
    Processing helix  chain 'C' and resid 205 through 225
    Processing helix  chain 'C' and resid 229 through 252
    Processing helix  chain 'C' and resid 256 through 269
      removed outlier: 3.687A  pdb=" N   GLU C 265 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 273
    Processing helix  chain 'C' and resid 275 through 279
    Processing helix  chain 'C' and resid 283 through 290
    Processing helix  chain 'C' and resid 292 through 305
    Processing helix  chain 'C' and resid 308 through 330
    Processing helix  chain 'C' and resid 337 through 359
    Processing helix  chain 'C' and resid 363 through 381
      removed outlier: 3.837A  pdb=" N   ASN C 379 " --> pdb=" O   GLU C 375 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU C 380 " --> pdb=" O   TYR C 376 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASN C 381 " --> pdb=" O   PHE C 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 389
    Processing helix  chain 'C' and resid 392 through 397
    Processing helix  chain 'C' and resid 404 through 422
    Processing helix  chain 'C' and resid 424 through 442
    Processing helix  chain 'C' and resid 447 through 461
    Processing helix  chain 'C' and resid 463 through 495
    Processing helix  chain 'C' and resid 525 through 543
    Processing helix  chain 'C' and resid 595 through 608
    Processing helix  chain 'C' and resid 613 through 621
    Processing helix  chain 'C' and resid 630 through 636
    Processing helix  chain 'C' and resid 684 through 714
    Processing helix  chain 'C' and resid 718 through 731
    Processing helix  chain 'C' and resid 737 through 751
    Processing helix  chain 'K' and resid 32 through 43
    Processing helix  chain 'K' and resid 64 through 69
    Processing helix  chain 'K' and resid 74 through 80
    Processing helix  chain 'K' and resid 97 through 109
    Processing helix  chain 'K' and resid 120 through 130
    Processing helix  chain 'K' and resid 132 through 146
      removed outlier: 3.842A  pdb=" N   ILE K 136 " --> pdb=" O   ILE K 132 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 36 through 46
    Processing helix  chain 'L' and resid 64 through 72
    Processing helix  chain 'L' and resid 103 through 110
    Processing helix  chain 'L' and resid 122 through 130
    Processing helix  chain 'L' and resid 132 through 142
    Processing helix  chain 'R' and resid 53 through 58
    Processing sheet with id=AA1, first strand: chain 'C' and resid 549 through 550
    Processing sheet with id=AA2, first strand: chain 'C' and resid 558 through 559
      removed outlier: 5.597A  pdb=" N   ILE C 591 " --> pdb=" O   VAL C 672 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 610 through 612
    Processing sheet with id=AA4, first strand: chain 'C' and resid 716 through 717
    Processing sheet with id=AA5, first strand: chain 'K' and resid 52 through 54
    Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 54

    464 hydrogen bonds defined for protein.
    1365 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: 1.23

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.48: 3457
        1.48 -     1.74: 4219
        1.74 -     2.00: 91
        2.00 -     2.26: 0
        2.26 -     2.52: 1
  Bond restraints: 7768
  Sorted by residual:
  bond pdb=" C   GLU L  57 "
       pdb=" N   ARG L  59 "
    ideal  model  delta    sigma   weight residual
    1.329  2.524 -1.195 1.40e-02 5.10e+03 7.29e+03
  bond pdb=" N   ILE C 269 "
       pdb=" CA  ILE C 269 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 9.00e-03 1.23e+04 1.72e+01
  bond pdb=" N   VAL K  56 "
       pdb=" CA  VAL K  56 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.08e-02 8.57e+03 1.29e+01
  bond pdb=" N   ILE C 122 "
       pdb=" CA  ILE C 122 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.19e-02 7.06e+03 1.15e+01
  bond pdb=" N   ILE K  48 "
       pdb=" CA  ILE K  48 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.14e-02 7.69e+03 1.08e+01
  ... (remaining 7763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.74: 10413
        6.74 -    13.48: 2
       13.48 -    20.22: 1
       20.22 -    26.96: 0
       26.96 -    33.70: 1
  Bond angle restraints: 10417
  Sorted by residual:
  angle pdb=" O   GLU L  57 "
        pdb=" C   GLU L  57 "
        pdb=" N   ARG L  59 "
      ideal   model   delta    sigma   weight residual
     122.59   88.89   33.70 1.33e+00 5.65e-01 6.42e+02
  angle pdb=" C   GLU L  57 "
        pdb=" N   ARG L  59 "
        pdb=" CA  ARG L  59 "
      ideal   model   delta    sigma   weight residual
     121.70  140.50  -18.80 1.80e+00 3.09e-01 1.09e+02
  angle pdb=" C   GLU C 752 "
        pdb=" CA  GLU C 752 "
        pdb=" CB  GLU C 752 "
      ideal   model   delta    sigma   weight residual
     116.54  110.58    5.96 1.15e+00 7.56e-01 2.69e+01
  angle pdb=" CA  VAL L  55 "
        pdb=" C   VAL L  55 "
        pdb=" O   VAL L  55 "
      ideal   model   delta    sigma   weight residual
     122.63  118.27    4.36 8.70e-01 1.32e+00 2.51e+01
  angle pdb=" CA  GLU L  57 "
        pdb=" C   GLU L  57 "
        pdb=" N   ARG L  59 "
      ideal   model   delta    sigma   weight residual
     116.84  125.05   -8.21 1.71e+00 3.42e-01 2.31e+01
  ... (remaining 10412 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.29: 4027
       13.29 -    26.58: 398
       26.58 -    39.87: 200
       39.87 -    53.16: 33
       53.16 -    66.45: 72
  Dihedral angle restraints: 4730
    sinusoidal: 1989
      harmonic: 2741
  Sorted by residual:
  dihedral pdb=" CA  GLU L  57 "
           pdb=" C   GLU L  57 "
           pdb=" N   ARG L  59 "
           pdb=" CA  ARG L  59 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   20.64  -20.64     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ARG C 671 "
           pdb=" CB  ARG C 671 "
           pdb=" CG  ARG C 671 "
           pdb=" CD  ARG C 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.17   58.83     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   VAL K  52 "
           pdb=" CA  VAL K  52 "
           pdb=" CB  VAL K  52 "
           pdb=" CG1 VAL K  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.79   58.21     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 4727 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 337
       0.045 -    0.089: 276
       0.089 -    0.134: 325
       0.134 -    0.179: 195
       0.179 -    0.224: 39
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CA  ILE C 741 "
            pdb=" N   ILE C 741 "
            pdb=" C   ILE C 741 "
            pdb=" CB  ILE C 741 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE C 183 "
            pdb=" N   ILE C 183 "
            pdb=" C   ILE C 183 "
            pdb=" CB  ILE C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE C 241 "
            pdb=" N   ILE C 241 "
            pdb=" C   ILE C 241 "
            pdb=" CB  ILE C 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1169 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU L  57 "   -0.155 2.00e-02 2.50e+03   2.13e-01 4.54e+02
        pdb=" C   GLU L  57 "    0.364 2.00e-02 2.50e+03
        pdb=" O   GLU L  57 "   -0.144 2.00e-02 2.50e+03
        pdb=" N   ARG L  59 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 153 "   -0.279 9.50e-02 1.11e+02   1.25e-01 9.59e+00
        pdb=" NE  ARG C 153 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 153 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 153 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 153 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 180 "    0.273 9.50e-02 1.11e+02   1.22e-01 9.19e+00
        pdb=" NE  ARG C 180 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 180 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 180 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 180 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.90: 3170
        2.90 -     3.40: 8894
        3.40 -     3.90: 14890
        3.90 -     4.40: 16936
        4.40 -     4.90: 24664
  Nonbonded interactions: 68554
  Sorted by model distance:
  nonbonded pdb=" O   LEU K  54 "
            pdb=" OH  TYR K  98 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" O   LEU C 252 "
            pdb=" OG1 THR C 256 "
     model   vdw
     2.416 3.040
  nonbonded pdb=" O   ARG C 642 "
            pdb=" ND2 ASN C 662 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" O   LYS C 457 "
            pdb=" OG1 THR C 460 "
     model   vdw
     2.465 3.040
  nonbonded pdb=" N   GLN C 551 "
            pdb=" O   VAL R  30 "
     model   vdw
     2.468 3.120
  ... (remaining 68549 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:             9.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.880
  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:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5289
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      :  0.018   1.195   7768  Z= 1.315
  Angle     :  1.410  33.696  10417  Z= 1.135
  Chirality :  0.100   0.224   1172
  Planarity :  0.015   0.213   1323
  Dihedral  : 15.708  66.448   2928
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 21.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 10.74 %
    Favored  : 83.59 %
  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: -1.38 (0.26), residues: 880
  helix: -0.14 (0.19), residues: 600
  sheet: -4.08 (1.35), residues: 10
  loop : -2.44 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  38 
 TYR   0.019   0.002   TYR C 233 
 PHE   0.015   0.002   PHE C  54 
 TRP   0.019   0.001   TRP R  33 
 HIS   0.007   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.01777 ( 7768)
  covalent geometry    : angle       1.40964 (10417)
  hydrogen bonds       : bond        0.19061 (  464)
  hydrogen bonds       : angle       6.76531 ( 1365)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 147
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7240 (mt)
REVERT: C   83 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7263 (tt0)
REVERT: C  124 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6488 (ptm)
REVERT: C  141 ASN cc_start: 0.5804 (OUTLIER) cc_final: 0.5604 (m-40)
REVERT: C  152 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.6705 (p)
REVERT: C  163 GLN cc_start: 0.6487 (pt0) cc_final: 0.6077 (pt0)
REVERT: C  167 ASP cc_start: 0.6536 (m-30) cc_final: 0.6053 (m-30)
REVERT: C  243 GLU cc_start: 0.6605 (tp30) cc_final: 0.6102 (tp30)
REVERT: C  289 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7344 (mtmt)
REVERT: C  321 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6485 (tt)
REVERT: C  377 PHE cc_start: 0.6537 (p90) cc_final: 0.6151 (p90)
REVERT: C  383 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6217 (ttm170)
REVERT: C  414 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7301 (mtmt)
REVERT: C  416 MET cc_start: 0.7612 (tpt) cc_final: 0.7313 (tpt)
REVERT: C  434 GLN cc_start: 0.6093 (mt0) cc_final: 0.5512 (mt0)
REVERT: C  454 MET cc_start: 0.6804 (tpt) cc_final: 0.6453 (tpp)
REVERT: C  457 LYS cc_start: 0.7370 (tptt) cc_final: 0.7035 (tptt)
REVERT: C  536 ARG cc_start: 0.6673 (ttp-110) cc_final: 0.6344 (ttp-170)
REVERT: C  599 MET cc_start: 0.5267 (mtm) cc_final: 0.4812 (mtm)
REVERT: C  766 TYR cc_start: 0.6493 (t80) cc_final: 0.5954 (t80)
  outliers start: 48
  outliers final: 14
  residues processed: 179
  average time/residue: 0.1167
  time to fit residues: 26.8612
Evaluate side-chains
  158 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.0876

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

Flipped N/Q/H residues before XYZ refinement:
C  45 GLN
** C  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 ASN
C 103 GLN
C 150 GLN
C 361 ASN
C 530 HIS
C 547 GLN
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 106 HIS
K 137 HIS
L  31 GLN
R  28 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.218177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.192477 restraints weight = 13794.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.197062 restraints weight = 8355.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.200136 restraints weight = 5560.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.202324 restraints weight = 3997.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.203854 restraints weight = 3065.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5390
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7768  Z= 0.152
  Angle     :  0.641  13.152  10417  Z= 0.343
  Chirality :  0.043   0.268   1172
  Planarity :  0.005   0.103   1323
  Dihedral  :  3.882  19.409   1000
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.38 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.75 (0.28), residues: 882
  helix:  1.51 (0.21), residues: 604
  sheet: -2.97 (1.13), residues: 20
  loop : -1.67 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K  59 
 TYR   0.029   0.002   TYR K  74 
 PHE   0.021   0.002   PHE C 377 
 TRP   0.015   0.001   TRP R  33 
 HIS   0.008   0.001   HIS K 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7768)
  covalent geometry    : angle       0.64145 (10417)
  hydrogen bonds       : bond        0.05518 (  464)
  hydrogen bonds       : angle       4.91243 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6469 (ttt) cc_final: 0.5977 (ttt)
REVERT: C   83 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7291 (tm-30)
REVERT: C  151 VAL cc_start: 0.8344 (t) cc_final: 0.8135 (t)
REVERT: C  152 VAL cc_start: 0.7527 (t) cc_final: 0.7220 (p)
REVERT: C  167 ASP cc_start: 0.6754 (m-30) cc_final: 0.6215 (m-30)
REVERT: C  191 MET cc_start: 0.6386 (mmt) cc_final: 0.5483 (mmt)
REVERT: C  237 VAL cc_start: 0.6765 (t) cc_final: 0.6547 (t)
REVERT: C  287 MET cc_start: 0.6126 (mtt) cc_final: 0.5910 (mtt)
REVERT: C  289 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7978 (mmmm)
REVERT: C  301 LYS cc_start: 0.6618 (tmmt) cc_final: 0.6214 (ttpp)
REVERT: C  326 LYS cc_start: 0.7464 (tttt) cc_final: 0.7167 (tttt)
REVERT: C  356 LEU cc_start: 0.7532 (tt) cc_final: 0.7196 (tt)
REVERT: C  377 PHE cc_start: 0.7000 (p90) cc_final: 0.6733 (p90)
REVERT: C  416 MET cc_start: 0.7455 (tpt) cc_final: 0.7237 (tpt)
REVERT: C  426 ASP cc_start: 0.7624 (p0) cc_final: 0.7372 (p0)
REVERT: C  434 GLN cc_start: 0.6636 (mt0) cc_final: 0.6223 (mt0)
REVERT: C  456 SER cc_start: 0.7230 (p) cc_final: 0.6994 (m)
REVERT: C  457 LYS cc_start: 0.7625 (tptt) cc_final: 0.7030 (tptt)
REVERT: C  536 ARG cc_start: 0.7005 (ttp-110) cc_final: 0.6739 (ttp80)
REVERT: C  599 MET cc_start: 0.5247 (mtm) cc_final: 0.4480 (mtm)
REVERT: C  673 LYS cc_start: 0.7514 (ptmm) cc_final: 0.7173 (ptmm)
REVERT: C  734 PHE cc_start: 0.7691 (p90) cc_final: 0.7374 (p90)
REVERT: C  766 TYR cc_start: 0.6477 (t80) cc_final: 0.5792 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1010
  time to fit residues: 20.2434
Evaluate side-chains
  141 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0070
   chunk 43 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0470
   chunk 26 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0980
   chunk 53 optimal weight:    0.0870
   chunk 73 optimal weight:    0.4980
   chunk 40 optimal weight:    0.3980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.1274

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

Flipped N/Q/H residues before XYZ refinement:
C 218 GLN
C 361 ASN
C 543 HIS
C 547 GLN
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.219078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.195186 restraints weight = 13416.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.199378 restraints weight = 8302.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.202192 restraints weight = 5568.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.204229 restraints weight = 4017.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.205438 restraints weight = 3090.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5475
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7768  Z= 0.130
  Angle     :  0.575  13.914  10417  Z= 0.310
  Chirality :  0.040   0.329   1172
  Planarity :  0.003   0.042   1323
  Dihedral  :  3.830  18.199   1000
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.60 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.18 (0.28), residues: 882
  helix:  1.78 (0.21), residues: 603
  sheet: -2.35 (1.24), residues: 21
  loop : -1.38 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 629 
 TYR   0.023   0.002   TYR K  74 
 PHE   0.024   0.002   PHE C 377 
 TRP   0.011   0.001   TRP R  33 
 HIS   0.004   0.001   HIS K 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7768)
  covalent geometry    : angle       0.57475 (10417)
  hydrogen bonds       : bond        0.04777 (  464)
  hydrogen bonds       : angle       4.53956 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6369 (ttt) cc_final: 0.5841 (ttt)
REVERT: C  183 ILE cc_start: 0.7408 (mt) cc_final: 0.7139 (mt)
REVERT: C  203 GLU cc_start: 0.6421 (mt-10) cc_final: 0.6184 (mt-10)
REVERT: C  206 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6971 (tm-30)
REVERT: C  237 VAL cc_start: 0.6872 (t) cc_final: 0.6561 (t)
REVERT: C  243 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6234 (mt-10)
REVERT: C  274 LYS cc_start: 0.7244 (pttp) cc_final: 0.6713 (tptp)
REVERT: C  289 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7268 (mtmt)
REVERT: C  301 LYS cc_start: 0.6550 (tmmt) cc_final: 0.6272 (ttpp)
REVERT: C  356 LEU cc_start: 0.7718 (tt) cc_final: 0.7401 (tt)
REVERT: C  361 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7862 (t0)
REVERT: C  377 PHE cc_start: 0.7286 (p90) cc_final: 0.6637 (p90)
REVERT: C  395 LYS cc_start: 0.7353 (mmmt) cc_final: 0.6778 (mmtm)
REVERT: C  457 LYS cc_start: 0.7653 (tptt) cc_final: 0.7258 (tptt)
REVERT: C  484 MET cc_start: 0.4584 (tpt) cc_final: 0.3502 (tpt)
REVERT: C  524 ILE cc_start: 0.7829 (mm) cc_final: 0.7544 (mm)
REVERT: C  629 ARG cc_start: 0.6891 (mmm160) cc_final: 0.6616 (mmm160)
REVERT: C  766 TYR cc_start: 0.6415 (t80) cc_final: 0.5936 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1134
  time to fit residues: 21.0637
Evaluate side-chains
  133 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 45 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C  67 HIS
** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 HIS
C 434 GLN
C 543 HIS
** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 662 ASN
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  88 GLN
K 131 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.206527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.179606 restraints weight = 13458.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.183964 restraints weight = 8374.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.187089 restraints weight = 5715.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.189224 restraints weight = 4165.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.190807 restraints weight = 3224.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5793
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7768  Z= 0.226
  Angle     :  0.693  13.879  10417  Z= 0.380
  Chirality :  0.045   0.308   1172
  Planarity :  0.004   0.035   1323
  Dihedral  :  4.305  20.811   1000
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.28), residues: 882
  helix:  1.35 (0.20), residues: 604
  sheet: -2.36 (1.02), residues: 22
  loop : -1.34 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 714 
 TYR   0.041   0.003   TYR C  62 
 PHE   0.024   0.002   PHE C 377 
 TRP   0.032   0.002   TRP C 513 
 HIS   0.008   0.001   HIS C 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 7768)
  covalent geometry    : angle       0.69297 (10417)
  hydrogen bonds       : bond        0.05738 (  464)
  hydrogen bonds       : angle       4.87212 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 VAL cc_start: 0.7483 (t) cc_final: 0.7261 (t)
REVERT: C  203 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6703 (mt-10)
REVERT: C  254 LYS cc_start: 0.7184 (mppt) cc_final: 0.6865 (mppt)
REVERT: C  274 LYS cc_start: 0.7749 (pttp) cc_final: 0.6935 (tptp)
REVERT: C  279 MET cc_start: 0.4883 (tmm) cc_final: 0.4589 (tmm)
REVERT: C  289 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8083 (mmmm)
REVERT: C  323 GLU cc_start: 0.7026 (tp30) cc_final: 0.6662 (tp30)
REVERT: C  361 ASN cc_start: 0.8090 (t0) cc_final: 0.7805 (t0)
REVERT: C  377 PHE cc_start: 0.7548 (p90) cc_final: 0.7324 (p90)
REVERT: C  381 ASN cc_start: 0.7873 (t0) cc_final: 0.7550 (t0)
REVERT: C  383 ARG cc_start: 0.6676 (ttm170) cc_final: 0.6279 (ttm170)
REVERT: C  420 ARG cc_start: 0.6476 (ttm110) cc_final: 0.6077 (ttm110)
REVERT: C  457 LYS cc_start: 0.7733 (tptt) cc_final: 0.7494 (tptt)
REVERT: C  538 PHE cc_start: 0.6837 (t80) cc_final: 0.6499 (t80)
REVERT: C  590 HIS cc_start: 0.6841 (m-70) cc_final: 0.5948 (m-70)
REVERT: C  766 TYR cc_start: 0.6543 (t80) cc_final: 0.6052 (t80)
REVERT: K  101 MET cc_start: 0.6519 (mmm) cc_final: 0.5781 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1155
  time to fit residues: 22.4810
Evaluate side-chains
  147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0170
   chunk 49 optimal weight:    0.9980
   chunk 91 optimal weight:    0.2980
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.2216

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

Flipped N/Q/H residues before XYZ refinement:
C  49 ASN
** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 551 GLN
** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.215948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.187290 restraints weight = 14118.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.191804 restraints weight = 9051.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.194937 restraints weight = 6280.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.197140 restraints weight = 4665.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.198440 restraints weight = 3676.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.4408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5747
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7768  Z= 0.137
  Angle     :  0.578  13.879  10417  Z= 0.312
  Chirality :  0.041   0.310   1172
  Planarity :  0.003   0.031   1323
  Dihedral  :  3.966  18.378   1000
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.06 (0.28), residues: 882
  helix:  1.59 (0.21), residues: 606
  sheet: -1.99 (1.14), residues: 20
  loop : -1.23 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 714 
 TYR   0.019   0.002   TYR K  74 
 PHE   0.025   0.002   PHE C 377 
 TRP   0.007   0.001   TRP R  33 
 HIS   0.003   0.001   HIS C 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7768)
  covalent geometry    : angle       0.57799 (10417)
  hydrogen bonds       : bond        0.04556 (  464)
  hydrogen bonds       : angle       4.48029 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 VAL cc_start: 0.7044 (t) cc_final: 0.6834 (t)
REVERT: C  139 VAL cc_start: 0.7093 (t) cc_final: 0.6839 (t)
REVERT: C  198 ARG cc_start: 0.7132 (ptt90) cc_final: 0.6878 (ttt-90)
REVERT: C  237 VAL cc_start: 0.6811 (t) cc_final: 0.6577 (t)
REVERT: C  243 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6379 (mm-30)
REVERT: C  254 LYS cc_start: 0.7079 (mppt) cc_final: 0.6754 (mppt)
REVERT: C  274 LYS cc_start: 0.7375 (pttp) cc_final: 0.6825 (tptp)
REVERT: C  278 GLU cc_start: 0.2746 (tp30) cc_final: 0.2366 (tp30)
REVERT: C  279 MET cc_start: 0.4682 (tmm) cc_final: 0.4449 (tmm)
REVERT: C  289 LYS cc_start: 0.8343 (mmtm) cc_final: 0.7283 (mtmt)
REVERT: C  323 GLU cc_start: 0.6887 (tp30) cc_final: 0.6498 (tp30)
REVERT: C  356 LEU cc_start: 0.7793 (tp) cc_final: 0.7536 (tt)
REVERT: C  361 ASN cc_start: 0.8061 (t0) cc_final: 0.7831 (t0)
REVERT: C  377 PHE cc_start: 0.7544 (p90) cc_final: 0.7240 (p90)
REVERT: C  381 ASN cc_start: 0.7888 (t0) cc_final: 0.7601 (t0)
REVERT: C  383 ARG cc_start: 0.6591 (ttm170) cc_final: 0.6282 (ttm170)
REVERT: C  392 ILE cc_start: 0.7955 (mm) cc_final: 0.7728 (mm)
REVERT: C  395 LYS cc_start: 0.7670 (mmmt) cc_final: 0.6839 (mmtm)
REVERT: C  413 ASP cc_start: 0.7320 (m-30) cc_final: 0.7049 (m-30)
REVERT: C  457 LYS cc_start: 0.7844 (tptt) cc_final: 0.7558 (tptt)
REVERT: C  469 LYS cc_start: 0.8275 (mttm) cc_final: 0.7651 (mtmt)
REVERT: C  673 LYS cc_start: 0.7987 (ptmm) cc_final: 0.7693 (ptmm)
REVERT: C  714 ARG cc_start: 0.5521 (pmt-80) cc_final: 0.4762 (pmt-80)
REVERT: C  766 TYR cc_start: 0.6379 (t80) cc_final: 0.5911 (t80)
REVERT: K  101 MET cc_start: 0.6621 (mmm) cc_final: 0.5828 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1083
  time to fit residues: 21.3296
Evaluate side-chains
  146 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   chunk 40 optimal weight:    0.4980
   chunk 64 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0370
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.2858

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

Flipped N/Q/H residues before XYZ refinement:
C  87 ASN
** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.213393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.184091 restraints weight = 14184.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.188881 restraints weight = 8897.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.192103 restraints weight = 6097.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.194422 restraints weight = 4503.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.195804 restraints weight = 3517.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5757
moved from start:          0.5553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7768  Z= 0.149
  Angle     :  0.600  13.723  10417  Z= 0.323
  Chirality :  0.042   0.308   1172
  Planarity :  0.003   0.029   1323
  Dihedral  :  4.083  17.707   1000
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.08 (0.28), residues: 882
  helix:  1.64 (0.21), residues: 604
  sheet: -2.33 (1.09), residues: 20
  loop : -1.25 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 430 
 TYR   0.024   0.002   TYR C 611 
 PHE   0.023   0.002   PHE C 377 
 TRP   0.012   0.001   TRP C 513 
 HIS   0.005   0.001   HIS C 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7768)
  covalent geometry    : angle       0.60037 (10417)
  hydrogen bonds       : bond        0.04640 (  464)
  hydrogen bonds       : angle       4.47742 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6133 (ttt) cc_final: 0.5795 (ttt)
REVERT: C  254 LYS cc_start: 0.7085 (mppt) cc_final: 0.6732 (mppt)
REVERT: C  274 LYS cc_start: 0.7177 (pttp) cc_final: 0.6738 (tptt)
REVERT: C  279 MET cc_start: 0.5102 (tmm) cc_final: 0.4902 (tmm)
REVERT: C  323 GLU cc_start: 0.6679 (tp30) cc_final: 0.6431 (tp30)
REVERT: C  356 LEU cc_start: 0.7956 (tp) cc_final: 0.7672 (tt)
REVERT: C  381 ASN cc_start: 0.7937 (t0) cc_final: 0.7638 (t0)
REVERT: C  383 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6253 (ttm170)
REVERT: C  413 ASP cc_start: 0.7064 (m-30) cc_final: 0.6850 (m-30)
REVERT: C  457 LYS cc_start: 0.7839 (tptt) cc_final: 0.7540 (tptt)
REVERT: C  469 LYS cc_start: 0.8237 (mttm) cc_final: 0.7737 (mtmt)
REVERT: C  544 SER cc_start: 0.6758 (t) cc_final: 0.6500 (p)
REVERT: C  589 LYS cc_start: 0.7034 (mmmt) cc_final: 0.6820 (mmmt)
REVERT: C  673 LYS cc_start: 0.8020 (ptmm) cc_final: 0.7705 (ptmm)
REVERT: C  717 MET cc_start: 0.2666 (mtp) cc_final: 0.1136 (mtp)
REVERT: C  766 TYR cc_start: 0.6310 (t80) cc_final: 0.5742 (t80)
REVERT: K  101 MET cc_start: 0.6443 (mmm) cc_final: 0.5756 (mmm)
REVERT: K  130 LEU cc_start: 0.6757 (tp) cc_final: 0.6499 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0924
  time to fit residues: 18.5413
Evaluate side-chains
  148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 29 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0980
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0970
   chunk 40 optimal weight:    0.0270
   overall best weight:    0.1836

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

Flipped N/Q/H residues before XYZ refinement:
** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 131 GLN
K 137 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.214867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.185503 restraints weight = 14018.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.190249 restraints weight = 8759.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.193483 restraints weight = 6006.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.195701 restraints weight = 4426.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.197451 restraints weight = 3494.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5729
moved from start:          0.5849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7768  Z= 0.132
  Angle     :  0.608  13.740  10417  Z= 0.322
  Chirality :  0.041   0.307   1172
  Planarity :  0.003   0.046   1323
  Dihedral  :  4.019  17.696   1000
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.15 (0.29), residues: 882
  helix:  1.69 (0.21), residues: 604
  sheet: -2.32 (1.07), residues: 20
  loop : -1.22 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 322 
 TYR   0.020   0.002   TYR K  74 
 PHE   0.034   0.002   PHE C 216 
 TRP   0.006   0.001   TRP C  34 
 HIS   0.003   0.001   HIS K  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7768)
  covalent geometry    : angle       0.60753 (10417)
  hydrogen bonds       : bond        0.04473 (  464)
  hydrogen bonds       : angle       4.41629 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6285 (ttt) cc_final: 0.5986 (ttt)
REVERT: C  203 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6577 (mt-10)
REVERT: C  211 GLU cc_start: 0.7065 (pt0) cc_final: 0.6858 (pt0)
REVERT: C  237 VAL cc_start: 0.6876 (t) cc_final: 0.6640 (t)
REVERT: C  254 LYS cc_start: 0.7002 (mppt) cc_final: 0.6612 (mppt)
REVERT: C  274 LYS cc_start: 0.7207 (pttp) cc_final: 0.6782 (tptt)
REVERT: C  279 MET cc_start: 0.5142 (tmm) cc_final: 0.4704 (tmm)
REVERT: C  323 GLU cc_start: 0.6832 (tp30) cc_final: 0.6502 (tp30)
REVERT: C  377 PHE cc_start: 0.7503 (p90) cc_final: 0.7209 (p90)
REVERT: C  381 ASN cc_start: 0.7884 (t0) cc_final: 0.7611 (t0)
REVERT: C  413 ASP cc_start: 0.7213 (m-30) cc_final: 0.7008 (m-30)
REVERT: C  457 LYS cc_start: 0.7803 (tptt) cc_final: 0.7570 (tptt)
REVERT: C  469 LYS cc_start: 0.8273 (mttm) cc_final: 0.7659 (mtmt)
REVERT: C  503 LEU cc_start: 0.7595 (tp) cc_final: 0.7310 (tp)
REVERT: C  554 MET cc_start: 0.7082 (mtt) cc_final: 0.6871 (mtt)
REVERT: C  589 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6902 (mmmt)
REVERT: C  673 LYS cc_start: 0.8011 (ptmm) cc_final: 0.7789 (ptmm)
REVERT: C  766 TYR cc_start: 0.6307 (t80) cc_final: 0.5968 (t80)
REVERT: K  101 MET cc_start: 0.6576 (mmm) cc_final: 0.5756 (mmm)
REVERT: K  130 LEU cc_start: 0.6736 (tp) cc_final: 0.6492 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0944
  time to fit residues: 19.2143
Evaluate side-chains
  150 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 64 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C 150 GLN
** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 131 GLN
R  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.210373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.180878 restraints weight = 13958.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.185462 restraints weight = 8768.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.188700 restraints weight = 6063.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.191076 restraints weight = 4480.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.192542 restraints weight = 3503.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.6321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7768  Z= 0.206
  Angle     :  0.691  13.686  10417  Z= 0.373
  Chirality :  0.044   0.305   1172
  Planarity :  0.005   0.060   1323
  Dihedral  :  4.410  19.966   1000
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.75 (0.28), residues: 882
  helix:  1.45 (0.21), residues: 600
  sheet: -2.60 (0.94), residues: 22
  loop : -1.49 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 322 
 TYR   0.035   0.003   TYR C 130 
 PHE   0.025   0.002   PHE C 209 
 TRP   0.018   0.002   TRP C 513 
 HIS   0.007   0.001   HIS C 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 7768)
  covalent geometry    : angle       0.69148 (10417)
  hydrogen bonds       : bond        0.05151 (  464)
  hydrogen bonds       : angle       4.74090 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 VAL cc_start: 0.6954 (t) cc_final: 0.6724 (t)
REVERT: C  183 ILE cc_start: 0.7773 (mt) cc_final: 0.7488 (mt)
REVERT: C  211 GLU cc_start: 0.7120 (pt0) cc_final: 0.6610 (pt0)
REVERT: C  237 VAL cc_start: 0.6965 (t) cc_final: 0.6734 (t)
REVERT: C  254 LYS cc_start: 0.7002 (mppt) cc_final: 0.6597 (mppt)
REVERT: C  274 LYS cc_start: 0.7377 (pttp) cc_final: 0.6928 (tptt)
REVERT: C  279 MET cc_start: 0.5360 (tmm) cc_final: 0.5007 (tmm)
REVERT: C  323 GLU cc_start: 0.6769 (tp30) cc_final: 0.6477 (tp30)
REVERT: C  377 PHE cc_start: 0.7658 (p90) cc_final: 0.7428 (p90)
REVERT: C  469 LYS cc_start: 0.8296 (mttm) cc_final: 0.8045 (mtpp)
REVERT: C  536 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6863 (ttm110)
REVERT: C  554 MET cc_start: 0.7187 (mtt) cc_final: 0.6946 (mtt)
REVERT: C  590 HIS cc_start: 0.6965 (m-70) cc_final: 0.6212 (m-70)
REVERT: C  592 LEU cc_start: 0.7171 (mm) cc_final: 0.6735 (mt)
REVERT: C  673 LYS cc_start: 0.8228 (ptmm) cc_final: 0.7930 (ptmm)
REVERT: C  734 PHE cc_start: 0.8284 (p90) cc_final: 0.7987 (p90)
REVERT: C  746 GLU cc_start: 0.7094 (tp30) cc_final: 0.6655 (tp30)
REVERT: C  766 TYR cc_start: 0.6433 (t80) cc_final: 0.6065 (t80)
REVERT: K  101 MET cc_start: 0.6596 (mmm) cc_final: 0.5892 (mmm)
REVERT: K  130 LEU cc_start: 0.6666 (tp) cc_final: 0.6440 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1061
  time to fit residues: 21.7504
Evaluate side-chains
  150 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0980
   chunk 12 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 47 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0970
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.0956

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

Flipped N/Q/H residues before XYZ refinement:
C  67 HIS
** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.212300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.184147 restraints weight = 13948.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.188620 restraints weight = 8759.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.191637 restraints weight = 6018.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.193737 restraints weight = 4456.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.195104 restraints weight = 3510.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5725
moved from start:          0.6418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7768  Z= 0.125
  Angle     :  0.628  13.702  10417  Z= 0.327
  Chirality :  0.041   0.308   1172
  Planarity :  0.004   0.040   1323
  Dihedral  :  4.098  20.253   1000
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.05 (0.28), residues: 882
  helix:  1.68 (0.21), residues: 601
  sheet: -2.45 (1.05), residues: 20
  loop : -1.40 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 322 
 TYR   0.018   0.002   TYR K  74 
 PHE   0.024   0.001   PHE C 216 
 TRP   0.010   0.001   TRP R  35 
 HIS   0.004   0.001   HIS K  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7768)
  covalent geometry    : angle       0.62777 (10417)
  hydrogen bonds       : bond        0.04302 (  464)
  hydrogen bonds       : angle       4.45265 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 VAL cc_start: 0.6815 (t) cc_final: 0.6615 (t)
REVERT: C  139 VAL cc_start: 0.6878 (t) cc_final: 0.6677 (t)
REVERT: C  219 MET cc_start: 0.7417 (tpp) cc_final: 0.7179 (tpp)
REVERT: C  237 VAL cc_start: 0.6799 (t) cc_final: 0.6549 (t)
REVERT: C  254 LYS cc_start: 0.6864 (mppt) cc_final: 0.6465 (mppt)
REVERT: C  274 LYS cc_start: 0.7103 (pttp) cc_final: 0.6717 (tptt)
REVERT: C  279 MET cc_start: 0.5128 (tmm) cc_final: 0.4745 (tmm)
REVERT: C  323 GLU cc_start: 0.6731 (tp30) cc_final: 0.6400 (tp30)
REVERT: C  377 PHE cc_start: 0.7607 (p90) cc_final: 0.7249 (p90)
REVERT: C  405 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6805 (tm-30)
REVERT: C  457 LYS cc_start: 0.7746 (tptp) cc_final: 0.7252 (tptp)
REVERT: C  503 LEU cc_start: 0.7514 (tp) cc_final: 0.7302 (tp)
REVERT: C  524 ILE cc_start: 0.7793 (mm) cc_final: 0.7556 (mm)
REVERT: C  536 ARG cc_start: 0.6978 (ttm170) cc_final: 0.6758 (ttm110)
REVERT: C  589 LYS cc_start: 0.7395 (mmpt) cc_final: 0.7120 (mmpt)
REVERT: C  611 TYR cc_start: 0.6076 (t80) cc_final: 0.5671 (t80)
REVERT: C  673 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7778 (ptmm)
REVERT: C  766 TYR cc_start: 0.6446 (t80) cc_final: 0.6137 (t80)
REVERT: K  101 MET cc_start: 0.6624 (mmm) cc_final: 0.5773 (mmm)
REVERT: K  119 ASN cc_start: 0.6066 (t0) cc_final: 0.5793 (p0)
REVERT: K  130 LEU cc_start: 0.6531 (tp) cc_final: 0.6291 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1014
  time to fit residues: 20.4040
Evaluate side-chains
  151 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    0.0570
   chunk 82 optimal weight:    0.3980
   chunk 90 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.3980
   chunk 75 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.2698

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

Flipped N/Q/H residues before XYZ refinement:
C  67 HIS
** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.208053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.179696 restraints weight = 13889.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.184106 restraints weight = 8853.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.187158 restraints weight = 6141.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.189101 restraints weight = 4569.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.190694 restraints weight = 3624.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5791
moved from start:          0.6652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7768  Z= 0.152
  Angle     :  0.654  13.744  10417  Z= 0.345
  Chirality :  0.042   0.306   1172
  Planarity :  0.004   0.048   1323
  Dihedral  :  4.156  21.192   1000
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.28), residues: 882
  helix:  1.67 (0.21), residues: 602
  sheet: -2.58 (1.01), residues: 20
  loop : -1.46 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 322 
 TYR   0.021   0.002   TYR C 387 
 PHE   0.034   0.002   PHE C 216 
 TRP   0.011   0.002   TRP C 513 
 HIS   0.004   0.001   HIS K  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7768)
  covalent geometry    : angle       0.65399 (10417)
  hydrogen bonds       : bond        0.04698 (  464)
  hydrogen bonds       : angle       4.51824 ( 1365)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6189 (ttt) cc_final: 0.5568 (ttt)
REVERT: C  166 LEU cc_start: 0.6842 (mt) cc_final: 0.6516 (mt)
REVERT: C  219 MET cc_start: 0.7466 (tpp) cc_final: 0.7234 (tpp)
REVERT: C  237 VAL cc_start: 0.6822 (t) cc_final: 0.6603 (t)
REVERT: C  254 LYS cc_start: 0.6865 (mppt) cc_final: 0.6428 (mppt)
REVERT: C  274 LYS cc_start: 0.7195 (pttp) cc_final: 0.6769 (tptt)
REVERT: C  279 MET cc_start: 0.5198 (tmm) cc_final: 0.4840 (tmm)
REVERT: C  323 GLU cc_start: 0.6792 (tp30) cc_final: 0.6410 (tp30)
REVERT: C  326 LYS cc_start: 0.7316 (tttt) cc_final: 0.7076 (tttt)
REVERT: C  405 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: C  426 ASP cc_start: 0.7989 (p0) cc_final: 0.7745 (p0)
REVERT: C  457 LYS cc_start: 0.7707 (tptp) cc_final: 0.7198 (tptp)
REVERT: C  503 LEU cc_start: 0.7528 (tp) cc_final: 0.7323 (tp)
REVERT: C  524 ILE cc_start: 0.7775 (mm) cc_final: 0.7555 (mm)
REVERT: C  536 ARG cc_start: 0.7048 (ttm170) cc_final: 0.6841 (ttm110)
REVERT: C  554 MET cc_start: 0.7219 (mtt) cc_final: 0.6963 (mtt)
REVERT: C  589 LYS cc_start: 0.7384 (mmpt) cc_final: 0.7140 (mmpt)
REVERT: C  592 LEU cc_start: 0.7181 (mm) cc_final: 0.6783 (mt)
REVERT: C  611 TYR cc_start: 0.6176 (t80) cc_final: 0.5737 (t80)
REVERT: C  673 LYS cc_start: 0.8170 (ptmm) cc_final: 0.7874 (ptmm)
REVERT: C  734 PHE cc_start: 0.8251 (p90) cc_final: 0.7911 (p90)
REVERT: C  766 TYR cc_start: 0.6596 (t80) cc_final: 0.6250 (t80)
REVERT: K  101 MET cc_start: 0.6709 (mmm) cc_final: 0.5865 (mmm)
REVERT: K  130 LEU cc_start: 0.6586 (tp) cc_final: 0.6346 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1094
  time to fit residues: 21.8470
Evaluate side-chains
  152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:    0.0980
   chunk 87 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** C 543 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 = 0.4507 r_free = 0.4507 target = 0.206047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.178430 restraints weight = 12963.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.183006 restraints weight = 8064.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.185938 restraints weight = 5433.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.187812 restraints weight = 3970.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.189503 restraints weight = 3113.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5861
moved from start:          0.7002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7768  Z= 0.216
  Angle     :  0.706  13.605  10417  Z= 0.378
  Chirality :  0.044   0.303   1172
  Planarity :  0.005   0.059   1323
  Dihedral  :  4.533  21.780   1000
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  0.50 (0.27), residues: 882
  helix:  1.29 (0.20), residues: 601
  sheet: -2.70 (0.88), residues: 22
  loop : -1.68 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 383 
 TYR   0.033   0.003   TYR C 130 
 PHE   0.025   0.002   PHE C 209 
 TRP   0.017   0.002   TRP C 513 
 HIS   0.007   0.001   HIS C 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7768)
  covalent geometry    : angle       0.70580 (10417)
  hydrogen bonds       : bond        0.05348 (  464)
  hydrogen bonds       : angle       4.89214 ( 1365)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1645.20 seconds
wall clock time: 29 minutes 11.89 seconds (1751.89 seconds total)