Starting phenix.real_space_refine
on Wed Mar 12 09:09:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k9i_36987/03_2025/8k9i_36987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k9i_36987/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k9i_36987/03_2025/8k9i_36987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k9i_36987/03_2025/8k9i_36987.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k9i_36987/03_2025/8k9i_36987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k9i_36987/03_2025/8k9i_36987.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.87, per 1000 atoms: 0.90
  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: 1.65
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.79
  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: 2.27

  Time building geometry restraints manager: 2.01 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:             7.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.520
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.540
-------------------------------------------------------------------------------
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= 1.292
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.019   0.001   TRP R  33 
 HIS   0.007   0.001   HIS C 112 
 PHE   0.015   0.002   PHE C  54 
 TYR   0.019   0.002   TYR C 233 
 ARG   0.005   0.001   ARG K  38 

*********************** 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  : 0.783 
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: 0.2479
  time to fit residues: 56.8144
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  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0020
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.2988

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

Flipped N/Q/H residues before XYZ refinement:
C  45 GLN
C 218 GLN
** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 361 ASN
** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.213913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.189131 restraints weight = 13565.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.193588 restraints weight = 8257.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.196606 restraints weight = 5494.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5607
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7768  Z= 0.243
  Angle     :  0.666  13.577  10417  Z= 0.358
  Chirality :  0.044   0.264   1172
  Planarity :  0.005   0.101   1323
  Dihedral  :  3.899  19.660   1000
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.49 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.28), residues: 882
  helix:  1.41 (0.20), residues: 606
  sheet: -2.92 (1.12), residues: 20
  loop : -1.71 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 513 
 HIS   0.007   0.001   HIS K 137 
 PHE   0.022   0.002   PHE C 428 
 TYR   0.030   0.002   TYR K  74 
 ARG   0.010   0.001   ARG C 322 

*********************** 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
  155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6747 (ttt) cc_final: 0.6168 (ttt)
REVERT: C  152 VAL cc_start: 0.7704 (t) cc_final: 0.7377 (p)
REVERT: C  189 MET cc_start: 0.7146 (ttp) cc_final: 0.6567 (tmm)
REVERT: C  191 MET cc_start: 0.6757 (mmt) cc_final: 0.6120 (mmt)
REVERT: C  237 VAL cc_start: 0.6795 (t) cc_final: 0.6525 (t)
REVERT: C  254 LYS cc_start: 0.7258 (mptt) cc_final: 0.6988 (mptt)
REVERT: C  289 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7864 (mmmm)
REVERT: C  301 LYS cc_start: 0.6550 (tmmt) cc_final: 0.6185 (ttpp)
REVERT: C  356 LEU cc_start: 0.7755 (tt) cc_final: 0.7518 (tt)
REVERT: C  377 PHE cc_start: 0.7163 (p90) cc_final: 0.6870 (p90)
REVERT: C  426 ASP cc_start: 0.7803 (p0) cc_final: 0.7550 (p0)
REVERT: C  434 GLN cc_start: 0.6779 (mt0) cc_final: 0.6548 (mt0)
REVERT: C  457 LYS cc_start: 0.7653 (tptt) cc_final: 0.7084 (tptt)
REVERT: C  599 MET cc_start: 0.5254 (mtm) cc_final: 0.4547 (mtm)
REVERT: C  673 LYS cc_start: 0.7706 (ptmm) cc_final: 0.7296 (ptpp)
REVERT: C  734 PHE cc_start: 0.7928 (p90) cc_final: 0.7614 (p90)
REVERT: C  766 TYR cc_start: 0.6712 (t80) cc_final: 0.6120 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2239
  time to fit residues: 45.9976
Evaluate side-chains
  136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0770
   chunk 65 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS
C 361 ASN
C 543 HIS
** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 131 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.204905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.179849 restraints weight = 13367.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.183848 restraints weight = 8568.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.186556 restraints weight = 5945.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5826
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7768  Z= 0.300
  Angle     :  0.672  13.938  10417  Z= 0.368
  Chirality :  0.045   0.322   1172
  Planarity :  0.004   0.048   1323
  Dihedral  :  4.326  20.388   1000
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.28), residues: 882
  helix:  1.36 (0.21), residues: 601
  sheet: -2.22 (1.13), residues: 22
  loop : -1.49 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 513 
 HIS   0.006   0.002   HIS C 670 
 PHE   0.027   0.002   PHE C 377 
 TYR   0.033   0.003   TYR C  62 
 ARG   0.007   0.001   ARG C 629 

*********************** 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
  144 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6539 (ttt) cc_final: 0.6298 (ttt)
REVERT: C   65 VAL cc_start: 0.7629 (t) cc_final: 0.6504 (t)
REVERT: C  152 VAL cc_start: 0.7963 (t) cc_final: 0.7740 (p)
REVERT: C  168 MET cc_start: 0.6894 (mmm) cc_final: 0.6675 (mmm)
REVERT: C  198 ARG cc_start: 0.6969 (ptt90) cc_final: 0.6721 (ttt-90)
REVERT: C  206 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: C  236 LYS cc_start: 0.6658 (mmpt) cc_final: 0.6343 (mmtt)
REVERT: C  243 GLU cc_start: 0.6870 (tp30) cc_final: 0.6390 (tp30)
REVERT: C  274 LYS cc_start: 0.7722 (pttp) cc_final: 0.6842 (tptp)
REVERT: C  279 MET cc_start: 0.4508 (tmm) cc_final: 0.4182 (tmm)
REVERT: C  289 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7886 (mmtm)
REVERT: C  301 LYS cc_start: 0.6414 (tmmt) cc_final: 0.5992 (ttpp)
REVERT: C  315 GLU cc_start: 0.6858 (pt0) cc_final: 0.6650 (pt0)
REVERT: C  323 GLU cc_start: 0.6917 (tp30) cc_final: 0.6657 (tp30)
REVERT: C  361 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7880 (t0)
REVERT: C  377 PHE cc_start: 0.7563 (p90) cc_final: 0.7284 (p90)
REVERT: C  381 ASN cc_start: 0.7766 (t0) cc_final: 0.7440 (t0)
REVERT: C  395 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7038 (mmtm)
REVERT: C  420 ARG cc_start: 0.6492 (ttm110) cc_final: 0.6090 (ttm110)
REVERT: C  589 LYS cc_start: 0.7218 (mmpt) cc_final: 0.6913 (mmpt)
REVERT: C  673 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7724 (ptmm)
REVERT: C  707 ILE cc_start: 0.8019 (mt) cc_final: 0.7773 (mt)
REVERT: C  766 TYR cc_start: 0.6513 (t80) cc_final: 0.6045 (t80)
REVERT: K  101 MET cc_start: 0.6478 (mmm) cc_final: 0.5854 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2727
  time to fit residues: 49.5727
Evaluate side-chains
  140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 68 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0040
   chunk 90 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.4170

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

Flipped N/Q/H residues before XYZ refinement:
C 434 GLN
C 530 HIS
** C 606 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 = 0.4522 r_free = 0.4522 target = 0.206334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.180828 restraints weight = 13083.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.184842 restraints weight = 8319.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.187591 restraints weight = 5691.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5850
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7768  Z= 0.249
  Angle     :  0.622  13.962  10417  Z= 0.340
  Chirality :  0.042   0.306   1172
  Planarity :  0.004   0.034   1323
  Dihedral  :  4.168  19.805   1000
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.28), residues: 882
  helix:  1.39 (0.20), residues: 604
  sheet: -2.10 (1.19), residues: 21
  loop : -1.37 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 513 
 HIS   0.007   0.001   HIS C 553 
 PHE   0.025   0.002   PHE C 377 
 TYR   0.023   0.003   TYR K  74 
 ARG   0.005   0.001   ARG C 430 

*********************** 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
  159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7883 (mmtm)
REVERT: C   64 MET cc_start: 0.6426 (ttt) cc_final: 0.6112 (ttt)
REVERT: C  191 MET cc_start: 0.7243 (mmt) cc_final: 0.6474 (mmt)
REVERT: C  206 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6791 (tm-30)
REVERT: C  243 GLU cc_start: 0.6804 (tp30) cc_final: 0.6320 (tp30)
REVERT: C  274 LYS cc_start: 0.7600 (pttp) cc_final: 0.7048 (tptt)
REVERT: C  279 MET cc_start: 0.4996 (tmm) cc_final: 0.4649 (tmm)
REVERT: C  289 LYS cc_start: 0.8336 (mmtm) cc_final: 0.7909 (mmtm)
REVERT: C  294 GLU cc_start: 0.6528 (pm20) cc_final: 0.6266 (pm20)
REVERT: C  301 LYS cc_start: 0.6484 (tmmt) cc_final: 0.6152 (ttpp)
REVERT: C  323 GLU cc_start: 0.6886 (tp30) cc_final: 0.6517 (tp30)
REVERT: C  356 LEU cc_start: 0.7962 (tp) cc_final: 0.7637 (tt)
REVERT: C  361 ASN cc_start: 0.8069 (t0) cc_final: 0.7850 (t0)
REVERT: C  381 ASN cc_start: 0.7916 (t0) cc_final: 0.7630 (t0)
REVERT: C  383 ARG cc_start: 0.6548 (ttm170) cc_final: 0.6170 (ttm170)
REVERT: C  395 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7262 (mmtm)
REVERT: C  413 ASP cc_start: 0.7222 (m-30) cc_final: 0.6914 (m-30)
REVERT: C  432 TYR cc_start: 0.7524 (t80) cc_final: 0.7224 (t80)
REVERT: C  457 LYS cc_start: 0.7896 (tptt) cc_final: 0.7616 (tptt)
REVERT: C  469 LYS cc_start: 0.8279 (mttm) cc_final: 0.7723 (mttt)
REVERT: C  544 SER cc_start: 0.6946 (t) cc_final: 0.6729 (p)
REVERT: C  590 HIS cc_start: 0.7058 (m-70) cc_final: 0.6056 (m-70)
REVERT: C  673 LYS cc_start: 0.8181 (ptmm) cc_final: 0.7946 (ptmm)
REVERT: C  707 ILE cc_start: 0.8067 (mt) cc_final: 0.7791 (mt)
REVERT: C  766 TYR cc_start: 0.6552 (t80) cc_final: 0.6157 (t80)
REVERT: K  101 MET cc_start: 0.6621 (mmm) cc_final: 0.5860 (mmm)
REVERT: K  130 LEU cc_start: 0.6751 (tp) cc_final: 0.6494 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2379
  time to fit residues: 49.3361
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  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 84 optimal weight:    0.1980
   chunk 63 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0770
   chunk 19 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0670
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
C 551 GLN
** C 606 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 = 0.4521 r_free = 0.4521 target = 0.205730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178314 restraints weight = 13122.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.182804 restraints weight = 8193.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.185941 restraints weight = 5579.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5866
moved from start:          0.5562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7768  Z= 0.217
  Angle     :  0.599  13.835  10417  Z= 0.323
  Chirality :  0.042   0.309   1172
  Planarity :  0.003   0.031   1323
  Dihedral  :  4.151  18.695   1000
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.28), residues: 882
  helix:  1.49 (0.21), residues: 602
  sheet: -2.76 (1.01), residues: 21
  loop : -1.42 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 513 
 HIS   0.005   0.001   HIS C 553 
 PHE   0.018   0.002   PHE C 209 
 TYR   0.024   0.002   TYR C 611 
 ARG   0.006   0.000   ARG C 171 

*********************** 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
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 ILE cc_start: 0.8277 (mt) cc_final: 0.8061 (mt)
REVERT: C   47 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7793 (mmtm)
REVERT: C   64 MET cc_start: 0.6332 (ttt) cc_final: 0.6096 (ttt)
REVERT: C   65 VAL cc_start: 0.7473 (t) cc_final: 0.7268 (t)
REVERT: C  198 ARG cc_start: 0.6971 (ptt90) cc_final: 0.6758 (ttt-90)
REVERT: C  203 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6738 (mt-10)
REVERT: C  243 GLU cc_start: 0.6770 (tp30) cc_final: 0.6354 (tp30)
REVERT: C  274 LYS cc_start: 0.7563 (pttp) cc_final: 0.6949 (tptt)
REVERT: C  279 MET cc_start: 0.5212 (tmm) cc_final: 0.4955 (tmm)
REVERT: C  294 GLU cc_start: 0.6676 (pm20) cc_final: 0.6425 (pm20)
REVERT: C  301 LYS cc_start: 0.6505 (tmmt) cc_final: 0.6153 (ttpp)
REVERT: C  323 GLU cc_start: 0.6893 (tp30) cc_final: 0.6495 (tp30)
REVERT: C  356 LEU cc_start: 0.7916 (tp) cc_final: 0.7662 (tt)
REVERT: C  361 ASN cc_start: 0.8022 (t0) cc_final: 0.7782 (t0)
REVERT: C  377 PHE cc_start: 0.7591 (p90) cc_final: 0.7349 (p90)
REVERT: C  381 ASN cc_start: 0.8010 (t0) cc_final: 0.7752 (t0)
REVERT: C  383 ARG cc_start: 0.6717 (ttm170) cc_final: 0.6291 (ttm170)
REVERT: C  413 ASP cc_start: 0.7318 (m-30) cc_final: 0.6999 (m-30)
REVERT: C  432 TYR cc_start: 0.7556 (t80) cc_final: 0.7321 (t80)
REVERT: C  457 LYS cc_start: 0.7975 (tptt) cc_final: 0.7775 (tptt)
REVERT: C  469 LYS cc_start: 0.8294 (mttm) cc_final: 0.7750 (mtmt)
REVERT: C  503 LEU cc_start: 0.7652 (tp) cc_final: 0.7442 (tp)
REVERT: C  554 MET cc_start: 0.7285 (mtt) cc_final: 0.7013 (mtt)
REVERT: C  590 HIS cc_start: 0.6952 (m-70) cc_final: 0.6033 (m-70)
REVERT: C  673 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7959 (ptmm)
REVERT: C  707 ILE cc_start: 0.8093 (mt) cc_final: 0.7831 (mt)
REVERT: C  746 GLU cc_start: 0.7096 (tp30) cc_final: 0.6621 (tp30)
REVERT: K  101 MET cc_start: 0.6653 (mmm) cc_final: 0.5864 (mmm)
REVERT: K  130 LEU cc_start: 0.6723 (tp) cc_final: 0.6505 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2484
  time to fit residues: 49.2717
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  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 64 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0670
   chunk 71 optimal weight:    0.1980
   chunk 53 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.1496

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.205784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.178995 restraints weight = 13076.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.183478 restraints weight = 8118.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.186495 restraints weight = 5501.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5811
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7768  Z= 0.167
  Angle     :  0.576  13.818  10417  Z= 0.307
  Chirality :  0.041   0.310   1172
  Planarity :  0.003   0.039   1323
  Dihedral  :  4.000  17.202   1000
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.28), residues: 882
  helix:  1.63 (0.21), residues: 604
  sheet: -2.47 (1.10), residues: 21
  loop : -1.25 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 109 
 HIS   0.003   0.001   HIS K  64 
 PHE   0.026   0.001   PHE C 216 
 TYR   0.018   0.002   TYR K  74 
 ARG   0.009   0.000   ARG C 430 

*********************** 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
  157 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.745 
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: 0.6367 (ttt) cc_final: 0.6060 (ttt)
REVERT: C  129 VAL cc_start: 0.8004 (p) cc_final: 0.7744 (p)
REVERT: C  203 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6547 (mt-10)
REVERT: C  243 GLU cc_start: 0.6678 (tp30) cc_final: 0.6440 (mm-30)
REVERT: C  274 LYS cc_start: 0.7301 (pttp) cc_final: 0.6758 (tptt)
REVERT: C  279 MET cc_start: 0.5315 (tmm) cc_final: 0.4871 (tmm)
REVERT: C  294 GLU cc_start: 0.6753 (pm20) cc_final: 0.6453 (pm20)
REVERT: C  323 GLU cc_start: 0.6833 (tp30) cc_final: 0.6366 (tp30)
REVERT: C  356 LEU cc_start: 0.7946 (tp) cc_final: 0.7666 (tt)
REVERT: C  361 ASN cc_start: 0.7930 (t0) cc_final: 0.7715 (t0)
REVERT: C  381 ASN cc_start: 0.7954 (t0) cc_final: 0.7743 (t0)
REVERT: C  383 ARG cc_start: 0.6630 (ttm170) cc_final: 0.6386 (ttm170)
REVERT: C  413 ASP cc_start: 0.7410 (m-30) cc_final: 0.7015 (m-30)
REVERT: C  457 LYS cc_start: 0.7922 (tptt) cc_final: 0.7531 (tptt)
REVERT: C  469 LYS cc_start: 0.8264 (mttm) cc_final: 0.7678 (mtmt)
REVERT: C  503 LEU cc_start: 0.7571 (tp) cc_final: 0.7334 (tp)
REVERT: C  524 ILE cc_start: 0.7810 (mm) cc_final: 0.7581 (mm)
REVERT: C  536 ARG cc_start: 0.7282 (ttm170) cc_final: 0.7024 (ttp80)
REVERT: C  554 MET cc_start: 0.7195 (mtt) cc_final: 0.6930 (mtt)
REVERT: C  589 LYS cc_start: 0.7339 (mmpt) cc_final: 0.7005 (mmpt)
REVERT: C  707 ILE cc_start: 0.8062 (mt) cc_final: 0.7785 (mt)
REVERT: C  766 TYR cc_start: 0.6515 (t80) cc_final: 0.6093 (t80)
REVERT: K  101 MET cc_start: 0.6653 (mmm) cc_final: 0.5882 (mmm)
REVERT: K  105 LEU cc_start: 0.7090 (mt) cc_final: 0.6855 (pp)
REVERT: K  130 LEU cc_start: 0.6677 (tp) cc_final: 0.6444 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2438
  time to fit residues: 49.5256
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  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0470
   chunk 65 optimal weight:    0.0020
   chunk 67 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0870
   chunk 78 optimal weight:    0.3980
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.2464

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

Flipped N/Q/H residues before XYZ refinement:
K 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.205949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.180665 restraints weight = 13087.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.184590 restraints weight = 8308.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.187275 restraints weight = 5765.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5802
moved from start:          0.5981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7768  Z= 0.192
  Angle     :  0.607  13.736  10417  Z= 0.323
  Chirality :  0.041   0.306   1172
  Planarity :  0.003   0.052   1323
  Dihedral  :  4.043  18.514   1000
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.28), residues: 882
  helix:  1.61 (0.21), residues: 604
  sheet: -2.47 (1.11), residues: 21
  loop : -1.28 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 513 
 HIS   0.004   0.001   HIS C 553 
 PHE   0.031   0.002   PHE C 224 
 TYR   0.017   0.002   TYR K  74 
 ARG   0.006   0.000   ARG C 322 

*********************** 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
  158 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6202 (ttt) cc_final: 0.5974 (ttt)
REVERT: C   65 VAL cc_start: 0.7516 (t) cc_final: 0.6926 (t)
REVERT: C  180 ARG cc_start: 0.6297 (mtp180) cc_final: 0.6064 (mtp85)
REVERT: C  211 GLU cc_start: 0.6939 (pt0) cc_final: 0.6488 (pt0)
REVERT: C  237 VAL cc_start: 0.6886 (t) cc_final: 0.6670 (t)
REVERT: C  243 GLU cc_start: 0.6622 (tp30) cc_final: 0.6165 (tp30)
REVERT: C  263 VAL cc_start: 0.7942 (p) cc_final: 0.7729 (m)
REVERT: C  274 LYS cc_start: 0.7178 (pttp) cc_final: 0.6809 (tptt)
REVERT: C  279 MET cc_start: 0.5413 (tmm) cc_final: 0.4989 (tmm)
REVERT: C  294 GLU cc_start: 0.6680 (pm20) cc_final: 0.6376 (pm20)
REVERT: C  323 GLU cc_start: 0.6750 (tp30) cc_final: 0.6384 (tp30)
REVERT: C  381 ASN cc_start: 0.7970 (t0) cc_final: 0.7691 (t0)
REVERT: C  413 ASP cc_start: 0.7272 (m-30) cc_final: 0.6911 (m-30)
REVERT: C  457 LYS cc_start: 0.7848 (tptt) cc_final: 0.7603 (tptt)
REVERT: C  469 LYS cc_start: 0.8222 (mttm) cc_final: 0.7986 (mtpp)
REVERT: C  524 ILE cc_start: 0.7716 (mm) cc_final: 0.7459 (mm)
REVERT: C  536 ARG cc_start: 0.7210 (ttm170) cc_final: 0.6980 (ttp80)
REVERT: C  554 MET cc_start: 0.7173 (mtt) cc_final: 0.6932 (mtt)
REVERT: C  589 LYS cc_start: 0.7278 (mmpt) cc_final: 0.6945 (mmpt)
REVERT: C  611 TYR cc_start: 0.6332 (t80) cc_final: 0.5984 (t80)
REVERT: C  673 LYS cc_start: 0.8015 (ptmm) cc_final: 0.7811 (ptmm)
REVERT: C  707 ILE cc_start: 0.8047 (mt) cc_final: 0.7819 (mt)
REVERT: C  734 PHE cc_start: 0.8198 (p90) cc_final: 0.7965 (p90)
REVERT: C  746 GLU cc_start: 0.6979 (tp30) cc_final: 0.6529 (tp30)
REVERT: C  766 TYR cc_start: 0.6449 (t80) cc_final: 0.6038 (t80)
REVERT: K  101 MET cc_start: 0.6549 (mmm) cc_final: 0.5840 (mmm)
REVERT: K  130 LEU cc_start: 0.6637 (tp) cc_final: 0.6390 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2598
  time to fit residues: 52.3386
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  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0040
   chunk 13 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   chunk 56 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 38 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0970
   overall best weight:    0.2348

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.213100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.184215 restraints weight = 14170.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.189094 restraints weight = 8826.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.192388 restraints weight = 5983.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5849
moved from start:          0.6192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7768  Z= 0.186
  Angle     :  0.595  13.734  10417  Z= 0.319
  Chirality :  0.041   0.308   1172
  Planarity :  0.003   0.031   1323
  Dihedral  :  4.066  17.047   1000
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.28), residues: 882
  helix:  1.65 (0.21), residues: 604
  sheet: -2.24 (1.14), residues: 20
  loop : -1.29 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 513 
 HIS   0.004   0.001   HIS C 553 
 PHE   0.030   0.002   PHE C 224 
 TYR   0.020   0.002   TYR C 130 
 ARG   0.006   0.001   ARG C 322 

*********************** 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
  165 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6347 (ttt) cc_final: 0.5962 (ttt)
REVERT: C   65 VAL cc_start: 0.6994 (t) cc_final: 0.6792 (t)
REVERT: C   83 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7253 (tm-30)
REVERT: C  166 LEU cc_start: 0.6863 (mt) cc_final: 0.6590 (mm)
REVERT: C  211 GLU cc_start: 0.7012 (pt0) cc_final: 0.6618 (pt0)
REVERT: C  237 VAL cc_start: 0.6891 (t) cc_final: 0.6678 (t)
REVERT: C  274 LYS cc_start: 0.7248 (pttp) cc_final: 0.6820 (tptt)
REVERT: C  279 MET cc_start: 0.5458 (tmm) cc_final: 0.5063 (tmm)
REVERT: C  294 GLU cc_start: 0.6737 (pm20) cc_final: 0.6400 (pm20)
REVERT: C  377 PHE cc_start: 0.7701 (p90) cc_final: 0.7410 (p90)
REVERT: C  381 ASN cc_start: 0.7952 (t0) cc_final: 0.7651 (t0)
REVERT: C  392 ILE cc_start: 0.7965 (mm) cc_final: 0.7666 (mm)
REVERT: C  413 ASP cc_start: 0.7264 (m-30) cc_final: 0.7020 (m-30)
REVERT: C  457 LYS cc_start: 0.7929 (tptt) cc_final: 0.7680 (tptt)
REVERT: C  503 LEU cc_start: 0.7508 (tp) cc_final: 0.7288 (tp)
REVERT: C  536 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6983 (ttp80)
REVERT: C  554 MET cc_start: 0.7069 (mtt) cc_final: 0.6862 (mtt)
REVERT: C  589 LYS cc_start: 0.7189 (mmpt) cc_final: 0.6845 (mmpt)
REVERT: C  593 GLN cc_start: 0.6957 (tp-100) cc_final: 0.6395 (tp-100)
REVERT: C  611 TYR cc_start: 0.6411 (t80) cc_final: 0.5976 (t80)
REVERT: C  687 GLU cc_start: 0.6587 (mp0) cc_final: 0.6245 (mp0)
REVERT: C  707 ILE cc_start: 0.8067 (mt) cc_final: 0.7848 (mt)
REVERT: C  766 TYR cc_start: 0.6525 (t80) cc_final: 0.6119 (t80)
REVERT: K  101 MET cc_start: 0.6558 (mmm) cc_final: 0.5815 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2422
  time to fit residues: 51.5728
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  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    0.0980
   chunk 51 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 6 optimal weight:    0.1980
   chunk 27 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.3580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.205899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.179895 restraints weight = 13258.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.183951 restraints weight = 8460.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.186522 restraints weight = 5858.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5866
moved from start:          0.6478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7768  Z= 0.239
  Angle     :  0.643  13.701  10417  Z= 0.342
  Chirality :  0.043   0.306   1172
  Planarity :  0.004   0.041   1323
  Dihedral  :  4.233  17.151   1000
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 882
  helix:  1.53 (0.21), residues: 602
  sheet: -2.33 (1.12), residues: 20
  loop : -1.49 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 513 
 HIS   0.005   0.001   HIS C 553 
 PHE   0.027   0.002   PHE C 224 
 TYR   0.020   0.002   TYR C  62 
 ARG   0.008   0.001   ARG C 322 

*********************** 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  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6264 (ttt) cc_final: 0.6033 (ttt)
REVERT: C   65 VAL cc_start: 0.7114 (t) cc_final: 0.6903 (t)
REVERT: C  163 GLN cc_start: 0.6838 (pt0) cc_final: 0.6546 (pt0)
REVERT: C  211 GLU cc_start: 0.7045 (pt0) cc_final: 0.6614 (pt0)
REVERT: C  237 VAL cc_start: 0.6915 (t) cc_final: 0.6682 (t)
REVERT: C  274 LYS cc_start: 0.7326 (pttp) cc_final: 0.6869 (tptt)
REVERT: C  278 GLU cc_start: 0.3221 (tm-30) cc_final: 0.2218 (tm-30)
REVERT: C  279 MET cc_start: 0.5493 (tmm) cc_final: 0.5025 (tmm)
REVERT: C  294 GLU cc_start: 0.6712 (pm20) cc_final: 0.6404 (pm20)
REVERT: C  301 LYS cc_start: 0.6481 (tmmt) cc_final: 0.6141 (tmmt)
REVERT: C  323 GLU cc_start: 0.6737 (tp30) cc_final: 0.6353 (tp30)
REVERT: C  361 ASN cc_start: 0.7582 (t0) cc_final: 0.7382 (t0)
REVERT: C  377 PHE cc_start: 0.7778 (p90) cc_final: 0.7538 (p90)
REVERT: C  383 ARG cc_start: 0.7183 (ttp-110) cc_final: 0.6169 (ttm170)
REVERT: C  413 ASP cc_start: 0.7241 (m-30) cc_final: 0.6946 (m-30)
REVERT: C  457 LYS cc_start: 0.7903 (tptt) cc_final: 0.7616 (tptt)
REVERT: C  524 ILE cc_start: 0.7722 (mm) cc_final: 0.7483 (mm)
REVERT: C  536 ARG cc_start: 0.7264 (ttm170) cc_final: 0.7039 (ttp80)
REVERT: C  554 MET cc_start: 0.7192 (mtt) cc_final: 0.6971 (mtt)
REVERT: C  589 LYS cc_start: 0.7379 (mmpt) cc_final: 0.7017 (mmpt)
REVERT: C  592 LEU cc_start: 0.7237 (mm) cc_final: 0.6835 (mt)
REVERT: C  593 GLN cc_start: 0.6766 (tp-100) cc_final: 0.6180 (tp-100)
REVERT: C  707 ILE cc_start: 0.8092 (mt) cc_final: 0.7851 (mt)
REVERT: C  766 TYR cc_start: 0.6596 (t80) cc_final: 0.6151 (t80)
REVERT: K  101 MET cc_start: 0.6617 (mmm) cc_final: 0.5852 (mmm)
REVERT: K  130 LEU cc_start: 0.6643 (tp) cc_final: 0.6417 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2585
  time to fit residues: 50.9198
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  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0770
   chunk 39 optimal weight:    0.0980
   chunk 83 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0070
   chunk 64 optimal weight:    0.0070
   chunk 60 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0270
   overall best weight:    0.0432

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

Flipped N/Q/H residues before XYZ refinement:
K 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.204299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.179094 restraints weight = 13449.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.183537 restraints weight = 8294.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.186557 restraints weight = 5492.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5711
moved from start:          0.6609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7768  Z= 0.161
  Angle     :  0.602  13.831  10417  Z= 0.319
  Chirality :  0.040   0.306   1172
  Planarity :  0.003   0.029   1323
  Dihedral  :  4.016  16.592   1000
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.28), residues: 882
  helix:  1.69 (0.21), residues: 605
  sheet: -1.71 (1.26), residues: 20
  loop : -1.35 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 109 
 HIS   0.009   0.001   HIS C 701 
 PHE   0.037   0.001   PHE C 216 
 TYR   0.016   0.001   TYR K  74 
 ARG   0.007   0.000   ARG C 699 

********************** 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
  161 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 ILE cc_start: 0.8058 (mt) cc_final: 0.7827 (mt)
REVERT: C   45 GLN cc_start: 0.7937 (tt0) cc_final: 0.6925 (tt0)
REVERT: C  191 MET cc_start: 0.7156 (mmt) cc_final: 0.6887 (mmt)
REVERT: C  211 GLU cc_start: 0.7090 (pt0) cc_final: 0.6716 (pt0)
REVERT: C  237 VAL cc_start: 0.6877 (t) cc_final: 0.6627 (t)
REVERT: C  243 GLU cc_start: 0.6532 (tp30) cc_final: 0.6223 (tp30)
REVERT: C  274 LYS cc_start: 0.6984 (pttp) cc_final: 0.6586 (tptt)
REVERT: C  278 GLU cc_start: 0.2587 (tm-30) cc_final: 0.1895 (tm-30)
REVERT: C  279 MET cc_start: 0.5145 (tmm) cc_final: 0.4666 (tmm)
REVERT: C  294 GLU cc_start: 0.6754 (pm20) cc_final: 0.6407 (pm20)
REVERT: C  323 GLU cc_start: 0.6687 (tp30) cc_final: 0.6225 (tp30)
REVERT: C  377 PHE cc_start: 0.7759 (p90) cc_final: 0.7400 (p90)
REVERT: C  383 ARG cc_start: 0.7002 (ttp-110) cc_final: 0.6477 (ttm170)
REVERT: C  413 ASP cc_start: 0.7400 (m-30) cc_final: 0.7117 (m-30)
REVERT: C  457 LYS cc_start: 0.7790 (tptt) cc_final: 0.7569 (tptt)
REVERT: C  503 LEU cc_start: 0.7408 (tp) cc_final: 0.7171 (tp)
REVERT: C  524 ILE cc_start: 0.7639 (mm) cc_final: 0.7370 (mm)
REVERT: C  536 ARG cc_start: 0.7227 (ttm170) cc_final: 0.7008 (ttp80)
REVERT: C  589 LYS cc_start: 0.7358 (mmpt) cc_final: 0.7024 (mmpt)
REVERT: C  593 GLN cc_start: 0.6580 (tp-100) cc_final: 0.6172 (tp-100)
REVERT: C  611 TYR cc_start: 0.6310 (t80) cc_final: 0.5784 (t80)
REVERT: C  766 TYR cc_start: 0.6531 (t80) cc_final: 0.6043 (t80)
REVERT: K  101 MET cc_start: 0.6474 (mmm) cc_final: 0.5690 (mmm)
REVERT: K  130 LEU cc_start: 0.6557 (tp) cc_final: 0.6300 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2704
  time to fit residues: 54.9153
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  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    0.0060
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0970
   chunk 24 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
C  67 HIS
K  64 HIS
** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 119 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 = 0.4542 r_free = 0.4542 target = 0.207108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.179065 restraints weight = 13059.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.183588 restraints weight = 8213.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.186713 restraints weight = 5610.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          0.6794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   7768  Z= 0.228
  Angle     :  0.623  13.674  10417  Z= 0.336
  Chirality :  0.042   0.307   1172
  Planarity :  0.004   0.053   1323
  Dihedral  :  4.051  16.077   1000
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.28), residues: 882
  helix:  1.65 (0.21), residues: 604
  sheet: -1.88 (1.23), residues: 20
  loop : -1.47 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 513 
 HIS   0.004   0.001   HIS C 553 
 PHE   0.025   0.002   PHE C 224 
 TYR   0.014   0.002   TYR C 432 
 ARG   0.008   0.001   ARG C 322 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3490.98 seconds
wall clock time: 61 minutes 43.04 seconds (3703.04 seconds total)