Starting phenix.real_space_refine
on Sun May 11 06:44:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k9i_36987/05_2025/8k9i_36987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k9i_36987/05_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_36987/05_2025/8k9i_36987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k9i_36987/05_2025/8k9i_36987.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k9i_36987/05_2025/8k9i_36987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k9i_36987/05_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-5687/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: 7.28, per 1000 atoms: 0.95
  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: 1.71
  Conformation dependent library (CDL) restraints added in 976.5 milliseconds
  

  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: 2.28

  Time building geometry restraints manager: 2.02 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:             13.670
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.140
  Process input model:                     22.700
  Find NCS groups from input model:        0.080
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.780
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.768 
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: 0.2418
  time to fit residues: 55.4163
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  : 0.767 
-------------------------------------------------------------------------------
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 = 0.213915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.189147 restraints weight = 13564.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.193594 restraints weight = 8268.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.196625 restraints weight = 5480.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5600
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= 0.180
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05845 (  464)
  hydrogen bonds       : angle       4.96366 ( 1365)
  covalent geometry    : bond        0.00373 ( 7768)
  covalent geometry    : angle       0.66635 (10417)

*********************** 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  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6672 (ttt) cc_final: 0.6115 (ttt)
REVERT: C  152 VAL cc_start: 0.7748 (t) cc_final: 0.7427 (p)
REVERT: C  189 MET cc_start: 0.7153 (ttp) cc_final: 0.6601 (tmm)
REVERT: C  191 MET cc_start: 0.6838 (mmt) cc_final: 0.6175 (mmt)
REVERT: C  237 VAL cc_start: 0.6847 (t) cc_final: 0.6580 (t)
REVERT: C  254 LYS cc_start: 0.7260 (mptt) cc_final: 0.6997 (mptt)
REVERT: C  289 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7845 (mmmm)
REVERT: C  301 LYS cc_start: 0.6573 (tmmt) cc_final: 0.6199 (ttpp)
REVERT: C  356 LEU cc_start: 0.7785 (tt) cc_final: 0.7532 (tt)
REVERT: C  377 PHE cc_start: 0.7186 (p90) cc_final: 0.6879 (p90)
REVERT: C  426 ASP cc_start: 0.7774 (p0) cc_final: 0.7530 (p0)
REVERT: C  434 GLN cc_start: 0.6779 (mt0) cc_final: 0.6557 (mt0)
REVERT: C  456 SER cc_start: 0.7303 (p) cc_final: 0.7096 (m)
REVERT: C  457 LYS cc_start: 0.7640 (tptt) cc_final: 0.7104 (tptt)
REVERT: C  599 MET cc_start: 0.5217 (mtm) cc_final: 0.4526 (mtm)
REVERT: C  673 LYS cc_start: 0.7692 (ptmm) cc_final: 0.7292 (ptpp)
REVERT: C  734 PHE cc_start: 0.7942 (p90) cc_final: 0.7629 (p90)
REVERT: C  766 TYR cc_start: 0.6672 (t80) cc_final: 0.6078 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2290
  time to fit residues: 46.4609
Evaluate side-chains
  137 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 48 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0970
   chunk 65 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 434 GLN
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.206737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.182310 restraints weight = 13339.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.186096 restraints weight = 8534.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.188850 restraints weight = 5926.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5736
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7768  Z= 0.174
  Angle     :  0.624  13.837  10417  Z= 0.340
  Chirality :  0.043   0.324   1172
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.088  19.907   1000
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.19 %
    Favored  : 96.69 %
  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:  0.91 (0.28), residues: 882
  helix:  1.55 (0.21), residues: 602
  sheet: -2.33 (1.10), residues: 23
  loop : -1.41 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 513 
 HIS   0.005   0.001   HIS C 670 
 PHE   0.027   0.002   PHE C 377 
 TYR   0.029   0.003   TYR C  62 
 ARG   0.006   0.001   ARG C 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05290 (  464)
  hydrogen bonds       : angle       4.75539 ( 1365)
  covalent geometry    : bond        0.00367 ( 7768)
  covalent geometry    : angle       0.62356 (10417)

*********************** 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
  146 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6461 (ttt) cc_final: 0.5964 (ttt)
REVERT: C   65 VAL cc_start: 0.7613 (t) cc_final: 0.6468 (t)
REVERT: C  139 VAL cc_start: 0.7137 (t) cc_final: 0.6926 (t)
REVERT: C  152 VAL cc_start: 0.7918 (t) cc_final: 0.7650 (p)
REVERT: C  183 ILE cc_start: 0.7687 (mt) cc_final: 0.7449 (mt)
REVERT: C  236 LYS cc_start: 0.6650 (mmpt) cc_final: 0.6342 (mmtt)
REVERT: C  243 GLU cc_start: 0.6908 (tp30) cc_final: 0.6609 (tp30)
REVERT: C  274 LYS cc_start: 0.7500 (pttp) cc_final: 0.6777 (tptp)
REVERT: C  289 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7866 (mmtm)
REVERT: C  301 LYS cc_start: 0.6522 (tmmt) cc_final: 0.6115 (ttpp)
REVERT: C  315 GLU cc_start: 0.6837 (pt0) cc_final: 0.6627 (pt0)
REVERT: C  323 GLU cc_start: 0.6851 (tp30) cc_final: 0.6576 (tp30)
REVERT: C  361 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7846 (t0)
REVERT: C  377 PHE cc_start: 0.7502 (p90) cc_final: 0.7110 (p90)
REVERT: C  381 ASN cc_start: 0.7635 (t0) cc_final: 0.7273 (t0)
REVERT: C  395 LYS cc_start: 0.7614 (mmmt) cc_final: 0.7230 (mmpt)
REVERT: C  589 LYS cc_start: 0.7154 (mmpt) cc_final: 0.6854 (mmpt)
REVERT: C  673 LYS cc_start: 0.7815 (ptmm) cc_final: 0.7480 (ptmm)
REVERT: C  707 ILE cc_start: 0.7960 (mt) cc_final: 0.7717 (mt)
REVERT: C  766 TYR cc_start: 0.6439 (t80) cc_final: 0.5927 (t80)
REVERT: K  138 PHE cc_start: 0.4623 (m-10) cc_final: 0.4205 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2523
  time to fit residues: 46.8307
Evaluate side-chains
  136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0020
   chunk 68 optimal weight:    0.0870
   chunk 67 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0980
   chunk 90 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.1966

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

Flipped N/Q/H residues before XYZ refinement:
C 530 HIS
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 = 0.4565 r_free = 0.4565 target = 0.208261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.182226 restraints weight = 13193.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.186507 restraints weight = 8163.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.189688 restraints weight = 5547.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5735
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7768  Z= 0.133
  Angle     :  0.582  13.977  10417  Z= 0.314
  Chirality :  0.041   0.315   1172
  Planarity :  0.003   0.034   1323
  Dihedral  :  3.871  18.565   1000
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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:  1.16 (0.28), residues: 882
  helix:  1.68 (0.21), residues: 607
  sheet: -2.00 (1.15), residues: 21
  loop : -1.24 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R  33 
 HIS   0.004   0.001   HIS C 553 
 PHE   0.025   0.002   PHE C 377 
 TYR   0.024   0.002   TYR C 130 
 ARG   0.003   0.000   ARG C 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 (  464)
  hydrogen bonds       : angle       4.45500 ( 1365)
  covalent geometry    : bond        0.00271 ( 7768)
  covalent geometry    : angle       0.58231 (10417)

*********************** 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
  141 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6360 (ttt) cc_final: 0.6085 (ttt)
REVERT: C   65 VAL cc_start: 0.7000 (t) cc_final: 0.6791 (t)
REVERT: C  124 MET cc_start: 0.6832 (ptt) cc_final: 0.6594 (ptt)
REVERT: C  203 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6361 (mt-10)
REVERT: C  206 GLU cc_start: 0.7375 (pp20) cc_final: 0.7101 (pp20)
REVERT: C  243 GLU cc_start: 0.6789 (tp30) cc_final: 0.6561 (mm-30)
REVERT: C  274 LYS cc_start: 0.7431 (pttp) cc_final: 0.6800 (tptt)
REVERT: C  279 MET cc_start: 0.4534 (tmm) cc_final: 0.4213 (tmm)
REVERT: C  289 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7933 (mmtm)
REVERT: C  294 GLU cc_start: 0.6591 (pm20) cc_final: 0.6270 (pm20)
REVERT: C  301 LYS cc_start: 0.6526 (tmmt) cc_final: 0.6242 (ttpp)
REVERT: C  323 GLU cc_start: 0.6863 (tp30) cc_final: 0.6486 (tp30)
REVERT: C  361 ASN cc_start: 0.8090 (t0) cc_final: 0.7827 (t0)
REVERT: C  377 PHE cc_start: 0.7463 (p90) cc_final: 0.7116 (p90)
REVERT: C  381 ASN cc_start: 0.7693 (t0) cc_final: 0.7441 (t0)
REVERT: C  395 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7130 (mmtt)
REVERT: C  405 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6876 (tm-30)
REVERT: C  413 ASP cc_start: 0.7266 (m-30) cc_final: 0.6931 (m-30)
REVERT: C  457 LYS cc_start: 0.7882 (tptt) cc_final: 0.7533 (tptt)
REVERT: C  469 LYS cc_start: 0.8276 (mttm) cc_final: 0.7609 (mttt)
REVERT: C  503 LEU cc_start: 0.7574 (tp) cc_final: 0.7360 (tp)
REVERT: C  538 PHE cc_start: 0.6676 (t80) cc_final: 0.6390 (t80)
REVERT: C  589 LYS cc_start: 0.7288 (mmpt) cc_final: 0.7008 (mmpt)
REVERT: C  673 LYS cc_start: 0.7886 (ptmm) cc_final: 0.7507 (ptmm)
REVERT: C  707 ILE cc_start: 0.8035 (mt) cc_final: 0.7795 (mt)
REVERT: K  101 MET cc_start: 0.6545 (mmm) cc_final: 0.5810 (mmm)
REVERT: K  130 LEU cc_start: 0.6691 (tp) cc_final: 0.6481 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2351
  time to fit residues: 43.1084
Evaluate side-chains
  132 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 84 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0270
   chunk 10 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4036

-------------------------------------------------------------------------------
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 662 ASN

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 = 0.206252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.180802 restraints weight = 13142.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.184614 restraints weight = 8341.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.187297 restraints weight = 5797.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7768  Z= 0.181
  Angle     :  0.642  13.739  10417  Z= 0.344
  Chirality :  0.043   0.309   1172
  Planarity :  0.004   0.032   1323
  Dihedral  :  4.180  21.933   1000
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  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:  0.91 (0.28), residues: 882
  helix:  1.49 (0.20), residues: 605
  sheet: -2.40 (0.98), residues: 20
  loop : -1.25 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 513 
 HIS   0.008   0.001   HIS C 553 
 PHE   0.023   0.002   PHE C 209 
 TYR   0.024   0.003   TYR C  62 
 ARG   0.005   0.001   ARG C 430 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05193 (  464)
  hydrogen bonds       : angle       4.66286 ( 1365)
  covalent geometry    : bond        0.00385 ( 7768)
  covalent geometry    : angle       0.64228 (10417)

*********************** 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
  155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.859 
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: 0.6330 (ttt) cc_final: 0.6068 (ttt)
REVERT: C  180 ARG cc_start: 0.6324 (mtt180) cc_final: 0.5999 (mtp85)
REVERT: C  203 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6529 (mt-10)
REVERT: C  243 GLU cc_start: 0.6754 (tp30) cc_final: 0.6275 (tp30)
REVERT: C  274 LYS cc_start: 0.7495 (pttp) cc_final: 0.6985 (tptt)
REVERT: C  289 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8159 (mmmm)
REVERT: C  301 LYS cc_start: 0.6465 (tmmt) cc_final: 0.6135 (ttpp)
REVERT: C  323 GLU cc_start: 0.6927 (tp30) cc_final: 0.6531 (tp30)
REVERT: C  361 ASN cc_start: 0.8048 (t0) cc_final: 0.7795 (t0)
REVERT: C  381 ASN cc_start: 0.7934 (t0) cc_final: 0.7659 (t0)
REVERT: C  413 ASP cc_start: 0.7201 (m-30) cc_final: 0.6817 (m-30)
REVERT: C  426 ASP cc_start: 0.7919 (p0) cc_final: 0.7666 (p0)
REVERT: C  469 LYS cc_start: 0.8295 (mttm) cc_final: 0.7726 (mtmt)
REVERT: C  538 PHE cc_start: 0.6687 (t80) cc_final: 0.6458 (t80)
REVERT: C  544 SER cc_start: 0.6933 (t) cc_final: 0.6712 (p)
REVERT: C  590 HIS cc_start: 0.6989 (m-70) cc_final: 0.5979 (m-70)
REVERT: C  593 GLN cc_start: 0.7024 (tm-30) cc_final: 0.6795 (tm-30)
REVERT: C  707 ILE cc_start: 0.8021 (mt) cc_final: 0.7775 (mt)
REVERT: C  734 PHE cc_start: 0.8113 (p90) cc_final: 0.7837 (p90)
REVERT: C  746 GLU cc_start: 0.7090 (tp30) cc_final: 0.6485 (tp30)
REVERT: K  101 MET cc_start: 0.6592 (mmm) cc_final: 0.5819 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2541
  time to fit residues: 50.6094
Evaluate side-chains
  145 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 23 optimal weight:    0.2980
   chunk 71 optimal weight:    0.2980
   chunk 53 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0570
   chunk 7 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   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 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.207114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.179152 restraints weight = 13277.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.183728 restraints weight = 8344.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.186875 restraints weight = 5702.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5844
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7768  Z= 0.143
  Angle     :  0.604  13.744  10417  Z= 0.321
  Chirality :  0.042   0.309   1172
  Planarity :  0.004   0.031   1323
  Dihedral  :  4.095  23.249   1000
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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: -2.12 (1.05), residues: 22
  loop : -1.28 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 513 
 HIS   0.005   0.001   HIS C 553 
 PHE   0.036   0.002   PHE C 377 
 TYR   0.018   0.002   TYR K  74 
 ARG   0.005   0.001   ARG C 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04616 (  464)
  hydrogen bonds       : angle       4.52847 ( 1365)
  covalent geometry    : bond        0.00301 ( 7768)
  covalent geometry    : angle       0.60416 (10417)

*********************** 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
  149 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6461 (ttt) cc_final: 0.6242 (ttt)
REVERT: C  180 ARG cc_start: 0.6149 (mtt180) cc_final: 0.5930 (mtp85)
REVERT: C  203 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6576 (mt-10)
REVERT: C  206 GLU cc_start: 0.7400 (pp20) cc_final: 0.7120 (pp20)
REVERT: C  237 VAL cc_start: 0.6762 (t) cc_final: 0.6550 (t)
REVERT: C  243 GLU cc_start: 0.6698 (tp30) cc_final: 0.6203 (tp30)
REVERT: C  274 LYS cc_start: 0.7432 (pttp) cc_final: 0.6770 (tptt)
REVERT: C  279 MET cc_start: 0.4894 (tmm) cc_final: 0.4542 (tmm)
REVERT: C  301 LYS cc_start: 0.6490 (tmmt) cc_final: 0.6235 (ttpp)
REVERT: C  323 GLU cc_start: 0.6857 (tp30) cc_final: 0.6380 (tp30)
REVERT: C  361 ASN cc_start: 0.8063 (t0) cc_final: 0.7819 (t0)
REVERT: C  377 PHE cc_start: 0.7573 (p90) cc_final: 0.7189 (p90)
REVERT: C  381 ASN cc_start: 0.7927 (t0) cc_final: 0.7680 (t0)
REVERT: C  413 ASP cc_start: 0.7375 (m-30) cc_final: 0.6997 (m-30)
REVERT: C  457 LYS cc_start: 0.7957 (tptt) cc_final: 0.7585 (tptt)
REVERT: C  469 LYS cc_start: 0.8257 (mttm) cc_final: 0.7675 (mtmt)
REVERT: C  503 LEU cc_start: 0.7575 (tp) cc_final: 0.7352 (tp)
REVERT: C  538 PHE cc_start: 0.6660 (t80) cc_final: 0.6404 (t80)
REVERT: C  544 SER cc_start: 0.6850 (t) cc_final: 0.6629 (p)
REVERT: C  554 MET cc_start: 0.7262 (mtt) cc_final: 0.6936 (mtt)
REVERT: C  589 LYS cc_start: 0.7481 (mmpt) cc_final: 0.7120 (mmpt)
REVERT: C  673 LYS cc_start: 0.8090 (ptmm) cc_final: 0.7877 (ptmm)
REVERT: C  707 ILE cc_start: 0.8061 (mt) cc_final: 0.7834 (mt)
REVERT: K  101 MET cc_start: 0.6677 (mmm) cc_final: 0.5871 (mmm)
REVERT: K  130 LEU cc_start: 0.6722 (tp) cc_final: 0.6474 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2427
  time to fit residues: 46.7695
Evaluate side-chains
  142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 65 optimal weight:    0.4980
   chunk 67 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.4499 r_free = 0.4499 target = 0.203338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.177398 restraints weight = 13000.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.181288 restraints weight = 8395.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.183950 restraints weight = 5846.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5905
moved from start:          0.6169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7768  Z= 0.195
  Angle     :  0.666  13.624  10417  Z= 0.356
  Chirality :  0.043   0.302   1172
  Planarity :  0.004   0.033   1323
  Dihedral  :  4.309  24.627   1000
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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:  0.83 (0.28), residues: 882
  helix:  1.50 (0.21), residues: 600
  sheet: -2.57 (1.00), residues: 22
  loop : -1.43 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 513 
 HIS   0.008   0.001   HIS C 543 
 PHE   0.023   0.002   PHE C 216 
 TYR   0.022   0.002   TYR C  62 
 ARG   0.011   0.001   ARG C 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05325 (  464)
  hydrogen bonds       : angle       4.74767 ( 1365)
  covalent geometry    : bond        0.00417 ( 7768)
  covalent geometry    : angle       0.66574 (10417)

*********************** 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
  160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.779 
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: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.6329 (ttt) cc_final: 0.6126 (ttt)
REVERT: C  198 ARG cc_start: 0.7153 (ptt90) cc_final: 0.6919 (ptm-80)
REVERT: C  243 GLU cc_start: 0.6665 (tp30) cc_final: 0.6223 (tp30)
REVERT: C  274 LYS cc_start: 0.7436 (pttp) cc_final: 0.6979 (tptt)
REVERT: C  279 MET cc_start: 0.4848 (tmm) cc_final: 0.4551 (tmm)
REVERT: C  383 ARG cc_start: 0.6601 (ttm170) cc_final: 0.6330 (ttm170)
REVERT: C  413 ASP cc_start: 0.7188 (m-30) cc_final: 0.6881 (m-30)
REVERT: C  457 LYS cc_start: 0.7894 (tptt) cc_final: 0.7664 (tptt)
REVERT: C  554 MET cc_start: 0.7275 (mtt) cc_final: 0.6941 (mtt)
REVERT: C  589 LYS cc_start: 0.7410 (mmpt) cc_final: 0.7035 (mmpt)
REVERT: C  592 LEU cc_start: 0.7291 (mm) cc_final: 0.6764 (mt)
REVERT: C  611 TYR cc_start: 0.6204 (t80) cc_final: 0.5787 (t80)
REVERT: C  673 LYS cc_start: 0.8258 (ptmm) cc_final: 0.7889 (ptmm)
REVERT: C  707 ILE cc_start: 0.8029 (mt) cc_final: 0.7808 (mt)
REVERT: C  734 PHE cc_start: 0.8148 (p90) cc_final: 0.7912 (p90)
REVERT: C  746 GLU cc_start: 0.7132 (tp30) cc_final: 0.6106 (tp30)
REVERT: C  766 TYR cc_start: 0.6542 (t80) cc_final: 0.6144 (t80)
REVERT: K  101 MET cc_start: 0.6657 (mmm) cc_final: 0.5991 (mmm)
REVERT: K  105 LEU cc_start: 0.7044 (mt) cc_final: 0.6640 (pp)
REVERT: K  130 LEU cc_start: 0.6625 (tp) cc_final: 0.6360 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2401
  time to fit residues: 49.2443
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  : 0.777 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 52 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0050
   chunk 70 optimal weight:    0.0170
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0770
   chunk 38 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.1590

-------------------------------------------------------------------------------
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**
K 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.212158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.184800 restraints weight = 13975.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.189365 restraints weight = 8668.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.192432 restraints weight = 5891.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.6315

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= 0.128
  Angle     :  0.592  13.736  10417  Z= 0.314
  Chirality :  0.040   0.307   1172
  Planarity :  0.003   0.030   1323
  Dihedral  :  4.058  23.520   1000
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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:  1.19 (0.28), residues: 882
  helix:  1.74 (0.21), residues: 604
  sheet: -2.23 (1.04), residues: 22
  loop : -1.24 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 109 
 HIS   0.003   0.001   HIS K  94 
 PHE   0.019   0.001   PHE C 216 
 TYR   0.018   0.002   TYR C 130 
 ARG   0.006   0.001   ARG C 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04456 (  464)
  hydrogen bonds       : angle       4.41816 ( 1365)
  covalent geometry    : bond        0.00261 ( 7768)
  covalent geometry    : angle       0.59156 (10417)

*********************** 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
  160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.746 
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: symmetry clash
REVERT: C   65 VAL cc_start: 0.7254 (t) cc_final: 0.6823 (t)
REVERT: C  210 LEU cc_start: 0.8205 (mm) cc_final: 0.7988 (mm)
REVERT: C  237 VAL cc_start: 0.6773 (t) cc_final: 0.6556 (t)
REVERT: C  243 GLU cc_start: 0.6612 (tp30) cc_final: 0.6180 (tp30)
REVERT: C  263 VAL cc_start: 0.7862 (p) cc_final: 0.7645 (m)
REVERT: C  274 LYS cc_start: 0.7262 (pttp) cc_final: 0.6829 (tptt)
REVERT: C  279 MET cc_start: 0.4724 (tmm) cc_final: 0.4381 (tmm)
REVERT: C  301 LYS cc_start: 0.6546 (tmmt) cc_final: 0.6295 (ttpp)
REVERT: C  377 PHE cc_start: 0.7548 (p90) cc_final: 0.7178 (p90)
REVERT: C  383 ARG cc_start: 0.6546 (ttm170) cc_final: 0.6342 (ttm170)
REVERT: C  392 ILE cc_start: 0.8097 (mm) cc_final: 0.7847 (mm)
REVERT: C  413 ASP cc_start: 0.7315 (m-30) cc_final: 0.6999 (m-30)
REVERT: C  457 LYS cc_start: 0.7825 (tptt) cc_final: 0.7564 (tptt)
REVERT: C  524 ILE cc_start: 0.7705 (mm) cc_final: 0.7418 (mm)
REVERT: C  554 MET cc_start: 0.7101 (mtt) cc_final: 0.6833 (mtt)
REVERT: C  589 LYS cc_start: 0.7383 (mmpt) cc_final: 0.6991 (mmpt)
REVERT: C  611 TYR cc_start: 0.6205 (t80) cc_final: 0.5706 (t80)
REVERT: C  673 LYS cc_start: 0.8182 (ptmm) cc_final: 0.7925 (ptmm)
REVERT: C  707 ILE cc_start: 0.8048 (mt) cc_final: 0.7826 (mt)
REVERT: C  766 TYR cc_start: 0.6490 (t80) cc_final: 0.6096 (t80)
REVERT: K  101 MET cc_start: 0.6656 (mmm) cc_final: 0.5856 (mmm)
REVERT: K  130 LEU cc_start: 0.6694 (tp) cc_final: 0.6438 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2537
  time to fit residues: 52.2889
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  : 0.770 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 81 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4456 r_free = 0.4456 target = 0.195443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.169919 restraints weight = 13330.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.173789 restraints weight = 8490.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.176497 restraints weight = 5883.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5942
moved from start:          0.6725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7768  Z= 0.229
  Angle     :  0.711  13.594  10417  Z= 0.381
  Chirality :  0.045   0.304   1172
  Planarity :  0.004   0.036   1323
  Dihedral  :  4.489  23.341   1000
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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:  0.62 (0.27), residues: 882
  helix:  1.36 (0.20), residues: 600
  sheet: -2.69 (1.00), residues: 22
  loop : -1.53 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 513 
 HIS   0.008   0.001   HIS C 553 
 PHE   0.020   0.002   PHE C 216 
 TYR   0.034   0.003   TYR C 130 
 ARG   0.007   0.001   ARG C 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05531 (  464)
  hydrogen bonds       : angle       4.81450 ( 1365)
  covalent geometry    : bond        0.00497 ( 7768)
  covalent geometry    : angle       0.71095 (10417)

*********************** 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
  157 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 LYS cc_start: 0.7993 (mptt) cc_final: 0.7486 (mptt)
REVERT: C  237 VAL cc_start: 0.6916 (t) cc_final: 0.6658 (t)
REVERT: C  243 GLU cc_start: 0.6735 (tp30) cc_final: 0.6278 (tp30)
REVERT: C  274 LYS cc_start: 0.7451 (pttp) cc_final: 0.7027 (tptt)
REVERT: C  275 THR cc_start: 0.7654 (p) cc_final: 0.7185 (t)
REVERT: C  279 MET cc_start: 0.4803 (tmm) cc_final: 0.4459 (tmm)
REVERT: C  301 LYS cc_start: 0.6603 (tmmt) cc_final: 0.6357 (tmmt)
REVERT: C  383 ARG cc_start: 0.6678 (ttm170) cc_final: 0.6419 (ttm170)
REVERT: C  413 ASP cc_start: 0.7239 (m-30) cc_final: 0.6955 (m-30)
REVERT: C  457 LYS cc_start: 0.7954 (tptt) cc_final: 0.7717 (tptt)
REVERT: C  554 MET cc_start: 0.7314 (mtt) cc_final: 0.6978 (mtt)
REVERT: C  589 LYS cc_start: 0.7442 (mmpt) cc_final: 0.7027 (mmpt)
REVERT: C  592 LEU cc_start: 0.7450 (mm) cc_final: 0.7197 (mt)
REVERT: C  611 TYR cc_start: 0.6529 (t80) cc_final: 0.5987 (t80)
REVERT: C  673 LYS cc_start: 0.8357 (ptmm) cc_final: 0.7968 (ptmm)
REVERT: C  707 ILE cc_start: 0.8094 (mt) cc_final: 0.7848 (mt)
REVERT: C  746 GLU cc_start: 0.6944 (tp30) cc_final: 0.6563 (tp30)
REVERT: C  766 TYR cc_start: 0.6617 (t80) cc_final: 0.6319 (t80)
REVERT: K  101 MET cc_start: 0.6665 (mmm) cc_final: 0.6033 (mmm)
REVERT: K  105 LEU cc_start: 0.7136 (mt) cc_final: 0.6715 (pp)
REVERT: K  129 GLN cc_start: 0.7586 (tt0) cc_final: 0.7282 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2415
  time to fit residues: 48.8024
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  : 0.777 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 85 optimal weight:    0.0010
   chunk 42 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 39 optimal weight:    0.1980
   chunk 83 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 64 optimal weight:    0.0050
   chunk 60 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.1600

-------------------------------------------------------------------------------
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**
K 137 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.208583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.181149 restraints weight = 13192.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.185852 restraints weight = 8121.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.188806 restraints weight = 5415.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5836
moved from start:          0.6790

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= 0.128
  Angle     :  0.619  13.765  10417  Z= 0.325
  Chirality :  0.041   0.306   1172
  Planarity :  0.003   0.031   1323
  Dihedral  :  4.200  23.022   1000
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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:  1.04 (0.28), residues: 882
  helix:  1.69 (0.21), residues: 602
  sheet: -2.32 (1.06), residues: 22
  loop : -1.46 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R  35 
 HIS   0.005   0.001   HIS K 137 
 PHE   0.016   0.001   PHE C 205 
 TYR   0.028   0.002   TYR C 130 
 ARG   0.005   0.001   ARG C 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  464)
  hydrogen bonds       : angle       4.46699 ( 1365)
  covalent geometry    : bond        0.00266 ( 7768)
  covalent geometry    : angle       0.61919 (10417)

********************** 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  : 0.879 
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  237 VAL cc_start: 0.6747 (t) cc_final: 0.6505 (t)
REVERT: C  243 GLU cc_start: 0.6624 (tp30) cc_final: 0.6140 (tp30)
REVERT: C  274 LYS cc_start: 0.7192 (pttp) cc_final: 0.6859 (tptt)
REVERT: C  279 MET cc_start: 0.4561 (tmm) cc_final: 0.4141 (tmm)
REVERT: C  377 PHE cc_start: 0.7641 (p90) cc_final: 0.7352 (p90)
REVERT: C  383 ARG cc_start: 0.6528 (ttm170) cc_final: 0.6294 (ttm170)
REVERT: C  413 ASP cc_start: 0.7277 (m-30) cc_final: 0.7004 (m-30)
REVERT: C  457 LYS cc_start: 0.7836 (tptt) cc_final: 0.7586 (tptt)
REVERT: C  503 LEU cc_start: 0.7496 (tp) cc_final: 0.7284 (tp)
REVERT: C  524 ILE cc_start: 0.7725 (mm) cc_final: 0.7433 (mm)
REVERT: C  536 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7401 (tpt90)
REVERT: C  554 MET cc_start: 0.7189 (mtt) cc_final: 0.6881 (mtt)
REVERT: C  589 LYS cc_start: 0.7408 (mmpt) cc_final: 0.6988 (mmpt)
REVERT: C  611 TYR cc_start: 0.6315 (t80) cc_final: 0.5722 (t80)
REVERT: C  673 LYS cc_start: 0.8241 (ptmm) cc_final: 0.7850 (ptmm)
REVERT: C  707 ILE cc_start: 0.8060 (mt) cc_final: 0.7856 (mt)
REVERT: C  734 PHE cc_start: 0.8122 (p90) cc_final: 0.7917 (p90)
REVERT: C  766 TYR cc_start: 0.6555 (t80) cc_final: 0.6149 (t80)
REVERT: K  101 MET cc_start: 0.6694 (mmm) cc_final: 0.5850 (mmm)
REVERT: K  130 LEU cc_start: 0.6469 (tp) cc_final: 0.6240 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2678
  time to fit residues: 52.7885
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  : 0.769 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 46 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0870
   chunk 51 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0000
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0970
   chunk 8 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.2360

-------------------------------------------------------------------------------
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 = 0.4535 r_free = 0.4535 target = 0.206389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.179037 restraints weight = 13115.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.183692 restraints weight = 8228.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.186788 restraints weight = 5506.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5853
moved from start:          0.6927

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= 0.140
  Angle     :  0.632  13.638  10417  Z= 0.331
  Chirality :  0.041   0.307   1172
  Planarity :  0.003   0.033   1323
  Dihedral  :  4.148  19.786   1000
  Min Nonbonded Distance : 2.486

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:  1.01 (0.28), residues: 882
  helix:  1.69 (0.21), residues: 603
  sheet: -2.26 (1.08), residues: 20
  loop : -1.57 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP R  35 
 HIS   0.004   0.001   HIS C 543 
 PHE   0.019   0.002   PHE C 216 
 TYR   0.020   0.002   TYR C 130 
 ARG   0.005   0.000   ARG C 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04533 (  464)
  hydrogen bonds       : angle       4.49060 ( 1365)
  covalent geometry    : bond        0.00298 ( 7768)
  covalent geometry    : angle       0.63204 (10417)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3144.69 seconds
wall clock time: 56 minutes 21.96 seconds (3381.96 seconds total)