Starting phenix.real_space_refine
on Thu Mar  6 03:38:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uac_26420/03_2025/7uac_26420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uac_26420/03_2025/7uac_26420.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2025/7uac_26420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2025/7uac_26420.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2025/7uac_26420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2025/7uac_26420.cif"
  }
  resolution = 2.7
  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=   0.003 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     S      21      5.16       5
     C    2860      2.51       5
     N     759      2.21       5
     O     897      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4540
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 4404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 4404
          Classifications: {'peptide': 546}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 528}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.42, per 1000 atoms: 0.75
  Number of scatterers: 4540
  At special positions: 0
  Unit cell: (94.34, 77.38, 92.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      21     16.00
     O     897      8.00
     N     759      7.00
     C    2860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H 107 " - pdb=" SG  CYS H 259 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 128 " - pdb=" SG  CYS H 147 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 269 " - pdb=" SG  CYS H 277 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 343 " - pdb=" SG  CYS H 431 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 557 " - pdb=" SG  CYS H 559 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A   1 " - " ASN H 140 "
      " NAG B   1 " - " ASN H 222 "
      " NAG C   1 " - " ASN H 414 "
      " NAG D   1 " - " ASN H 440 "
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 523.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN H 702 "
        pdb="ZN    ZN H 702 " - pdb=" NE2 HIS H 159 "
        pdb="ZN    ZN H 702 " - pdb=" NE2 HIS H 165 "
        pdb="ZN    ZN H 702 " - pdb=" NE2 HIS H 155 "


  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 9 sheets defined
      21.8% alpha, 27.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'H' and resid 42 through 51
    Processing helix  chain 'H' and resid 88 through 106
    Processing helix  chain 'H' and resid 149 through 161
    Processing helix  chain 'H' and resid 165 through 169
      removed outlier: 3.606A  pdb=" N   SER H 168 " --> pdb=" O   HIS H 165 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 171 through 174
    Processing helix  chain 'H' and resid 180 through 183
    Processing helix  chain 'H' and resid 187 through 192
    Processing helix  chain 'H' and resid 232 through 238
    Processing helix  chain 'H' and resid 246 through 258
    Processing helix  chain 'H' and resid 275 through 279
    Processing helix  chain 'H' and resid 440 through 448
    Processing helix  chain 'H' and resid 516 through 520
    Processing helix  chain 'H' and resid 546 through 550
    Processing helix  chain 'H' and resid 573 through 577
    Processing helix  chain 'H' and resid 582 through 586
    Processing helix  chain 'H' and resid 597 through 600
    Processing sheet with id=AA1, first strand: chain 'H' and resid 110 through 112
      removed outlier: 7.939A  pdb=" N   PHE H 122 " --> pdb=" O   PRO H  80 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE H  82 " --> pdb=" O   PHE H 122 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 176 through 178
    Processing sheet with id=AA3, first strand: chain 'H' and resid 265 through 269
    Processing sheet with id=AA4, first strand: chain 'H' and resid 265 through 269
      removed outlier: 5.664A  pdb=" N   LEU H 421 " --> pdb=" O   LYS H 349 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   LYS H 349 " --> pdb=" O   LEU H 421 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   ASP H 423 " --> pdb=" O   PHE H 347 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   PHE H 347 " --> pdb=" O   ASP H 423 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 280 through 281
      removed outlier: 6.826A  pdb=" N   LEU H 358 " --> pdb=" O   THR H 379 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   THR H 379 " --> pdb=" O   LEU H 358 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL H 360 " --> pdb=" O   VAL H 377 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 434 through 438
    Processing sheet with id=AA7, first strand: chain 'H' and resid 454 through 455
    Processing sheet with id=AA8, first strand: chain 'H' and resid 454 through 455
      removed outlier: 3.961A  pdb=" N   GLY H 466 " --> pdb=" O   CYS H 489 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LEU H 482 " --> pdb=" O   GLY H 569 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU H 484 " --> pdb=" O   TRP H 567 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 551 through 554

    156 hydrogen bonds defined for protein.
    375 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 861
        1.32 -     1.45: 1258
        1.45 -     1.57: 2495
        1.57 -     1.69: 0
        1.69 -     1.82: 30
  Bond restraints: 4644
  Sorted by residual:
  bond pdb=" N   PRO H 412 "
       pdb=" CA  PRO H 412 "
    ideal  model  delta    sigma   weight residual
    1.471  1.410  0.061 1.29e-02 6.01e+03 2.26e+01
  bond pdb=" C   GLN H  40 "
       pdb=" N   LYS H  41 "
    ideal  model  delta    sigma   weight residual
    1.331  1.403 -0.072 1.51e-02 4.39e+03 2.26e+01
  bond pdb=" C   GLU H  39 "
       pdb=" N   GLN H  40 "
    ideal  model  delta    sigma   weight residual
    1.330  1.385 -0.055 1.32e-02 5.74e+03 1.75e+01
  bond pdb=" N   ILE H 276 "
       pdb=" CA  ILE H 276 "
    ideal  model  delta    sigma   weight residual
    1.459  1.506 -0.047 1.25e-02 6.40e+03 1.43e+01
  bond pdb=" CA  SER H 168 "
       pdb=" CB  SER H 168 "
    ideal  model  delta    sigma   weight residual
    1.530  1.472  0.058 1.54e-02 4.22e+03 1.40e+01
  ... (remaining 4639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 4534
        1.87 -     3.74: 1521
        3.74 -     5.61: 202
        5.61 -     7.48: 30
        7.48 -     9.35: 5
  Bond angle restraints: 6292
  Sorted by residual:
  angle pdb=" CA  PHE H 590 "
        pdb=" CB  PHE H 590 "
        pdb=" CG  PHE H 590 "
      ideal   model   delta    sigma   weight residual
     113.80  120.35   -6.55 1.00e+00 1.00e+00 4.28e+01
  angle pdb=" N   GLN H 135 "
        pdb=" CA  GLN H 135 "
        pdb=" C   GLN H 135 "
      ideal   model   delta    sigma   weight residual
     113.30  104.70    8.60 1.34e+00 5.57e-01 4.12e+01
  angle pdb=" C   PRO H 412 "
        pdb=" CA  PRO H 412 "
        pdb=" CB  PRO H 412 "
      ideal   model   delta    sigma   weight residual
     112.55  121.90   -9.35 1.50e+00 4.44e-01 3.88e+01
  angle pdb=" CA  GLY H 138 "
        pdb=" C   GLY H 138 "
        pdb=" O   GLY H 138 "
      ideal   model   delta    sigma   weight residual
     122.23  118.25    3.98 6.90e-01 2.10e+00 3.32e+01
  angle pdb=" CA  ASP H 134 "
        pdb=" CB  ASP H 134 "
        pdb=" CG  ASP H 134 "
      ideal   model   delta    sigma   weight residual
     112.60  118.31   -5.71 1.00e+00 1.00e+00 3.26e+01
  ... (remaining 6287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.46: 2693
       22.46 -    44.92: 116
       44.92 -    67.38: 22
       67.38 -    89.84: 7
       89.84 -   112.30: 22
  Dihedral angle restraints: 2860
    sinusoidal: 1279
      harmonic: 1581
  Sorted by residual:
  dihedral pdb=" CB  CYS H 128 "
           pdb=" SG  CYS H 128 "
           pdb=" SG  CYS H 147 "
           pdb=" CB  CYS H 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.89  -58.89     1      1.00e+01 1.00e-02 4.64e+01
  dihedral pdb=" C   PRO H 412 "
           pdb=" N   PRO H 412 "
           pdb=" CA  PRO H 412 "
           pdb=" CB  PRO H 412 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -134.70   14.00     0      2.50e+00 1.60e-01 3.14e+01
  dihedral pdb=" CA  ILE H 424 "
           pdb=" C   ILE H 424 "
           pdb=" N   THR H 425 "
           pdb=" CA  THR H 425 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.34   26.66     0      5.00e+00 4.00e-02 2.84e+01
  ... (remaining 2857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 571
       0.128 -    0.256: 109
       0.256 -    0.384: 18
       0.384 -    0.511: 2
       0.511 -    0.639: 1
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C1  FUC C   4 "
            pdb=" O6  NAG C   1 "
            pdb=" C2  FUC C   4 "
            pdb=" O5  FUC C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-02 2.50e+03 1.54e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 7.76e+01
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-02 2.50e+03 5.09e+01
  ... (remaining 698 not shown)

  Planarity restraints: 809
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.228 2.00e-02 2.50e+03   1.93e-01 4.64e+02
        pdb=" C7  NAG A   1 "    0.056 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.155 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.326 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.218 2.00e-02 2.50e+03   1.82e-01 4.12e+02
        pdb=" C7  NAG D   1 "    0.059 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.154 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.300 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.115 2.00e-02 2.50e+03   9.51e-02 1.13e+02
        pdb=" C7  NAG C   1 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.087 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.151 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 806 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.28: 3
        2.28 -     2.94: 1967
        2.94 -     3.59: 5970
        3.59 -     4.25: 11163
        4.25 -     4.90: 18169
  Nonbonded interactions: 37272
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H  58 "
            pdb="ZN    ZN H 702 "
     model   vdw
     1.626 2.230
  nonbonded pdb=" CG  ASP H  58 "
            pdb="ZN    ZN H 702 "
     model   vdw
     2.169 2.460
  nonbonded pdb=" OD2 ASP H  58 "
            pdb="ZN    ZN H 702 "
     model   vdw
     2.250 2.230
  nonbonded pdb=" OD1 ASP H 288 "
            pdb="CA    CA H 701 "
     model   vdw
     2.332 2.510
  nonbonded pdb=" OD1 ASP H 285 "
            pdb="CA    CA H 701 "
     model   vdw
     2.343 2.510
  ... (remaining 37267 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.300
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:13.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
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      :  0.012   0.072   4644  Z= 0.766
  Angle     :  1.786   9.345   6292  Z= 1.201
  Chirality :  0.109   0.639    701
  Planarity :  0.015   0.193    805
  Dihedral  : 17.447 112.300   1829
  Min Nonbonded Distance : 1.626

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.98 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.63 (0.33), residues: 538
  helix: -0.90 (0.48), residues: 78
  sheet:  0.08 (0.43), residues: 127
  loop : -0.44 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.012   TRP H 180 
 HIS   0.013   0.003   HIS H 159 
 PHE   0.060   0.011   PHE H 593 
 TYR   0.081   0.014   TYR H 119 
 ARG   0.007   0.001   ARG H 169 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: H  130 SER cc_start: 0.8444 (t) cc_final: 0.8059 (m)
REVERT: H  150 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7761 (ttmt)
REVERT: H  154 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7768 (mt-10)
REVERT: H  156 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7882 (mm-30)
REVERT: H  183 ILE cc_start: 0.9047 (mt) cc_final: 0.8817 (mt)
REVERT: H  192 ASP cc_start: 0.7554 (m-30) cc_final: 0.7349 (m-30)
REVERT: H  207 ASP cc_start: 0.7777 (t0) cc_final: 0.7274 (t0)
REVERT: H  212 MET cc_start: 0.8763 (mmm) cc_final: 0.8176 (mmp)
REVERT: H  225 VAL cc_start: 0.8804 (t) cc_final: 0.8522 (p)
REVERT: H  244 ASP cc_start: 0.7817 (t70) cc_final: 0.7600 (t0)
REVERT: H  249 ASP cc_start: 0.7589 (m-30) cc_final: 0.7367 (m-30)
REVERT: H  251 GLU cc_start: 0.7637 (tt0) cc_final: 0.7378 (tt0)
REVERT: H  256 MET cc_start: 0.8696 (ttp) cc_final: 0.8272 (ttt)
REVERT: H  323 SER cc_start: 0.8765 (t) cc_final: 0.8346 (p)
REVERT: H  326 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: H  423 ASP cc_start: 0.8088 (m-30) cc_final: 0.7654 (m-30)
REVERT: H  492 GLU cc_start: 0.7887 (pt0) cc_final: 0.7250 (tm-30)
REVERT: H  525 MET cc_start: 0.7589 (mmt) cc_final: 0.7310 (mmm)
REVERT: H  527 PHE cc_start: 0.8466 (p90) cc_final: 0.8030 (p90)
REVERT: H  543 ILE cc_start: 0.9345 (mt) cc_final: 0.9120 (mm)
REVERT: H  565 LEU cc_start: 0.9180 (tt) cc_final: 0.8928 (tm)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 1.2753
  time to fit residues: 214.5112
Evaluate side-chains
  98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
H  40 GLN
H 124 GLN
H 203 ASN
H 370 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.091533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.081852 restraints weight = 8484.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.39
r_work: 0.3148 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4644  Z= 0.261
  Angle     :  0.713   8.559   6292  Z= 0.370
  Chirality :  0.049   0.196    701
  Planarity :  0.004   0.035    805
  Dihedral  : 14.534 108.004    796
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.16 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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:  0.01 (0.33), residues: 538
  helix:  0.90 (0.62), residues: 71
  sheet:  0.42 (0.42), residues: 141
  loop : -0.34 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 129 
 HIS   0.003   0.001   HIS H 155 
 PHE   0.016   0.002   PHE H 593 
 TYR   0.017   0.002   TYR H 113 
 ARG   0.007   0.001   ARG H  74 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: H   42 ASP cc_start: 0.7291 (p0) cc_final: 0.6924 (p0)
REVERT: H  105 LYS cc_start: 0.8820 (mttt) cc_final: 0.8614 (mttt)
REVERT: H  116 GLU cc_start: 0.7370 (mp0) cc_final: 0.7015 (mp0)
REVERT: H  117 SER cc_start: 0.8294 (m) cc_final: 0.8027 (p)
REVERT: H  130 SER cc_start: 0.8822 (t) cc_final: 0.8331 (m)
REVERT: H  192 ASP cc_start: 0.8215 (m-30) cc_final: 0.7871 (m-30)
REVERT: H  207 ASP cc_start: 0.8303 (t0) cc_final: 0.7985 (t0)
REVERT: H  212 MET cc_start: 0.8893 (mmm) cc_final: 0.8641 (mmp)
REVERT: H  238 ILE cc_start: 0.9067 (mp) cc_final: 0.8857 (mp)
REVERT: H  244 ASP cc_start: 0.8408 (t70) cc_final: 0.8183 (t0)
REVERT: H  249 ASP cc_start: 0.8441 (m-30) cc_final: 0.8101 (m-30)
REVERT: H  251 GLU cc_start: 0.8714 (tt0) cc_final: 0.8205 (tp30)
REVERT: H  284 ARG cc_start: 0.5901 (ttt180) cc_final: 0.0618 (tmt170)
REVERT: H  304 LEU cc_start: 0.9349 (mt) cc_final: 0.8950 (mm)
REVERT: H  319 THR cc_start: 0.8862 (p) cc_final: 0.8567 (m)
REVERT: H  329 LEU cc_start: 0.9140 (mt) cc_final: 0.8933 (mt)
REVERT: H  331 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8054 (mp0)
REVERT: H  385 ASP cc_start: 0.8815 (t0) cc_final: 0.8518 (t0)
REVERT: H  415 SER cc_start: 0.8829 (t) cc_final: 0.8450 (p)
REVERT: H  428 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: H  483 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7912 (ttt180)
REVERT: H  499 TRP cc_start: 0.8858 (m100) cc_final: 0.8544 (m100)
REVERT: H  525 MET cc_start: 0.8497 (mmt) cc_final: 0.8244 (mmm)
REVERT: H  543 ILE cc_start: 0.9382 (mt) cc_final: 0.9149 (mm)
  outliers start: 12
  outliers final: 2
  residues processed: 114
  average time/residue: 1.1323
  time to fit residues: 134.0148
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  368 THR
Chi-restraints excluded: chain H residue  552 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 386 HIS
H 455 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.092365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.082582 restraints weight = 8574.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.44
r_work: 0.3153 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4644  Z= 0.206
  Angle     :  0.644   6.859   6292  Z= 0.333
  Chirality :  0.046   0.168    701
  Planarity :  0.004   0.043    805
  Dihedral  : 10.403 108.716    796
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.12 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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:  0.11 (0.34), residues: 538
  helix:  0.88 (0.61), residues: 77
  sheet:  0.48 (0.42), residues: 143
  loop : -0.27 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 289 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.026   0.002   PHE H 527 
 TYR   0.009   0.001   TYR H 403 
 ARG   0.009   0.001   ARG H 546 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.516 
Fit side-chains
REVERT: H   42 ASP cc_start: 0.7230 (p0) cc_final: 0.7002 (p0)
REVERT: H  116 GLU cc_start: 0.7558 (mp0) cc_final: 0.7217 (mp0)
REVERT: H  130 SER cc_start: 0.8824 (t) cc_final: 0.8338 (m)
REVERT: H  192 ASP cc_start: 0.8252 (m-30) cc_final: 0.7878 (m-30)
REVERT: H  207 ASP cc_start: 0.8307 (t0) cc_final: 0.7893 (t0)
REVERT: H  212 MET cc_start: 0.8924 (mmm) cc_final: 0.8599 (mmp)
REVERT: H  238 ILE cc_start: 0.9155 (mp) cc_final: 0.8934 (mp)
REVERT: H  244 ASP cc_start: 0.8418 (t70) cc_final: 0.8100 (t0)
REVERT: H  249 ASP cc_start: 0.8459 (m-30) cc_final: 0.7796 (m-30)
REVERT: H  252 ARG cc_start: 0.9104 (mtm-85) cc_final: 0.8672 (mtm-85)
REVERT: H  284 ARG cc_start: 0.5905 (ttt180) cc_final: 0.0751 (tmt170)
REVERT: H  301 ASP cc_start: 0.7899 (p0) cc_final: 0.7472 (p0)
REVERT: H  319 THR cc_start: 0.8928 (p) cc_final: 0.8383 (m)
REVERT: H  331 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8042 (mp0)
REVERT: H  385 ASP cc_start: 0.8913 (t0) cc_final: 0.8670 (t0)
REVERT: H  411 ASP cc_start: 0.8142 (t0) cc_final: 0.7893 (t0)
REVERT: H  415 SER cc_start: 0.8886 (t) cc_final: 0.8414 (p)
REVERT: H  428 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: H  483 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7905 (ttt180)
REVERT: H  489 CYS cc_start: 0.8536 (m) cc_final: 0.8325 (m)
REVERT: H  492 GLU cc_start: 0.8127 (pm20) cc_final: 0.7913 (pm20)
REVERT: H  494 ASP cc_start: 0.8460 (p0) cc_final: 0.7593 (t0)
REVERT: H  525 MET cc_start: 0.8537 (mmt) cc_final: 0.8310 (mmm)
REVERT: H  543 ILE cc_start: 0.9365 (mt) cc_final: 0.9096 (mm)
REVERT: H  546 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7157 (mmm160)
REVERT: H  578 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8254 (ptp90)
REVERT: H  586 ASP cc_start: 0.7601 (m-30) cc_final: 0.7326 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 108
  average time/residue: 1.1733
  time to fit residues: 131.8412
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  218 SER
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  368 THR
Chi-restraints excluded: chain H residue  448 THR
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  578 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0370
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.091680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.081978 restraints weight = 8646.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.44
r_work: 0.3141 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4644  Z= 0.195
  Angle     :  0.606   7.489   6292  Z= 0.317
  Chirality :  0.045   0.172    701
  Planarity :  0.004   0.042    805
  Dihedral  :  8.570  96.197    796
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.70 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.00 (0.35), residues: 538
  helix:  0.94 (0.61), residues: 77
  sheet:  0.23 (0.42), residues: 148
  loop : -0.30 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 289 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.028   0.002   PHE H 527 
 TYR   0.009   0.001   TYR H 403 
 ARG   0.005   0.001   ARG H  74 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.471 
Fit side-chains
REVERT: H  116 GLU cc_start: 0.7685 (mp0) cc_final: 0.7308 (mp0)
REVERT: H  130 SER cc_start: 0.8841 (t) cc_final: 0.8367 (m)
REVERT: H  192 ASP cc_start: 0.8217 (m-30) cc_final: 0.7860 (m-30)
REVERT: H  207 ASP cc_start: 0.8265 (t0) cc_final: 0.7865 (t0)
REVERT: H  212 MET cc_start: 0.8935 (mmm) cc_final: 0.8549 (mmp)
REVERT: H  249 ASP cc_start: 0.8460 (m-30) cc_final: 0.7829 (m-30)
REVERT: H  251 GLU cc_start: 0.8757 (tt0) cc_final: 0.8114 (tp30)
REVERT: H  252 ARG cc_start: 0.9061 (mtm-85) cc_final: 0.8680 (mtm-85)
REVERT: H  284 ARG cc_start: 0.6000 (ttt180) cc_final: 0.4757 (mtp180)
REVERT: H  301 ASP cc_start: 0.8022 (p0) cc_final: 0.7593 (p0)
REVERT: H  319 THR cc_start: 0.9008 (p) cc_final: 0.8578 (p)
REVERT: H  331 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8020 (mp0)
REVERT: H  385 ASP cc_start: 0.8958 (t0) cc_final: 0.8710 (t0)
REVERT: H  411 ASP cc_start: 0.8148 (t0) cc_final: 0.7850 (t0)
REVERT: H  415 SER cc_start: 0.8891 (t) cc_final: 0.8387 (p)
REVERT: H  423 ASP cc_start: 0.8567 (m-30) cc_final: 0.8209 (m-30)
REVERT: H  425 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8378 (p)
REVERT: H  428 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8176 (mt-10)
REVERT: H  483 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7875 (ttt180)
REVERT: H  489 CYS cc_start: 0.8557 (m) cc_final: 0.8251 (p)
REVERT: H  494 ASP cc_start: 0.8473 (p0) cc_final: 0.8148 (p0)
REVERT: H  525 MET cc_start: 0.8504 (mmt) cc_final: 0.8235 (mmm)
REVERT: H  543 ILE cc_start: 0.9333 (mt) cc_final: 0.9075 (mm)
REVERT: H  578 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8192 (ptp90)
REVERT: H  584 ASN cc_start: 0.8803 (t0) cc_final: 0.8198 (t160)
REVERT: H  586 ASP cc_start: 0.7476 (m-30) cc_final: 0.7097 (m-30)
  outliers start: 15
  outliers final: 3
  residues processed: 111
  average time/residue: 0.9965
  time to fit residues: 115.4074
Evaluate side-chains
  96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  448 THR
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  578 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 203 ASN
H 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.089194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.079692 restraints weight = 8738.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.43
r_work: 0.3099 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4644  Z= 0.302
  Angle     :  0.622   8.125   6292  Z= 0.327
  Chirality :  0.046   0.169    701
  Planarity :  0.004   0.041    805
  Dihedral  :  7.588  78.836    796
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.15 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.21 (0.35), residues: 538
  helix:  0.60 (0.57), residues: 84
  sheet:  0.30 (0.42), residues: 150
  loop : -0.54 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 567 
 HIS   0.006   0.001   HIS H 159 
 PHE   0.028   0.002   PHE H 527 
 TYR   0.011   0.001   TYR H  81 
 ARG   0.007   0.001   ARG H  74 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.464 
Fit side-chains
REVERT: H  116 GLU cc_start: 0.7791 (mp0) cc_final: 0.7404 (mp0)
REVERT: H  130 SER cc_start: 0.8820 (t) cc_final: 0.8339 (m)
REVERT: H  171 ASP cc_start: 0.8342 (p0) cc_final: 0.8043 (p0)
REVERT: H  192 ASP cc_start: 0.8207 (m-30) cc_final: 0.7827 (m-30)
REVERT: H  207 ASP cc_start: 0.8266 (t0) cc_final: 0.7873 (t0)
REVERT: H  212 MET cc_start: 0.9033 (mmm) cc_final: 0.8749 (mmp)
REVERT: H  249 ASP cc_start: 0.8443 (m-30) cc_final: 0.7845 (m-30)
REVERT: H  252 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.8697 (mtm-85)
REVERT: H  284 ARG cc_start: 0.6134 (ttt180) cc_final: 0.4869 (mtp180)
REVERT: H  301 ASP cc_start: 0.8285 (p0) cc_final: 0.7912 (p0)
REVERT: H  331 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8055 (mp0)
REVERT: H  385 ASP cc_start: 0.8947 (t0) cc_final: 0.8707 (t0)
REVERT: H  411 ASP cc_start: 0.8147 (t0) cc_final: 0.7920 (t0)
REVERT: H  415 SER cc_start: 0.8926 (t) cc_final: 0.8526 (p)
REVERT: H  428 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8162 (mt-10)
REVERT: H  483 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.8010 (ttt180)
REVERT: H  489 CYS cc_start: 0.8535 (m) cc_final: 0.8286 (p)
REVERT: H  530 SER cc_start: 0.9238 (t) cc_final: 0.8946 (t)
REVERT: H  543 ILE cc_start: 0.9334 (mt) cc_final: 0.9055 (mm)
REVERT: H  584 ASN cc_start: 0.8796 (t0) cc_final: 0.8545 (t160)
  outliers start: 11
  outliers final: 6
  residues processed: 96
  average time/residue: 1.0479
  time to fit residues: 105.0658
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  243 LEU
Chi-restraints excluded: chain H residue  329 LEU
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  576 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0010
   overall best weight:    0.8390

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.089973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.080527 restraints weight = 8582.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.39
r_work: 0.3121 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.4163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4644  Z= 0.219
  Angle     :  0.619   7.642   6292  Z= 0.322
  Chirality :  0.045   0.166    701
  Planarity :  0.004   0.042    805
  Dihedral  :  6.436  51.323    796
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.56 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.11 (0.35), residues: 538
  helix:  0.83 (0.59), residues: 83
  sheet:  0.25 (0.42), residues: 150
  loop : -0.44 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 567 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.028   0.002   PHE H 527 
 TYR   0.009   0.001   TYR H  81 
 ARG   0.005   0.001   ARG H  74 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.657 
Fit side-chains
REVERT: H  116 GLU cc_start: 0.7792 (mp0) cc_final: 0.7412 (mp0)
REVERT: H  130 SER cc_start: 0.8834 (t) cc_final: 0.8362 (m)
REVERT: H  166 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8367 (mm-30)
REVERT: H  171 ASP cc_start: 0.8309 (p0) cc_final: 0.8008 (p0)
REVERT: H  192 ASP cc_start: 0.8178 (m-30) cc_final: 0.7792 (m-30)
REVERT: H  207 ASP cc_start: 0.8239 (t0) cc_final: 0.7772 (t0)
REVERT: H  212 MET cc_start: 0.8966 (mmm) cc_final: 0.8711 (mmp)
REVERT: H  249 ASP cc_start: 0.8440 (m-30) cc_final: 0.7857 (m-30)
REVERT: H  252 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8639 (mtm-85)
REVERT: H  284 ARG cc_start: 0.6125 (ttt180) cc_final: 0.4820 (mtp180)
REVERT: H  301 ASP cc_start: 0.8289 (p0) cc_final: 0.7908 (p0)
REVERT: H  319 THR cc_start: 0.9013 (p) cc_final: 0.8594 (m)
REVERT: H  331 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8005 (mp0)
REVERT: H  385 ASP cc_start: 0.8980 (t0) cc_final: 0.8755 (t0)
REVERT: H  411 ASP cc_start: 0.8047 (t0) cc_final: 0.7842 (t0)
REVERT: H  415 SER cc_start: 0.8889 (t) cc_final: 0.8429 (p)
REVERT: H  428 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8143 (mt-10)
REVERT: H  483 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7886 (ttt180)
REVERT: H  489 CYS cc_start: 0.8535 (m) cc_final: 0.8283 (p)
REVERT: H  525 MET cc_start: 0.8516 (mmm) cc_final: 0.8108 (mmm)
REVERT: H  543 ILE cc_start: 0.9313 (mt) cc_final: 0.8998 (mm)
REVERT: H  584 ASN cc_start: 0.8883 (t0) cc_final: 0.8279 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 103
  average time/residue: 1.0905
  time to fit residues: 117.0711
Evaluate side-chains
  96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  329 LEU
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  576 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.088833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.079146 restraints weight = 8657.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.44
r_work: 0.3102 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4644  Z= 0.279
  Angle     :  0.645   7.917   6292  Z= 0.339
  Chirality :  0.045   0.162    701
  Planarity :  0.004   0.047    805
  Dihedral  :  5.701  51.007    796
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.25 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.17 (0.35), residues: 538
  helix:  0.79 (0.59), residues: 83
  sheet:  0.22 (0.42), residues: 150
  loop : -0.49 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP H 567 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.033   0.002   PHE H 527 
 TYR   0.010   0.001   TYR H  81 
 ARG   0.006   0.001   ARG H 546 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: H  106 SER cc_start: 0.8834 (t) cc_final: 0.8564 (p)
REVERT: H  116 GLU cc_start: 0.7836 (mp0) cc_final: 0.7460 (mp0)
REVERT: H  130 SER cc_start: 0.8821 (t) cc_final: 0.8337 (m)
REVERT: H  171 ASP cc_start: 0.8283 (p0) cc_final: 0.7995 (p0)
REVERT: H  192 ASP cc_start: 0.8234 (m-30) cc_final: 0.7777 (m-30)
REVERT: H  207 ASP cc_start: 0.8262 (t0) cc_final: 0.7805 (t0)
REVERT: H  212 MET cc_start: 0.9010 (mmm) cc_final: 0.8467 (mmm)
REVERT: H  249 ASP cc_start: 0.8499 (m-30) cc_final: 0.7900 (m-30)
REVERT: H  252 ARG cc_start: 0.9092 (mtm-85) cc_final: 0.8693 (mtm-85)
REVERT: H  284 ARG cc_start: 0.6131 (ttt180) cc_final: 0.4867 (mtp180)
REVERT: H  301 ASP cc_start: 0.8379 (p0) cc_final: 0.8005 (p0)
REVERT: H  319 THR cc_start: 0.9071 (p) cc_final: 0.8672 (m)
REVERT: H  331 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8099 (mp0)
REVERT: H  385 ASP cc_start: 0.8991 (t0) cc_final: 0.8754 (t0)
REVERT: H  411 ASP cc_start: 0.8083 (t0) cc_final: 0.7857 (t0)
REVERT: H  415 SER cc_start: 0.8876 (t) cc_final: 0.8458 (p)
REVERT: H  428 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8178 (mt-10)
REVERT: H  483 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7957 (ttt180)
REVERT: H  489 CYS cc_start: 0.8524 (m) cc_final: 0.8268 (p)
REVERT: H  525 MET cc_start: 0.8573 (mmm) cc_final: 0.8215 (mmm)
REVERT: H  543 ILE cc_start: 0.9309 (mt) cc_final: 0.9000 (mm)
REVERT: H  584 ASN cc_start: 0.8907 (t0) cc_final: 0.8348 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 99
  average time/residue: 1.0212
  time to fit residues: 105.3763
Evaluate side-chains
  93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  329 LEU
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  576 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.088803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.079159 restraints weight = 8571.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.41
r_work: 0.3099 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4644  Z= 0.281
  Angle     :  0.653  12.957   6292  Z= 0.339
  Chirality :  0.045   0.157    701
  Planarity :  0.004   0.049    805
  Dihedral  :  5.387  50.820    796
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.69 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.20 (0.35), residues: 538
  helix:  0.88 (0.59), residues: 83
  sheet:  0.22 (0.42), residues: 150
  loop : -0.56 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP H 567 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.034   0.002   PHE H 527 
 TYR   0.010   0.001   TYR H  81 
 ARG   0.006   0.001   ARG H 546 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: H  106 SER cc_start: 0.8802 (t) cc_final: 0.8500 (p)
REVERT: H  116 GLU cc_start: 0.7861 (mp0) cc_final: 0.7476 (mp0)
REVERT: H  130 SER cc_start: 0.8820 (t) cc_final: 0.8347 (m)
REVERT: H  171 ASP cc_start: 0.8271 (p0) cc_final: 0.7985 (p0)
REVERT: H  192 ASP cc_start: 0.8212 (m-30) cc_final: 0.7749 (m-30)
REVERT: H  207 ASP cc_start: 0.8276 (t0) cc_final: 0.7817 (t0)
REVERT: H  212 MET cc_start: 0.8985 (mmm) cc_final: 0.8434 (mmm)
REVERT: H  249 ASP cc_start: 0.8485 (m-30) cc_final: 0.7901 (m-30)
REVERT: H  252 ARG cc_start: 0.9086 (mtm-85) cc_final: 0.8669 (mtm-85)
REVERT: H  280 ILE cc_start: 0.9020 (pt) cc_final: 0.8706 (pp)
REVERT: H  284 ARG cc_start: 0.6151 (ttt180) cc_final: 0.4884 (mtp180)
REVERT: H  301 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8013 (p0)
REVERT: H  331 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8004 (mp0)
REVERT: H  385 ASP cc_start: 0.8972 (t0) cc_final: 0.8753 (t0)
REVERT: H  411 ASP cc_start: 0.8143 (t0) cc_final: 0.7905 (t0)
REVERT: H  415 SER cc_start: 0.8882 (t) cc_final: 0.8476 (p)
REVERT: H  428 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8176 (mt-10)
REVERT: H  483 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7962 (ttt180)
REVERT: H  489 CYS cc_start: 0.8532 (m) cc_final: 0.8270 (p)
REVERT: H  502 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: H  525 MET cc_start: 0.8593 (mmm) cc_final: 0.8221 (mmm)
REVERT: H  543 ILE cc_start: 0.9298 (mt) cc_final: 0.8996 (mm)
REVERT: H  584 ASN cc_start: 0.8942 (t0) cc_final: 0.8332 (t0)
REVERT: H  594 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7506 (mp0)
  outliers start: 9
  outliers final: 5
  residues processed: 95
  average time/residue: 1.1074
  time to fit residues: 109.5462
Evaluate side-chains
  97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  301 ASP
Chi-restraints excluded: chain H residue  329 LEU
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  576 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 49 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0670
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7898

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.089264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.079689 restraints weight = 8558.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.40
r_work: 0.3110 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4644  Z= 0.226
  Angle     :  0.654  11.923   6292  Z= 0.340
  Chirality :  0.044   0.163    701
  Planarity :  0.004   0.046    805
  Dihedral  :  5.239  51.296    796
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 21.28 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.10 (0.35), residues: 538
  helix:  0.91 (0.59), residues: 83
  sheet:  0.30 (0.42), residues: 150
  loop : -0.49 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP H 567 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.033   0.002   PHE H 527 
 TYR   0.009   0.001   TYR H  81 
 ARG   0.005   0.001   ARG H 546 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: H  106 SER cc_start: 0.8734 (t) cc_final: 0.8415 (p)
REVERT: H  116 GLU cc_start: 0.7857 (mp0) cc_final: 0.7545 (mp0)
REVERT: H  130 SER cc_start: 0.8825 (t) cc_final: 0.8359 (m)
REVERT: H  171 ASP cc_start: 0.8258 (p0) cc_final: 0.7965 (p0)
REVERT: H  192 ASP cc_start: 0.8213 (m-30) cc_final: 0.7759 (m-30)
REVERT: H  207 ASP cc_start: 0.8273 (t0) cc_final: 0.7820 (t0)
REVERT: H  212 MET cc_start: 0.8984 (mmm) cc_final: 0.8527 (mmm)
REVERT: H  215 GLN cc_start: 0.8468 (pm20) cc_final: 0.8178 (pm20)
REVERT: H  249 ASP cc_start: 0.8495 (m-30) cc_final: 0.7913 (m-30)
REVERT: H  252 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8639 (mtm-85)
REVERT: H  280 ILE cc_start: 0.9006 (pt) cc_final: 0.8702 (pp)
REVERT: H  284 ARG cc_start: 0.6082 (ttt180) cc_final: 0.4830 (mtp180)
REVERT: H  301 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8018 (p0)
REVERT: H  319 THR cc_start: 0.9101 (p) cc_final: 0.8730 (m)
REVERT: H  331 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7935 (mp0)
REVERT: H  385 ASP cc_start: 0.9003 (t0) cc_final: 0.8779 (t0)
REVERT: H  411 ASP cc_start: 0.8123 (t0) cc_final: 0.7889 (t0)
REVERT: H  415 SER cc_start: 0.8828 (t) cc_final: 0.8326 (p)
REVERT: H  428 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8179 (mt-10)
REVERT: H  478 SER cc_start: 0.8149 (m) cc_final: 0.7594 (p)
REVERT: H  483 ARG cc_start: 0.8211 (ttt-90) cc_final: 0.7949 (ttt180)
REVERT: H  489 CYS cc_start: 0.8496 (m) cc_final: 0.8247 (p)
REVERT: H  502 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: H  525 MET cc_start: 0.8576 (mmm) cc_final: 0.8211 (mmm)
REVERT: H  543 ILE cc_start: 0.9273 (mt) cc_final: 0.8963 (mm)
REVERT: H  574 GLN cc_start: 0.8427 (tt0) cc_final: 0.8190 (tt0)
REVERT: H  584 ASN cc_start: 0.8945 (t0) cc_final: 0.8345 (t0)
REVERT: H  594 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7482 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 105
  average time/residue: 1.1685
  time to fit residues: 128.1285
Evaluate side-chains
  100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  301 ASP
Chi-restraints excluded: chain H residue  329 LEU
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  496 ILE
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  576 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0980
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 203 ASN
H 443 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.088977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.079450 restraints weight = 8520.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.40
r_work: 0.3106 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4644  Z= 0.258
  Angle     :  0.677  11.903   6292  Z= 0.350
  Chirality :  0.045   0.159    701
  Planarity :  0.004   0.050    805
  Dihedral  :  5.225  51.377    796
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 21.90 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.12 (0.35), residues: 538
  helix:  0.96 (0.59), residues: 83
  sheet:  0.32 (0.43), residues: 150
  loop : -0.55 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP H 567 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.034   0.002   PHE H 527 
 TYR   0.009   0.001   TYR H  81 
 ARG   0.008   0.001   ARG H  74 

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: H  106 SER cc_start: 0.8728 (t) cc_final: 0.8405 (p)
REVERT: H  116 GLU cc_start: 0.7843 (mp0) cc_final: 0.7553 (mp0)
REVERT: H  130 SER cc_start: 0.8832 (t) cc_final: 0.8368 (m)
REVERT: H  171 ASP cc_start: 0.8260 (p0) cc_final: 0.7951 (p0)
REVERT: H  192 ASP cc_start: 0.8203 (m-30) cc_final: 0.7673 (m-30)
REVERT: H  203 ASN cc_start: 0.8348 (m-40) cc_final: 0.7471 (t0)
REVERT: H  207 ASP cc_start: 0.8266 (t0) cc_final: 0.7796 (t0)
REVERT: H  212 MET cc_start: 0.8988 (mmm) cc_final: 0.8430 (mmm)
REVERT: H  249 ASP cc_start: 0.8465 (m-30) cc_final: 0.7913 (m-30)
REVERT: H  252 ARG cc_start: 0.9071 (mtm-85) cc_final: 0.8853 (mtm-85)
REVERT: H  280 ILE cc_start: 0.9003 (pt) cc_final: 0.8704 (pp)
REVERT: H  284 ARG cc_start: 0.6086 (ttt180) cc_final: 0.0982 (tmt170)
REVERT: H  301 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8025 (p0)
REVERT: H  319 THR cc_start: 0.9104 (p) cc_final: 0.8746 (m)
REVERT: H  331 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7926 (mp0)
REVERT: H  385 ASP cc_start: 0.8978 (t0) cc_final: 0.8757 (t0)
REVERT: H  411 ASP cc_start: 0.8121 (t0) cc_final: 0.7891 (t0)
REVERT: H  415 SER cc_start: 0.8827 (t) cc_final: 0.8320 (p)
REVERT: H  428 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8196 (mt-10)
REVERT: H  446 GLU cc_start: 0.8229 (pp20) cc_final: 0.7992 (pp20)
REVERT: H  478 SER cc_start: 0.8155 (m) cc_final: 0.7609 (p)
REVERT: H  489 CYS cc_start: 0.8487 (m) cc_final: 0.8248 (p)
REVERT: H  525 MET cc_start: 0.8584 (mmm) cc_final: 0.8213 (mmm)
REVERT: H  543 ILE cc_start: 0.9267 (mt) cc_final: 0.8964 (mm)
REVERT: H  574 GLN cc_start: 0.8420 (tt0) cc_final: 0.8185 (tt0)
REVERT: H  584 ASN cc_start: 0.8965 (t0) cc_final: 0.8346 (t0)
REVERT: H  594 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7438 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 101
  average time/residue: 1.7044
  time to fit residues: 180.7261
Evaluate side-chains
  101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  204 THR
Chi-restraints excluded: chain H residue  301 ASP
Chi-restraints excluded: chain H residue  329 LEU
Chi-restraints excluded: chain H residue  331 GLU
Chi-restraints excluded: chain H residue  425 THR
Chi-restraints excluded: chain H residue  496 ILE
Chi-restraints excluded: chain H residue  552 THR
Chi-restraints excluded: chain H residue  576 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
H 190 ASN
H 574 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.087459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.078024 restraints weight = 8555.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.39
r_work: 0.3078 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4644  Z= 0.359
  Angle     :  0.722  11.660   6292  Z= 0.374
  Chirality :  0.046   0.159    701
  Planarity :  0.004   0.047    805
  Dihedral  :  5.445  50.582    796
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.20 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 21.49 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.26 (0.35), residues: 538
  helix:  0.87 (0.59), residues: 83
  sheet:  0.22 (0.43), residues: 150
  loop : -0.64 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H 567 
 HIS   0.005   0.001   HIS H 155 
 PHE   0.035   0.002   PHE H 527 
 TYR   0.012   0.001   TYR H  81 
 ARG   0.009   0.001   ARG H 483 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4575.86 seconds
wall clock time: 80 minutes 16.75 seconds (4816.75 seconds total)