Starting phenix.real_space_refine
on Sun Mar 10 23:28:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/03_2024/8uyh_42806_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/03_2024/8uyh_42806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/03_2024/8uyh_42806.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/03_2024/8uyh_42806.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/03_2024/8uyh_42806_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/03_2024/8uyh_42806_updated.pdb"
  }
  resolution = 2.84
  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=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      3      5.21       5
     S      40      5.16       5
     C    3840      2.51       5
     N    1013      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  223": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6036
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3003
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 357}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2968
          Classifications: {'peptide': 370}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 352}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.87, per 1000 atoms: 0.64
  Number of scatterers: 6036
  At special positions: 0
  Unit cell: (116.352, 81.608, 72.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      40     16.00
     P       8     15.00
     Mg      3     11.99
     O    1132      8.00
     N    1013      7.00
     C    3840      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  - 3.50
        Amino acid           : False - 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: 2.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      39.5% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 135
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 204 through 214
    Processing helix  chain 'A' and resid 297 through 303
    Processing helix  chain 'A' and resid 308 through 327
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 389 through 392
      No H-bonds generated for 'chain 'A' and resid 389 through 392'
    Processing helix  chain 'A' and resid 407 through 419
      removed outlier: 3.590A  pdb=" N   GLY A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 414 " --> pdb=" O   TRP A 410 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 461
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 499 through 514
    Processing helix  chain 'A' and resid 543 through 555
      removed outlier: 3.928A  pdb=" N   ARG A 555 " --> pdb=" O   SER A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 3.580A  pdb=" N   LEU A 571 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 136
    Processing helix  chain 'B' and resid 156 through 158
      No H-bonds generated for 'chain 'B' and resid 156 through 158'
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 297 through 303
    Processing helix  chain 'B' and resid 308 through 327
    Processing helix  chain 'B' and resid 358 through 360
      No H-bonds generated for 'chain 'B' and resid 358 through 360'
    Processing helix  chain 'B' and resid 389 through 392
      No H-bonds generated for 'chain 'B' and resid 389 through 392'
    Processing helix  chain 'B' and resid 407 through 419
      removed outlier: 3.519A  pdb=" N   GLY B 413 " --> pdb=" O   LEU B 409 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA B 414 " --> pdb=" O   TRP B 410 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 461
    Processing helix  chain 'B' and resid 472 through 484
    Processing helix  chain 'B' and resid 487 through 490
    Processing helix  chain 'B' and resid 499 through 514
    Processing helix  chain 'B' and resid 543 through 553
    Processing helix  chain 'B' and resid 558 through 573
      removed outlier: 3.703A  pdb=" N   HIS B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 249 through 255
      removed outlier: 6.872A  pdb=" N   VAL A 289 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   VAL A 252 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   PHE A 287 " --> pdb=" O   VAL A 252 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ALA A 254 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   SER A 285 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   SER A 175 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 340 through 343
    Processing sheet with id=  C, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=  D, first strand: chain 'B' and resid 159 through 161
      removed outlier: 4.019A  pdb=" N   SER B 285 " --> pdb=" O   ASP B 255 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER B 251 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   SER B 220 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 8.851A  pdb=" N   ALA B 254 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   PHE B 222 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 340 through 343
    Processing sheet with id=  F, first strand: chain 'B' and resid 370 through 372
    Processing sheet with id=  G, first strand: chain 'B' and resid 164 through 167
      removed outlier: 6.715A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    657 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: 1.56

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1920
        1.34 -     1.46: 1237
        1.46 -     1.58: 2917
        1.58 -     1.69: 16
        1.69 -     1.81: 62
  Bond restraints: 6152
  Sorted by residual:
  bond pdb=" O3A ANP A 601 "
       pdb=" PB  ANP A 601 "
    ideal  model  delta    sigma   weight residual
    1.700  1.558  0.142 2.00e-02 2.50e+03 5.04e+01
  bond pdb=" O3A ANP B 601 "
       pdb=" PB  ANP B 601 "
    ideal  model  delta    sigma   weight residual
    1.700  1.558  0.142 2.00e-02 2.50e+03 5.02e+01
  bond pdb=" OG1 TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" OG1 TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" N3B ANP B 601 "
       pdb=" PG  ANP B 601 "
    ideal  model  delta    sigma   weight residual
    1.795  1.693  0.102 2.00e-02 2.50e+03 2.62e+01
  ... (remaining 6147 not shown)

  Histogram of bond angle deviations from ideal:
      100.47 -   107.18: 213
      107.18 -   113.90: 3520
      113.90 -   120.61: 2276
      120.61 -   127.32: 2263
      127.32 -   134.04: 70
  Bond angle restraints: 8342
  Sorted by residual:
  angle pdb=" PB  ANP B 601 "
        pdb=" N3B ANP B 601 "
        pdb=" PG  ANP B 601 "
      ideal   model   delta    sigma   weight residual
     126.95  109.08   17.87 3.00e+00 1.11e-01 3.55e+01
  angle pdb=" PB  ANP A 601 "
        pdb=" N3B ANP A 601 "
        pdb=" PG  ANP A 601 "
      ideal   model   delta    sigma   weight residual
     126.95  109.87   17.08 3.00e+00 1.11e-01 3.24e+01
  angle pdb=" CB  TPO A 305 "
        pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.60   11.71 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" CB  TPO B 305 "
        pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.87   11.44 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" O1B ANP A 601 "
        pdb=" PB  ANP A 601 "
        pdb=" O2B ANP A 601 "
      ideal   model   delta    sigma   weight residual
     120.08  109.30   10.78 3.00e+00 1.11e-01 1.29e+01
  ... (remaining 8337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.93: 3605
       21.93 -    43.87: 118
       43.87 -    65.80: 30
       65.80 -    87.73: 23
       87.73 -   109.66: 1
  Dihedral angle restraints: 3777
    sinusoidal: 1570
      harmonic: 2207
  Sorted by residual:
  dihedral pdb=" O1B ANP B 601 "
           pdb=" N3B ANP B 601 "
           pdb=" PB  ANP B 601 "
           pdb=" PG  ANP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -74.51  109.66     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" CA  LEU A 483 "
           pdb=" C   LEU A 483 "
           pdb=" N   TRP A 484 "
           pdb=" CA  TRP A 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.28  -15.72     0      5.00e+00 4.00e-02 9.89e+00
  dihedral pdb=" N   GLU B 376 "
           pdb=" CA  GLU B 376 "
           pdb=" CB  GLU B 376 "
           pdb=" CG  GLU B 376 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.43  -59.57     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 801
       0.055 -    0.111: 123
       0.111 -    0.166: 17
       0.166 -    0.221: 0
       0.221 -    0.277: 2
  Chirality restraints: 943
  Sorted by residual:
  chirality pdb=" C3' ANP B 601 "
            pdb=" C2' ANP B 601 "
            pdb=" C4' ANP B 601 "
            pdb=" O3' ANP B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C3' ANP A 601 "
            pdb=" C2' ANP A 601 "
            pdb=" C4' ANP A 601 "
            pdb=" O3' ANP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CA  ILE A 450 "
            pdb=" N   ILE A 450 "
            pdb=" C   ILE A 450 "
            pdb=" CB  ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.64e-01
  ... (remaining 940 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO B 451 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 450 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.88e+00
        pdb=" N   PRO A 451 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 243 "    0.030 5.00e-02 4.00e+02   4.46e-02 3.19e+00
        pdb=" N   PRO B 244 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 70
        2.64 -     3.20: 4988
        3.20 -     3.77: 9047
        3.77 -     4.33: 13424
        4.33 -     4.90: 21633
  Nonbonded interactions: 49162
  Sorted by model distance:
  nonbonded pdb=" O2B ANP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.074 2.170
  nonbonded pdb=" OD2 ASP B 357 "
            pdb="MG    MG B 603 "
     model   vdw
     2.131 2.170
  nonbonded pdb=" N3B ANP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.238 2.250
  nonbonded pdb=" O   THR A 215 "
            pdb=" OH  TYR A 221 "
     model   vdw
     2.280 2.440
  nonbonded pdb=" O2B ANP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.321 2.170
  ... (remaining 49157 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 121 through 223 or resid 238 through 515 or (resid 541 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 542 through 574 o \ 
r resid 601 through 602))
  selection = (chain 'B' and (resid 121 through 136 or resid 148 through 427 or (resid 432 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 433 through 540 o \ 
r resid 542 through 574 or resid 601 through 602))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.880
  Check model and map are aligned:         0.090
  Set scattering table:                    0.060
  Process input model:                     20.260
  Find NCS groups from input model:        0.390
  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:             0.010
  Load rotamer database and sin/cos tables:15.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.142   6152  Z= 0.348
  Angle     :  0.763  17.873   8342  Z= 0.361
  Chirality :  0.042   0.277    943
  Planarity :  0.005   0.050   1038
  Dihedral  : 13.962 109.665   2333
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  4.55 %
    Favored  : 93.94 %
  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: -1.53 (0.27), residues: 711
  helix: -1.14 (0.21), residues: 307
  sheet: -1.13 (0.49), residues: 103
  loop : -0.58 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 484 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.010   0.001   PHE B 253 
 TYR   0.011   0.001   TYR A 494 
 ARG   0.002   0.000   ARG B 384 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7289 (mttt) cc_final: 0.6642 (mttp)
REVERT: A  177 LYS cc_start: 0.6773 (tttt) cc_final: 0.6474 (ttpp)
REVERT: A  189 GLN cc_start: 0.7291 (mt0) cc_final: 0.7081 (mm110)
REVERT: A  211 MET cc_start: 0.8201 (mtt) cc_final: 0.7979 (mtt)
REVERT: A  248 ARG cc_start: 0.7539 (ttt90) cc_final: 0.7211 (ttm170)
REVERT: A  300 TYR cc_start: 0.7999 (t80) cc_final: 0.7729 (t80)
REVERT: A  343 ASP cc_start: 0.7352 (t0) cc_final: 0.7140 (t0)
REVERT: A  346 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6164 (mp0)
REVERT: A  350 TYR cc_start: 0.7705 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  545 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6534 (mt-10)
REVERT: A  554 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7658 (mtt-85)
REVERT: B  133 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7430 (mm-30)
REVERT: B  167 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7524 (mppt)
REVERT: B  177 LYS cc_start: 0.7401 (pttt) cc_final: 0.7129 (mtmm)
REVERT: B  189 GLN cc_start: 0.7820 (mt0) cc_final: 0.7124 (mm110)
REVERT: B  201 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6981 (mp0)
REVERT: B  212 TYR cc_start: 0.7892 (t80) cc_final: 0.6540 (m-10)
REVERT: B  290 MET cc_start: 0.8586 (mtm) cc_final: 0.8360 (mtp)
REVERT: B  510 SER cc_start: 0.8833 (p) cc_final: 0.8418 (m)
  outliers start: 10
  outliers final: 1
  residues processed: 182
  average time/residue: 1.1466
  time to fit residues: 218.5898
Evaluate side-chains
  139 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0470
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0470
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 ASN
A 569 GLN
B 197 ASN
B 572 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6152  Z= 0.172
  Angle     :  0.492   5.709   8342  Z= 0.249
  Chirality :  0.040   0.149    943
  Planarity :  0.005   0.045   1038
  Dihedral  : 10.776  91.402    867
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 11.67 %
    Favored  : 83.79 %
  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:  0.21 (0.30), residues: 711
  helix:  1.01 (0.27), residues: 304
  sheet: -0.50 (0.51), residues: 91
  loop : -0.42 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 324 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.014   0.001   TYR A 174 
 ARG   0.007   0.000   ARG A 557 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7351 (mttt) cc_final: 0.6639 (mttp)
REVERT: A  177 LYS cc_start: 0.6935 (tttt) cc_final: 0.6559 (ttpp)
REVERT: A  214 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8254 (mm-30)
REVERT: A  248 ARG cc_start: 0.7505 (ttt90) cc_final: 0.7087 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7937 (t80) cc_final: 0.7500 (t80)
REVERT: A  376 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7478 (mt-10)
REVERT: A  379 ASP cc_start: 0.7686 (p0) cc_final: 0.7357 (p0)
REVERT: A  554 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7096 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7229 (mtpt)
REVERT: B  167 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7421 (mppt)
REVERT: B  189 GLN cc_start: 0.7890 (mt0) cc_final: 0.7079 (mm-40)
REVERT: B  201 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7097 (mp0)
REVERT: B  212 TYR cc_start: 0.7896 (t80) cc_final: 0.6409 (m-10)
REVERT: B  239 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6986 (mtp85)
REVERT: B  423 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7566 (t70)
REVERT: B  436 LYS cc_start: 0.7389 (tttt) cc_final: 0.7021 (tttp)
REVERT: B  510 SER cc_start: 0.8892 (p) cc_final: 0.8497 (m)
  outliers start: 30
  outliers final: 9
  residues processed: 147
  average time/residue: 1.1469
  time to fit residues: 176.7144
Evaluate side-chains
  142 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  195 MET
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0060
   chunk 18 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
A 500 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6152  Z= 0.204
  Angle     :  0.481   5.310   8342  Z= 0.242
  Chirality :  0.041   0.144    943
  Planarity :  0.004   0.047   1038
  Dihedral  :  8.879  88.252    865
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 13.48 %
    Favored  : 81.21 %
  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:  0.81 (0.31), residues: 711
  helix:  1.79 (0.29), residues: 304
  sheet: -0.48 (0.50), residues: 96
  loop : -0.32 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.011   0.002   PHE B 452 
 TYR   0.011   0.001   TYR A 482 
 ARG   0.005   0.000   ARG A 557 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7431 (mttt) cc_final: 0.6728 (mttp)
REVERT: A  177 LYS cc_start: 0.6978 (tttt) cc_final: 0.6528 (ttpp)
REVERT: A  195 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8162 (mtp)
REVERT: A  214 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8270 (mm-30)
REVERT: A  248 ARG cc_start: 0.7466 (ttt90) cc_final: 0.7136 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7966 (t80) cc_final: 0.7547 (t80)
REVERT: A  302 ARG cc_start: 0.7063 (ttp80) cc_final: 0.6518 (ttp-110)
REVERT: A  376 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7463 (mt-10)
REVERT: A  379 ASP cc_start: 0.7735 (p0) cc_final: 0.7450 (p0)
REVERT: A  554 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7141 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.6994 (mtpt)
REVERT: B  167 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7369 (mppt)
REVERT: B  189 GLN cc_start: 0.7883 (mt0) cc_final: 0.6999 (mm110)
REVERT: B  196 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6629 (p90)
REVERT: B  201 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7203 (mm-30)
REVERT: B  212 TYR cc_start: 0.7932 (t80) cc_final: 0.6349 (m-10)
REVERT: B  239 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7065 (mtp85)
REVERT: B  309 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6918 (ttt-90)
REVERT: B  423 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7576 (t70)
REVERT: B  436 LYS cc_start: 0.7377 (tttt) cc_final: 0.6924 (tttp)
REVERT: B  439 LYS cc_start: 0.7820 (mttt) cc_final: 0.7547 (mtpp)
REVERT: B  504 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7648 (mp10)
REVERT: B  510 SER cc_start: 0.8848 (p) cc_final: 0.8473 (m)
REVERT: B  570 GLU cc_start: 0.7221 (pp20) cc_final: 0.6792 (tm-30)
  outliers start: 35
  outliers final: 10
  residues processed: 149
  average time/residue: 1.2463
  time to fit residues: 194.4518
Evaluate side-chains
  142 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0870
   chunk 45 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 500 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6152  Z= 0.135
  Angle     :  0.433   4.779   8342  Z= 0.219
  Chirality :  0.038   0.144    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.372  90.091    865
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 15.30 %
    Favored  : 80.30 %
  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:  1.10 (0.32), residues: 711
  helix:  2.12 (0.29), residues: 306
  sheet: -0.31 (0.50), residues: 96
  loop : -0.30 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.010   0.001   TYR A 174 
 ARG   0.004   0.000   ARG A 557 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7449 (mttt) cc_final: 0.6759 (mttp)
REVERT: A  177 LYS cc_start: 0.7057 (tttt) cc_final: 0.6579 (ttpp)
REVERT: A  248 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7118 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7939 (t80) cc_final: 0.7645 (t80)
REVERT: A  302 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6605 (ttp-110)
REVERT: A  308 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6667 (tpp)
REVERT: A  376 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7489 (mt-10)
REVERT: A  379 ASP cc_start: 0.7718 (p0) cc_final: 0.7458 (p0)
REVERT: A  384 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8171 (mtp-110)
REVERT: A  554 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7127 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7024 (mtpt)
REVERT: B  167 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7391 (mppt)
REVERT: B  189 GLN cc_start: 0.7778 (mt0) cc_final: 0.6970 (mm110)
REVERT: B  196 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.6554 (p90)
REVERT: B  212 TYR cc_start: 0.7952 (t80) cc_final: 0.6309 (m-10)
REVERT: B  239 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7105 (mtp85)
REVERT: B  423 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7590 (t70)
REVERT: B  436 LYS cc_start: 0.7344 (tttt) cc_final: 0.6896 (tttp)
REVERT: B  510 SER cc_start: 0.8812 (p) cc_final: 0.8467 (m)
REVERT: B  570 GLU cc_start: 0.7213 (pp20) cc_final: 0.6875 (tm-30)
  outliers start: 29
  outliers final: 11
  residues processed: 145
  average time/residue: 1.0889
  time to fit residues: 165.8929
Evaluate side-chains
  138 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 40 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 500 ASN
B 504 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6152  Z= 0.153
  Angle     :  0.437   4.876   8342  Z= 0.221
  Chirality :  0.039   0.142    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.283  92.527    865
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 15.45 %
    Favored  : 79.39 %
  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:  1.24 (0.32), residues: 711
  helix:  2.28 (0.29), residues: 306
  sheet: -0.04 (0.50), residues: 90
  loop : -0.36 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.010   0.001   TYR A 174 
 ARG   0.003   0.000   ARG A 557 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.678 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7039 (mt)
REVERT: A  167 LYS cc_start: 0.7454 (mttt) cc_final: 0.6736 (mttp)
REVERT: A  177 LYS cc_start: 0.7038 (tttt) cc_final: 0.6622 (ttpp)
REVERT: A  248 ARG cc_start: 0.7484 (ttt90) cc_final: 0.7137 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7938 (t80) cc_final: 0.7558 (t80)
REVERT: A  302 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6608 (ttp-110)
REVERT: A  308 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6678 (tpp)
REVERT: A  376 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7505 (mt-10)
REVERT: A  379 ASP cc_start: 0.7673 (p0) cc_final: 0.7448 (p0)
REVERT: A  384 ARG cc_start: 0.8387 (mtp85) cc_final: 0.8147 (mtp-110)
REVERT: A  554 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7126 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6973 (mtpt)
REVERT: B  167 LYS cc_start: 0.7703 (mtpt) cc_final: 0.7427 (mppt)
REVERT: B  189 GLN cc_start: 0.7710 (mt0) cc_final: 0.6882 (mm110)
REVERT: B  196 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6624 (p90)
REVERT: B  212 TYR cc_start: 0.7912 (t80) cc_final: 0.6276 (m-10)
REVERT: B  239 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7067 (mtp85)
REVERT: B  423 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7563 (t70)
REVERT: B  436 LYS cc_start: 0.7339 (tttt) cc_final: 0.6890 (tttp)
REVERT: B  473 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6159 (t0)
REVERT: B  510 SER cc_start: 0.8817 (p) cc_final: 0.8474 (m)
REVERT: B  570 GLU cc_start: 0.7222 (pp20) cc_final: 0.6879 (tm-30)
  outliers start: 34
  outliers final: 11
  residues processed: 146
  average time/residue: 1.1006
  time to fit residues: 168.6442
Evaluate side-chains
  144 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 500 ASN
B 155 ASN
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6152  Z= 0.169
  Angle     :  0.443   5.165   8342  Z= 0.224
  Chirality :  0.039   0.140    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.294  93.991    865
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 15.76 %
    Favored  : 79.09 %
  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:  1.29 (0.32), residues: 711
  helix:  2.32 (0.29), residues: 306
  sheet:  0.01 (0.50), residues: 90
  loop : -0.34 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.010   0.001   TYR A 482 
 ARG   0.003   0.000   ARG B 309 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7019 (mt)
REVERT: A  167 LYS cc_start: 0.7479 (mttt) cc_final: 0.6758 (mttp)
REVERT: A  177 LYS cc_start: 0.7097 (tttt) cc_final: 0.6680 (ttpp)
REVERT: A  248 ARG cc_start: 0.7457 (ttt90) cc_final: 0.7115 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7936 (t80) cc_final: 0.7597 (t80)
REVERT: A  302 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6578 (ttp-110)
REVERT: A  308 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6664 (tpp)
REVERT: A  376 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7484 (mt-10)
REVERT: A  384 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8158 (mtp-110)
REVERT: A  418 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6877 (mt-10)
REVERT: A  554 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7551 (mtt180)
REVERT: A  566 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.6975 (mtpt)
REVERT: B  161 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7296 (tp)
REVERT: B  167 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7412 (mppt)
REVERT: B  189 GLN cc_start: 0.7727 (mt0) cc_final: 0.6887 (mm110)
REVERT: B  196 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6625 (p90)
REVERT: B  201 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7239 (mm-30)
REVERT: B  212 TYR cc_start: 0.7934 (t80) cc_final: 0.6275 (m-10)
REVERT: B  239 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7073 (mtp85)
REVERT: B  423 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7578 (t70)
REVERT: B  436 LYS cc_start: 0.7353 (tttt) cc_final: 0.6907 (tttp)
REVERT: B  473 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6192 (t0)
REVERT: B  510 SER cc_start: 0.8824 (p) cc_final: 0.8474 (m)
REVERT: B  541 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6570 (mpt-90)
REVERT: B  570 GLU cc_start: 0.7228 (pp20) cc_final: 0.6867 (tm-30)
  outliers start: 34
  outliers final: 12
  residues processed: 144
  average time/residue: 1.1452
  time to fit residues: 173.1239
Evaluate side-chains
  151 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  541 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0570
   chunk 40 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.1902

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 504 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6152  Z= 0.192
  Angle     :  0.457   5.462   8342  Z= 0.232
  Chirality :  0.039   0.141    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.366  95.037    865
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 15.45 %
    Favored  : 78.94 %
  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:  1.31 (0.32), residues: 711
  helix:  2.39 (0.29), residues: 303
  sheet:  0.01 (0.50), residues: 90
  loop : -0.37 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.010   0.001   TYR A 482 
 ARG   0.003   0.000   ARG B 309 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 132
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7017 (mt)
REVERT: A  167 LYS cc_start: 0.7429 (mttt) cc_final: 0.6775 (mttm)
REVERT: A  177 LYS cc_start: 0.7142 (tttt) cc_final: 0.6701 (ttpp)
REVERT: A  248 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7110 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7950 (t80) cc_final: 0.7610 (t80)
REVERT: A  302 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6560 (ttp-110)
REVERT: A  308 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6684 (tpp)
REVERT: A  346 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6545 (mp0)
REVERT: A  376 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7495 (mt-10)
REVERT: A  384 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8194 (mtp-110)
REVERT: A  418 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6884 (mt-10)
REVERT: A  566 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7005 (mtpt)
REVERT: B  167 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7415 (mppt)
REVERT: B  189 GLN cc_start: 0.7770 (mt0) cc_final: 0.6913 (mm110)
REVERT: B  196 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.6632 (p90)
REVERT: B  201 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7236 (mm-30)
REVERT: B  212 TYR cc_start: 0.7940 (t80) cc_final: 0.6267 (m-10)
REVERT: B  239 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7069 (mtp85)
REVERT: B  423 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7591 (t70)
REVERT: B  436 LYS cc_start: 0.7365 (tttt) cc_final: 0.6862 (tttp)
REVERT: B  439 LYS cc_start: 0.7838 (mttt) cc_final: 0.7552 (mtpp)
REVERT: B  473 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6203 (t0)
REVERT: B  510 SER cc_start: 0.8831 (p) cc_final: 0.8473 (m)
REVERT: B  541 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6584 (mpt-90)
REVERT: B  570 GLU cc_start: 0.7240 (pp20) cc_final: 0.6838 (tm-30)
  outliers start: 37
  outliers final: 15
  residues processed: 148
  average time/residue: 1.1272
  time to fit residues: 175.0172
Evaluate side-chains
  156 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  541 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 21 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6152  Z= 0.146
  Angle     :  0.440   5.200   8342  Z= 0.223
  Chirality :  0.038   0.142    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.247  97.457    865
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.12 %
    Favored  : 78.79 %
  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:  1.41 (0.32), residues: 711
  helix:  2.47 (0.29), residues: 302
  sheet:  0.05 (0.50), residues: 90
  loop : -0.29 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.009   0.001   TYR A 482 
 ARG   0.003   0.000   ARG B 309 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7033 (mt)
REVERT: A  167 LYS cc_start: 0.7432 (mttt) cc_final: 0.6774 (mttm)
REVERT: A  177 LYS cc_start: 0.7172 (tttt) cc_final: 0.6952 (pttp)
REVERT: A  248 ARG cc_start: 0.7471 (ttt90) cc_final: 0.7094 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7924 (t80) cc_final: 0.7589 (t80)
REVERT: A  302 ARG cc_start: 0.7063 (ttp80) cc_final: 0.6598 (ttp-110)
REVERT: A  308 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6668 (tpp)
REVERT: A  376 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7468 (mt-10)
REVERT: A  379 ASP cc_start: 0.7554 (p0) cc_final: 0.7276 (p0)
REVERT: A  384 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8179 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7056 (mmtt)
REVERT: B  167 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7404 (mppt)
REVERT: B  196 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6498 (p90)
REVERT: B  201 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7156 (mm-30)
REVERT: B  212 TYR cc_start: 0.7950 (t80) cc_final: 0.6263 (m-10)
REVERT: B  239 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7099 (mtp85)
REVERT: B  423 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7593 (t70)
REVERT: B  436 LYS cc_start: 0.7321 (tttt) cc_final: 0.6881 (tttp)
REVERT: B  510 SER cc_start: 0.8793 (p) cc_final: 0.8464 (m)
REVERT: B  541 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6574 (mpt-90)
REVERT: B  570 GLU cc_start: 0.7227 (pp20) cc_final: 0.6893 (tm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 140
  average time/residue: 1.1125
  time to fit residues: 163.5560
Evaluate side-chains
  147 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  541 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.0060
   chunk 66 optimal weight:    0.0040
   chunk 68 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.7810

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 559 HIS
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6152  Z= 0.152
  Angle     :  0.444   4.967   8342  Z= 0.226
  Chirality :  0.038   0.142    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.168  98.720    865
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.27 %
    Favored  : 78.64 %
  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:  1.43 (0.32), residues: 711
  helix:  2.48 (0.29), residues: 302
  sheet:  0.07 (0.50), residues: 90
  loop : -0.28 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.009   0.001   TYR A 482 
 ARG   0.003   0.000   ARG A 557 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7042 (mt)
REVERT: A  167 LYS cc_start: 0.7502 (mttt) cc_final: 0.6821 (mttm)
REVERT: A  177 LYS cc_start: 0.7271 (tttt) cc_final: 0.7026 (pttp)
REVERT: A  248 ARG cc_start: 0.7456 (ttt90) cc_final: 0.7087 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7928 (t80) cc_final: 0.7584 (t80)
REVERT: A  302 ARG cc_start: 0.7063 (ttp80) cc_final: 0.6631 (ttp-110)
REVERT: A  308 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6657 (tpp)
REVERT: A  346 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6557 (mp0)
REVERT: A  350 TYR cc_start: 0.7629 (m-80) cc_final: 0.7324 (m-80)
REVERT: A  376 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7461 (mt-10)
REVERT: A  379 ASP cc_start: 0.7621 (p0) cc_final: 0.7295 (p0)
REVERT: A  566 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7059 (mmtt)
REVERT: B  167 LYS cc_start: 0.7720 (mtpt) cc_final: 0.7408 (mppt)
REVERT: B  189 GLN cc_start: 0.7901 (mt0) cc_final: 0.6913 (mm110)
REVERT: B  196 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.6509 (p90)
REVERT: B  201 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7176 (mm-30)
REVERT: B  212 TYR cc_start: 0.7956 (t80) cc_final: 0.6277 (m-10)
REVERT: B  239 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7068 (mtp85)
REVERT: B  423 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7576 (t70)
REVERT: B  436 LYS cc_start: 0.7341 (tttt) cc_final: 0.6898 (tttp)
REVERT: B  473 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6167 (t0)
REVERT: B  510 SER cc_start: 0.8798 (p) cc_final: 0.8466 (m)
REVERT: B  541 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6596 (mpt-90)
REVERT: B  570 GLU cc_start: 0.7230 (pp20) cc_final: 0.6846 (tm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 145
  average time/residue: 1.0814
  time to fit residues: 164.7402
Evaluate side-chains
  149 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  541 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0870
   chunk 6 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0870
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6152  Z= 0.129
  Angle     :  0.430   5.430   8342  Z= 0.220
  Chirality :  0.038   0.144    943
  Planarity :  0.004   0.044   1038
  Dihedral  :  7.946 101.229    865
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.09 %
    Favored  : 78.48 %
  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:  1.48 (0.32), residues: 711
  helix:  2.51 (0.29), residues: 303
  sheet: -0.06 (0.49), residues: 95
  loop : -0.18 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.008   0.001   TYR A 482 
 ARG   0.003   0.000   ARG A 557 

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7046 (mt)
REVERT: A  167 LYS cc_start: 0.7502 (mttt) cc_final: 0.6823 (mttm)
REVERT: A  177 LYS cc_start: 0.7245 (tttt) cc_final: 0.7010 (pttp)
REVERT: A  248 ARG cc_start: 0.7439 (ttt90) cc_final: 0.7081 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7909 (t80) cc_final: 0.7585 (t80)
REVERT: A  302 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6522 (ttp-110)
REVERT: A  308 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6568 (tpp)
REVERT: A  346 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6592 (mp0)
REVERT: A  350 TYR cc_start: 0.7622 (m-80) cc_final: 0.7302 (m-80)
REVERT: A  379 ASP cc_start: 0.7571 (p0) cc_final: 0.7238 (p0)
REVERT: A  566 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.6943 (mtpt)
REVERT: B  167 LYS cc_start: 0.7733 (mtpt) cc_final: 0.7419 (mppt)
REVERT: B  189 GLN cc_start: 0.7919 (mt0) cc_final: 0.6870 (mm110)
REVERT: B  196 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6556 (p90)
REVERT: B  201 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7320 (mm-30)
REVERT: B  212 TYR cc_start: 0.7968 (t80) cc_final: 0.6300 (m-10)
REVERT: B  436 LYS cc_start: 0.7276 (tttt) cc_final: 0.6848 (tttp)
REVERT: B  510 SER cc_start: 0.8791 (p) cc_final: 0.8467 (m)
REVERT: B  541 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6538 (mpt-90)
REVERT: B  570 GLU cc_start: 0.7232 (pp20) cc_final: 0.6788 (tm-30)
  outliers start: 16
  outliers final: 6
  residues processed: 137
  average time/residue: 1.1386
  time to fit residues: 163.9355
Evaluate side-chains
  140 residues out of total 668 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  541 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 16 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.177989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.153078 restraints weight = 6822.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.74
r_work: 0.3589 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6152  Z= 0.141
  Angle     :  0.445   5.287   8342  Z= 0.227
  Chirality :  0.038   0.158    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  7.882 102.011    865
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.24 %
    Favored  : 78.33 %
  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:  1.54 (0.32), residues: 711
  helix:  2.51 (0.29), residues: 304
  sheet:  0.07 (0.50), residues: 95
  loop : -0.14 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.008   0.001   TYR A 482 
 ARG   0.002   0.000   ARG A 557 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3188.49 seconds
wall clock time: 57 minutes 1.46 seconds (3421.46 seconds total)