Starting phenix.real_space_refine
on Mon Apr 28 16:43:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tel_41190/04_2025/8tel_41190.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tel_41190/04_2025/8tel_41190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tel_41190/04_2025/8tel_41190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tel_41190/04_2025/8tel_41190.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tel_41190/04_2025/8tel_41190.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tel_41190/04_2025/8tel_41190.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      52      5.16       5
     C    5110      2.51       5
     N    1290      2.21       5
     O    1352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7806
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3903
          Classifications: {'peptide': 494}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.30, per 1000 atoms: 0.94
  Number of scatterers: 7806
  At special positions: 0
  Unit cell: (85.49, 120.35, 93.79, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       2     15.00
     O    1352      8.00
     N    1290      7.00
     C    5110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      77.9% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 19
    Processing helix  chain 'A' and resid 21 through 32
      removed outlier: 3.634A  pdb=" N   ALA A  32 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 35
      No H-bonds generated for 'chain 'A' and resid 33 through 35'
    Processing helix  chain 'A' and resid 36 through 62
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 67 through 86
    Processing helix  chain 'A' and resid 96 through 112
      removed outlier: 3.686A  pdb=" N   ALA A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 142
    Processing helix  chain 'A' and resid 145 through 151
      removed outlier: 4.184A  pdb=" N   ASN A 149 " --> pdb=" O   CYS A 145 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ARG A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 178
      removed outlier: 3.792A  pdb=" N   GLY A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 192
    Processing helix  chain 'A' and resid 193 through 219
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 228 through 251
      removed outlier: 6.415A  pdb=" N   VAL A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      Proline residue:  A 241  - end of helix
    Processing helix  chain 'A' and resid 252 through 258
      removed outlier: 4.377A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL A 258 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.731A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 319
      removed outlier: 3.570A  pdb=" N   SER A 313 " --> pdb=" O   TYR A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'A' and resid 359 through 391
      removed outlier: 3.688A  pdb=" N   LYS A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 409
    Processing helix  chain 'A' and resid 424 through 431
    Processing helix  chain 'A' and resid 442 through 446
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 4.291A  pdb=" N   ASP A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 464 through 477
    Processing helix  chain 'A' and resid 480 through 485
    Processing helix  chain 'A' and resid 488 through 503
      removed outlier: 3.829A  pdb=" N   LEU A 492 " --> pdb=" O   PRO A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 516
    Processing helix  chain 'B' and resid 8 through 19
    Processing helix  chain 'B' and resid 21 through 32
      removed outlier: 3.634A  pdb=" N   ALA B  32 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 35
      No H-bonds generated for 'chain 'B' and resid 33 through 35'
    Processing helix  chain 'B' and resid 36 through 62
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 67 through 86
    Processing helix  chain 'B' and resid 96 through 112
      removed outlier: 3.686A  pdb=" N   ALA B 112 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 142
    Processing helix  chain 'B' and resid 145 through 151
      removed outlier: 4.184A  pdb=" N   ASN B 149 " --> pdb=" O   CYS B 145 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG B 150 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 178
      removed outlier: 3.792A  pdb=" N   GLY B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   PHE B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 192
    Processing helix  chain 'B' and resid 193 through 219
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 228 through 251
      removed outlier: 6.415A  pdb=" N   VAL B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
    Processing helix  chain 'B' and resid 252 through 258
      removed outlier: 4.377A  pdb=" N   GLY B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL B 258 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.732A  pdb=" N   LEU B 287 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 319
      removed outlier: 3.570A  pdb=" N   SER B 313 " --> pdb=" O   TYR B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 325
    Processing helix  chain 'B' and resid 331 through 350
    Processing helix  chain 'B' and resid 359 through 391
      removed outlier: 3.688A  pdb=" N   LYS B 389 " --> pdb=" O   ARG B 385 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 409
    Processing helix  chain 'B' and resid 424 through 431
    Processing helix  chain 'B' and resid 442 through 446
    Processing helix  chain 'B' and resid 447 through 453
      removed outlier: 4.292A  pdb=" N   ASP B 453 " --> pdb=" O   GLU B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 456
      No H-bonds generated for 'chain 'B' and resid 454 through 456'
    Processing helix  chain 'B' and resid 464 through 477
    Processing helix  chain 'B' and resid 480 through 485
    Processing helix  chain 'B' and resid 488 through 503
      removed outlier: 3.828A  pdb=" N   LEU B 492 " --> pdb=" O   PRO B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 516
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94
    Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94

    522 hydrogen bonds defined for protein.
    1506 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2420
        1.34 -     1.46: 1850
        1.46 -     1.58: 3630
        1.58 -     1.70: 6
        1.70 -     1.82: 90
  Bond restraints: 7996
  Sorted by residual:
  bond pdb=" OG1 TPO B 410 "
       pdb=" P   TPO B 410 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" OG1 TPO A 410 "
       pdb=" P   TPO A 410 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" O3P TPO B 410 "
       pdb=" P   TPO B 410 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" O3P TPO A 410 "
       pdb=" P   TPO A 410 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" O2P TPO A 410 "
       pdb=" P   TPO A 410 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  ... (remaining 7991 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 10748
        2.43 -     4.86: 90
        4.86 -     7.29: 4
        7.29 -     9.72: 2
        9.72 -    12.15: 2
  Bond angle restraints: 10846
  Sorted by residual:
  angle pdb=" CB  TPO A 410 "
        pdb=" OG1 TPO A 410 "
        pdb=" P   TPO A 410 "
      ideal   model   delta    sigma   weight residual
     119.31  107.16   12.15 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" CB  TPO B 410 "
        pdb=" OG1 TPO B 410 "
        pdb=" P   TPO B 410 "
      ideal   model   delta    sigma   weight residual
     119.31  107.16   12.15 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" N   VAL B 413 "
        pdb=" CA  VAL B 413 "
        pdb=" C   VAL B 413 "
      ideal   model   delta    sigma   weight residual
     113.53  110.46    3.07 9.80e-01 1.04e+00 9.83e+00
  angle pdb=" N   VAL A 413 "
        pdb=" CA  VAL A 413 "
        pdb=" C   VAL A 413 "
      ideal   model   delta    sigma   weight residual
     113.53  110.48    3.05 9.80e-01 1.04e+00 9.67e+00
  angle pdb=" OG1 TPO B 410 "
        pdb=" P   TPO B 410 "
        pdb=" O1P TPO B 410 "
      ideal   model   delta    sigma   weight residual
     100.43  109.76   -9.33 3.00e+00 1.11e-01 9.66e+00
  ... (remaining 10841 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4030
       17.68 -    35.37: 506
       35.37 -    53.05: 144
       53.05 -    70.73: 38
       70.73 -    88.42: 10
  Dihedral angle restraints: 4728
    sinusoidal: 1892
      harmonic: 2836
  Sorted by residual:
  dihedral pdb=" CA  ILE B 291 "
           pdb=" C   ILE B 291 "
           pdb=" N   VAL B 292 "
           pdb=" CA  VAL B 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.59   18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ILE A 291 "
           pdb=" C   ILE A 291 "
           pdb=" N   VAL A 292 "
           pdb=" CA  VAL A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.66   18.34     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CB  GLU B 323 "
           pdb=" CG  GLU B 323 "
           pdb=" CD  GLU B 323 "
           pdb=" OE1 GLU B 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.42   88.42     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4725 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 863
       0.029 -    0.057: 219
       0.057 -    0.086: 101
       0.086 -    0.114: 38
       0.114 -    0.143: 11
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CA  ILE A 181 "
            pdb=" N   ILE A 181 "
            pdb=" C   ILE A 181 "
            pdb=" CB  ILE A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  ILE B 181 "
            pdb=" N   ILE B 181 "
            pdb=" C   ILE B 181 "
            pdb=" CB  ILE B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  ILE A 262 "
            pdb=" N   ILE A 262 "
            pdb=" C   ILE A 262 "
            pdb=" CB  ILE A 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 1229 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 258 "   -0.023 5.00e-02 4.00e+02   3.51e-02 1.97e+00
        pdb=" N   PRO B 259 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 258 "   -0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO A 259 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 259 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 259 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 226 "    0.009 2.00e-02 2.50e+03   8.01e-03 1.28e+00
        pdb=" CG  TYR A 226 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 226 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 226 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 226 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 67
        2.64 -     3.20: 7220
        3.20 -     3.77: 12090
        3.77 -     4.33: 16309
        4.33 -     4.90: 27518
  Nonbonded interactions: 63204
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 298 "
            pdb=" OG  SER A 302 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" O   PHE B 298 "
            pdb=" OG  SER B 302 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" OG  SER A 195 "
            pdb=" OG  SER B 195 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   LYS A 424 "
            pdb=" OG1 THR A 427 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LYS B 424 "
            pdb=" OG1 THR B 427 "
     model   vdw
     2.197 3.040
  ... (remaining 63199 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             2.470
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.470
  Find NCS groups from input model:        0.140
  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:12.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   39.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
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      :  0.004   0.108   7996  Z= 0.167
  Angle     :  0.551  12.153  10846  Z= 0.264
  Chirality :  0.035   0.143   1232
  Planarity :  0.003   0.035   1346
  Dihedral  : 17.767  88.419   2904
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 22.97 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.33 (0.27), residues: 970
  helix:  2.14 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop :  0.22 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 247 
 HIS   0.002   0.000   HIS B 312 
 PHE   0.004   0.001   PHE A 192 
 TYR   0.019   0.001   TYR A 226 
 ARG   0.002   0.000   ARG B 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13239 (  522)
  hydrogen bonds       : angle       5.00729 ( 1506)
  covalent geometry    : bond        0.00355 ( 7996)
  covalent geometry    : angle       0.55126 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  226 TYR cc_start: 0.6885 (m-80) cc_final: 0.6522 (m-80)
REVERT: B  226 TYR cc_start: 0.6860 (m-80) cc_final: 0.6517 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 95
  average time/residue: 1.2983
  time to fit residues: 130.7906
Evaluate side-chains
  93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  490 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0870
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0670
   chunk 57 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.8298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.151571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.107530 restraints weight = 8662.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.81
r_work: 0.3012 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7996  Z= 0.121
  Angle     :  0.478   5.378  10846  Z= 0.243
  Chirality :  0.039   0.157   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  4.865  50.039   1076
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.77 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.60 (0.27), residues: 970
  helix:  2.39 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.15 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 247 
 HIS   0.004   0.001   HIS A 312 
 PHE   0.007   0.001   PHE A 105 
 TYR   0.014   0.001   TYR B 405 
 ARG   0.001   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  522)
  hydrogen bonds       : angle       4.04825 ( 1506)
  covalent geometry    : bond        0.00262 ( 7996)
  covalent geometry    : angle       0.47793 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.6389 (mpt180)
REVERT: A  150 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6853 (mpp80)
REVERT: A  242 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8250 (tp)
REVERT: A  385 ARG cc_start: 0.6398 (mtt90) cc_final: 0.5931 (mtm-85)
REVERT: B   20 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7814 (ptp)
REVERT: B   35 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.6431 (mpt180)
REVERT: B  150 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6806 (mpp80)
REVERT: B  242 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8255 (tp)
REVERT: B  385 ARG cc_start: 0.6408 (mtt90) cc_final: 0.5932 (mtm-85)
  outliers start: 24
  outliers final: 4
  residues processed: 105
  average time/residue: 1.6146
  time to fit residues: 178.6240
Evaluate side-chains
  96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 321 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.153062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.110297 restraints weight = 8904.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.76
r_work: 0.3024 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7996  Z= 0.132
  Angle     :  0.493   6.664  10846  Z= 0.249
  Chirality :  0.039   0.160   1232
  Planarity :  0.004   0.047   1346
  Dihedral  :  4.047  30.822   1064
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.93 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.48 (0.26), residues: 970
  helix:  2.28 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.15 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 247 
 HIS   0.003   0.001   HIS B 312 
 PHE   0.007   0.001   PHE A 498 
 TYR   0.017   0.001   TYR B 405 
 ARG   0.002   0.000   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05052 (  522)
  hydrogen bonds       : angle       4.00304 ( 1506)
  covalent geometry    : bond        0.00301 ( 7996)
  covalent geometry    : angle       0.49328 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.733 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7778 (ptp)
REVERT: A   35 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.6740 (mpt180)
REVERT: A  181 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6764 (mt)
REVERT: A  226 TYR cc_start: 0.7146 (m-80) cc_final: 0.6722 (m-80)
REVERT: A  242 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (tp)
REVERT: A  284 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7121 (mmpt)
REVERT: A  385 ARG cc_start: 0.6477 (mtt90) cc_final: 0.6182 (mtm-85)
REVERT: A  463 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7418 (pp30)
REVERT: B   20 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (ptp)
REVERT: B   35 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.6759 (mpt180)
REVERT: B  181 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6761 (mt)
REVERT: B  226 TYR cc_start: 0.7128 (m-80) cc_final: 0.6716 (m-80)
REVERT: B  242 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8259 (tp)
REVERT: B  284 LYS cc_start: 0.7659 (mmtt) cc_final: 0.7124 (mmpt)
REVERT: B  385 ARG cc_start: 0.6483 (mtt90) cc_final: 0.6181 (mtm-85)
REVERT: B  463 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7427 (pp30)
  outliers start: 27
  outliers final: 6
  residues processed: 105
  average time/residue: 2.3112
  time to fit residues: 256.4020
Evaluate side-chains
  98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 3 optimal weight:    0.1980
   chunk 18 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.154248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.111947 restraints weight = 8787.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.75
r_work: 0.3027 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.109
  Angle     :  0.456   6.388  10846  Z= 0.230
  Chirality :  0.038   0.156   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  3.823  19.506   1064
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.81 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.68 (0.26), residues: 970
  helix:  2.43 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.22 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 247 
 HIS   0.003   0.001   HIS B 312 
 PHE   0.006   0.001   PHE A 498 
 TYR   0.007   0.001   TYR B 495 
 ARG   0.001   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  522)
  hydrogen bonds       : angle       3.89680 ( 1506)
  covalent geometry    : bond        0.00232 ( 7996)
  covalent geometry    : angle       0.45560 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7770 (ptp)
REVERT: A   35 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.6643 (mpt180)
REVERT: A  135 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8251 (mtt)
REVERT: A  181 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6709 (mt)
REVERT: A  226 TYR cc_start: 0.7067 (m-80) cc_final: 0.6637 (m-80)
REVERT: A  284 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7125 (mmpt)
REVERT: A  385 ARG cc_start: 0.6457 (mtt90) cc_final: 0.6174 (mtm-85)
REVERT: B   20 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7736 (ptp)
REVERT: B   35 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.6661 (mpt180)
REVERT: B  135 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8270 (mtt)
REVERT: B  181 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6714 (mt)
REVERT: B  226 TYR cc_start: 0.7022 (m-80) cc_final: 0.6602 (m-80)
REVERT: B  284 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7117 (mmpt)
REVERT: B  385 ARG cc_start: 0.6440 (mtt90) cc_final: 0.6123 (mtm-85)
REVERT: B  448 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5546 (tp)
  outliers start: 28
  outliers final: 7
  residues processed: 101
  average time/residue: 1.4502
  time to fit residues: 154.2850
Evaluate side-chains
  94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 45 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.147969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.104363 restraints weight = 8883.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.74
r_work: 0.2983 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7996  Z= 0.142
  Angle     :  0.505   6.312  10846  Z= 0.255
  Chirality :  0.040   0.160   1232
  Planarity :  0.004   0.046   1346
  Dihedral  :  3.902  17.973   1062
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 20.93 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.38 (0.26), residues: 970
  helix:  2.21 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.11 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 247 
 HIS   0.004   0.001   HIS B 312 
 PHE   0.007   0.001   PHE A 498 
 TYR   0.017   0.001   TYR A 405 
 ARG   0.002   0.000   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05177 (  522)
  hydrogen bonds       : angle       4.01745 ( 1506)
  covalent geometry    : bond        0.00327 ( 7996)
  covalent geometry    : angle       0.50452 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7789 (ptp)
REVERT: A  135 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8240 (mtt)
REVERT: A  226 TYR cc_start: 0.6961 (m-80) cc_final: 0.6546 (m-80)
REVERT: A  242 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8284 (tp)
REVERT: A  284 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7038 (mmpt)
REVERT: A  385 ARG cc_start: 0.6473 (mtt90) cc_final: 0.6139 (mtm-85)
REVERT: A  448 ILE cc_start: 0.5912 (OUTLIER) cc_final: 0.5634 (tp)
REVERT: B  135 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8252 (mtt)
REVERT: B  226 TYR cc_start: 0.6953 (m-80) cc_final: 0.6548 (m-80)
REVERT: B  242 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8280 (tp)
REVERT: B  284 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7044 (mmpt)
REVERT: B  385 ARG cc_start: 0.6488 (mtt90) cc_final: 0.6172 (mtm-85)
REVERT: B  448 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5574 (tp)
  outliers start: 31
  outliers final: 6
  residues processed: 101
  average time/residue: 1.7263
  time to fit residues: 183.8193
Evaluate side-chains
  91 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 86 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.152843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.110519 restraints weight = 8862.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.74
r_work: 0.3004 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7996  Z= 0.115
  Angle     :  0.466   6.180  10846  Z= 0.236
  Chirality :  0.038   0.154   1232
  Planarity :  0.004   0.048   1346
  Dihedral  :  3.836  17.586   1062
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.17 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.55 (0.26), residues: 970
  helix:  2.34 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.14 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 312 
 PHE   0.006   0.001   PHE A 498 
 TYR   0.008   0.001   TYR A 495 
 ARG   0.001   0.000   ARG B 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04575 (  522)
  hydrogen bonds       : angle       3.91843 ( 1506)
  covalent geometry    : bond        0.00250 ( 7996)
  covalent geometry    : angle       0.46640 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7680 (ptp)
REVERT: A   30 PHE cc_start: 0.7888 (m-80) cc_final: 0.7578 (m-80)
REVERT: A  135 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8243 (mtt)
REVERT: A  150 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6798 (mpp80)
REVERT: A  217 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7196 (mtt90)
REVERT: A  226 TYR cc_start: 0.6979 (m-80) cc_final: 0.6567 (m-80)
REVERT: A  242 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8269 (tp)
REVERT: A  284 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7020 (mmpt)
REVERT: A  385 ARG cc_start: 0.6486 (mtt90) cc_final: 0.6149 (mtm-85)
REVERT: A  448 ILE cc_start: 0.5916 (OUTLIER) cc_final: 0.5682 (tp)
REVERT: B   20 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7741 (ptp)
REVERT: B   30 PHE cc_start: 0.7890 (m-80) cc_final: 0.7582 (m-80)
REVERT: B   35 ARG cc_start: 0.7885 (mtt-85) cc_final: 0.6755 (mpt180)
REVERT: B  135 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8271 (mtt)
REVERT: B  150 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6821 (mpp80)
REVERT: B  217 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7172 (mtt90)
REVERT: B  226 TYR cc_start: 0.6937 (m-80) cc_final: 0.6522 (m-80)
REVERT: B  242 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: B  284 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7026 (mmpt)
REVERT: B  385 ARG cc_start: 0.6511 (mtt90) cc_final: 0.6181 (mtm-85)
REVERT: B  448 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5634 (tp)
  outliers start: 32
  outliers final: 7
  residues processed: 101
  average time/residue: 1.5476
  time to fit residues: 164.7272
Evaluate side-chains
  102 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 40 optimal weight:    0.0030
   chunk 9 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 23 optimal weight:    0.1980
   chunk 61 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0870
   overall best weight:    1.4572

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.150314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.107595 restraints weight = 8860.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.75
r_work: 0.2976 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7996  Z= 0.142
  Angle     :  0.503   6.487  10846  Z= 0.254
  Chirality :  0.040   0.159   1232
  Planarity :  0.004   0.047   1346
  Dihedral  :  3.964  17.567   1062
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.57 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.34 (0.26), residues: 970
  helix:  2.18 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.08 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 230 
 HIS   0.003   0.001   HIS B 312 
 PHE   0.006   0.001   PHE A 179 
 TYR   0.021   0.002   TYR A 405 
 ARG   0.001   0.000   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05159 (  522)
  hydrogen bonds       : angle       4.01872 ( 1506)
  covalent geometry    : bond        0.00328 ( 7996)
  covalent geometry    : angle       0.50291 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7618 (ptp)
REVERT: A   30 PHE cc_start: 0.7845 (m-80) cc_final: 0.7561 (m-80)
REVERT: A  135 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8260 (mtt)
REVERT: A  150 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6841 (mpp80)
REVERT: A  191 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7594 (pt0)
REVERT: A  226 TYR cc_start: 0.7037 (m-80) cc_final: 0.6617 (m-80)
REVERT: A  242 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8284 (tp)
REVERT: A  284 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7011 (mmpt)
REVERT: A  385 ARG cc_start: 0.6482 (mtt90) cc_final: 0.6109 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6740 (m90) cc_final: 0.6013 (t70)
REVERT: A  448 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5671 (tp)
REVERT: A  463 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7407 (pp30)
REVERT: B   30 PHE cc_start: 0.7853 (m-80) cc_final: 0.7571 (m-80)
REVERT: B  135 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8268 (mtt)
REVERT: B  150 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6818 (mpp80)
REVERT: B  191 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7586 (pt0)
REVERT: B  226 TYR cc_start: 0.7026 (m-80) cc_final: 0.6647 (m-80)
REVERT: B  242 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8287 (tp)
REVERT: B  284 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7018 (mmpt)
REVERT: B  385 ARG cc_start: 0.6506 (mtt90) cc_final: 0.6146 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6737 (m90) cc_final: 0.6007 (t70)
REVERT: B  448 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5661 (tp)
REVERT: B  463 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7423 (pp30)
  outliers start: 34
  outliers final: 13
  residues processed: 103
  average time/residue: 1.2830
  time to fit residues: 139.7000
Evaluate side-chains
  106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 63 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0470
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.153545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.111528 restraints weight = 8916.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.74
r_work: 0.3020 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.105
  Angle     :  0.451   5.821  10846  Z= 0.228
  Chirality :  0.038   0.151   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  3.804  17.454   1062
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 21.65 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.54 (0.26), residues: 970
  helix:  2.34 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.12 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 247 
 HIS   0.002   0.001   HIS B 364 
 PHE   0.006   0.001   PHE B 498 
 TYR   0.008   0.001   TYR B 373 
 ARG   0.001   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04286 (  522)
  hydrogen bonds       : angle       3.87288 ( 1506)
  covalent geometry    : bond        0.00221 ( 7996)
  covalent geometry    : angle       0.45083 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 86
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  150 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6820 (mpp80)
REVERT: A  191 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7544 (pt0)
REVERT: A  217 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7168 (mtt90)
REVERT: A  226 TYR cc_start: 0.6956 (m-80) cc_final: 0.6545 (m-80)
REVERT: A  242 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8256 (tp)
REVERT: A  284 LYS cc_start: 0.7537 (mmtt) cc_final: 0.6999 (mmpt)
REVERT: A  385 ARG cc_start: 0.6457 (mtt90) cc_final: 0.6152 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6673 (m90) cc_final: 0.5940 (t70)
REVERT: A  448 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5769 (tp)
REVERT: A  463 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7353 (pp30)
REVERT: B   20 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7581 (ptp)
REVERT: B  150 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6799 (mpp80)
REVERT: B  191 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7544 (pt0)
REVERT: B  217 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7172 (mtt90)
REVERT: B  226 TYR cc_start: 0.7007 (m-80) cc_final: 0.6626 (m-80)
REVERT: B  242 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8258 (tp)
REVERT: B  284 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7015 (mmpt)
REVERT: B  385 ARG cc_start: 0.6499 (mtt90) cc_final: 0.6181 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6677 (m90) cc_final: 0.5940 (t70)
REVERT: B  448 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5741 (tp)
REVERT: B  463 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7378 (pp30)
  outliers start: 34
  outliers final: 9
  residues processed: 105
  average time/residue: 1.2710
  time to fit residues: 141.2152
Evaluate side-chains
  104 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 25 optimal weight:    0.1980
   chunk 67 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   chunk 52 optimal weight:    0.2980
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.154040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.111951 restraints weight = 8915.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.75
r_work: 0.3034 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.104
  Angle     :  0.454   7.833  10846  Z= 0.227
  Chirality :  0.038   0.150   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  3.731  16.883   1062
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.13 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.61 (0.27), residues: 970
  helix:  2.35 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.19 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 247 
 HIS   0.002   0.001   HIS B 312 
 PHE   0.006   0.001   PHE A 498 
 TYR   0.023   0.001   TYR B 405 
 ARG   0.001   0.000   ARG B 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 (  522)
  hydrogen bonds       : angle       3.83356 ( 1506)
  covalent geometry    : bond        0.00217 ( 7996)
  covalent geometry    : angle       0.45378 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8288 (mtt)
REVERT: A  150 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6872 (mpp80)
REVERT: A  191 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7562 (pt0)
REVERT: A  217 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7179 (mtt90)
REVERT: A  226 TYR cc_start: 0.6963 (m-80) cc_final: 0.6566 (m-80)
REVERT: A  242 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8237 (tp)
REVERT: A  284 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7001 (mmpt)
REVERT: A  385 ARG cc_start: 0.6432 (mtt90) cc_final: 0.6111 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6695 (m90) cc_final: 0.5944 (t70)
REVERT: A  448 ILE cc_start: 0.5936 (OUTLIER) cc_final: 0.5714 (tp)
REVERT: A  463 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7369 (pp30)
REVERT: B   20 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7570 (ptp)
REVERT: B  135 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8278 (mtt)
REVERT: B  150 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6842 (mpp80)
REVERT: B  191 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7559 (pt0)
REVERT: B  217 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7188 (mtt90)
REVERT: B  226 TYR cc_start: 0.6906 (m-80) cc_final: 0.6511 (m-80)
REVERT: B  242 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8242 (tp)
REVERT: B  284 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7017 (mmpt)
REVERT: B  385 ARG cc_start: 0.6484 (mtt90) cc_final: 0.6159 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6694 (m90) cc_final: 0.5938 (t70)
REVERT: B  448 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5712 (tp)
REVERT: B  463 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7388 (pp30)
  outliers start: 32
  outliers final: 9
  residues processed: 103
  average time/residue: 1.3867
  time to fit residues: 150.9993
Evaluate side-chains
  108 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 82 optimal weight:    0.0370
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.154704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.112905 restraints weight = 8881.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.74
r_work: 0.3023 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.101
  Angle     :  0.450   6.976  10846  Z= 0.225
  Chirality :  0.037   0.148   1232
  Planarity :  0.004   0.051   1346
  Dihedral  :  3.688  16.447   1062
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 23.56 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.72 (0.27), residues: 970
  helix:  2.42 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.26 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 247 
 HIS   0.002   0.001   HIS B 312 
 PHE   0.006   0.001   PHE A 498 
 TYR   0.007   0.001   TYR A 495 
 ARG   0.001   0.000   ARG B 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  522)
  hydrogen bonds       : angle       3.80185 ( 1506)
  covalent geometry    : bond        0.00210 ( 7996)
  covalent geometry    : angle       0.44954 (10846)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8285 (mtt)
REVERT: A  150 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6774 (mtp85)
REVERT: A  217 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7169 (mtt90)
REVERT: A  226 TYR cc_start: 0.6894 (m-80) cc_final: 0.6532 (m-80)
REVERT: A  242 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8226 (tp)
REVERT: A  284 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6985 (mmpt)
REVERT: A  385 ARG cc_start: 0.6441 (mtt90) cc_final: 0.6125 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6639 (m90) cc_final: 0.5928 (t70)
REVERT: A  448 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5732 (tp)
REVERT: A  463 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7340 (pp30)
REVERT: B   20 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7546 (ptp)
REVERT: B  135 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8272 (mtt)
REVERT: B  150 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6845 (mtp85)
REVERT: B  217 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7185 (mtt90)
REVERT: B  226 TYR cc_start: 0.6885 (m-80) cc_final: 0.6500 (m-80)
REVERT: B  242 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8224 (tp)
REVERT: B  284 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7003 (mmpt)
REVERT: B  385 ARG cc_start: 0.6509 (mtt90) cc_final: 0.6226 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6660 (m90) cc_final: 0.5936 (t70)
REVERT: B  463 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7357 (pp30)
  outliers start: 20
  outliers final: 6
  residues processed: 95
  average time/residue: 1.4746
  time to fit residues: 147.6521
Evaluate side-chains
  102 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.153728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.111673 restraints weight = 8915.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.74
r_work: 0.3042 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.109
  Angle     :  0.460   6.887  10846  Z= 0.231
  Chirality :  0.038   0.150   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  3.727  16.519   1062
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.85 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.65 (0.27), residues: 970
  helix:  2.35 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.26 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 247 
 HIS   0.002   0.001   HIS B 312 
 PHE   0.006   0.001   PHE A 498 
 TYR   0.024   0.001   TYR A 405 
 ARG   0.001   0.000   ARG B 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04337 (  522)
  hydrogen bonds       : angle       3.84213 ( 1506)
  covalent geometry    : bond        0.00234 ( 7996)
  covalent geometry    : angle       0.46042 (10846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6631.40 seconds
wall clock time: 116 minutes 12.97 seconds (6972.97 seconds total)