Starting phenix.real_space_refine
on Wed Feb 12 11:18:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tel_41190/02_2025/8tel_41190.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tel_41190/02_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_41190/02_2025/8tel_41190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tel_41190/02_2025/8tel_41190.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tel_41190/02_2025/8tel_41190.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tel_41190/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.00, per 1000 atoms: 0.90
  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: 2.25
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.75
  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: 2.19

  Time building geometry restraints manager: 2.43 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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.100
  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:12.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.110
-------------------------------------------------------------------------------
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= 0.225
  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 

*********************** 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  : 0.888 
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: 1.2806
  time to fit residues: 129.1136
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  : 0.930 
-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.151295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.107165 restraints weight = 8667.761|
|-----------------------------------------------------------------------------|
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: 0.8407
moved from start:          0.1040

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= 0.172
  Angle     :  0.477   5.346  10846  Z= 0.243
  Chirality :  0.039   0.155   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  4.865  50.024   1076
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.65 %
    Favored  : 75.48 %
  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 

*********************** 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  : 0.980 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.6392 (mpt180)
REVERT: A  150 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6854 (mpp80)
REVERT: A  242 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (tp)
REVERT: A  385 ARG cc_start: 0.6397 (mtt90) cc_final: 0.5929 (mtm-85)
REVERT: B   20 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7814 (ptp)
REVERT: B   35 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.6430 (mpt180)
REVERT: B  150 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6808 (mpp80)
REVERT: B  242 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8254 (tp)
REVERT: B  385 ARG cc_start: 0.6407 (mtt90) cc_final: 0.5931 (mtm-85)
  outliers start: 24
  outliers final: 4
  residues processed: 105
  average time/residue: 1.5890
  time to fit residues: 175.3309
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  : 0.888 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.153024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.110262 restraints weight = 8909.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.75
r_work: 0.3026 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1563

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= 0.193
  Angle     :  0.493   6.940  10846  Z= 0.250
  Chirality :  0.039   0.159   1232
  Planarity :  0.004   0.047   1346
  Dihedral  :  4.032  29.763   1064
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.29 %
    Favored  : 75.72 %
  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:  2.50 (0.26), residues: 970
  helix:  2.30 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.14 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 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 

*********************** 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
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7778 (ptp)
REVERT: A   35 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.6739 (mpt180)
REVERT: A  181 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6769 (mt)
REVERT: A  226 TYR cc_start: 0.7129 (m-80) cc_final: 0.6704 (m-80)
REVERT: A  242 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8277 (tp)
REVERT: A  284 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7120 (mmpt)
REVERT: A  363 MET cc_start: 0.9089 (mtp) cc_final: 0.8854 (mtp)
REVERT: A  385 ARG cc_start: 0.6484 (mtt90) cc_final: 0.6196 (mtm-85)
REVERT: A  463 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7420 (pp30)
REVERT: B   20 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7812 (ptp)
REVERT: B   35 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.6762 (mpt180)
REVERT: B  181 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6765 (mt)
REVERT: B  226 TYR cc_start: 0.7090 (m-80) cc_final: 0.6671 (m-80)
REVERT: B  242 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8277 (tp)
REVERT: B  284 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7124 (mmpt)
REVERT: B  385 ARG cc_start: 0.6494 (mtt90) cc_final: 0.6195 (mtm-85)
REVERT: B  463 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7426 (pp30)
  outliers start: 25
  outliers final: 6
  residues processed: 104
  average time/residue: 1.4287
  time to fit residues: 156.4444
Evaluate side-chains
  99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 18 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.154500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112269 restraints weight = 8790.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.74
r_work: 0.3036 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1688

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= 0.145
  Angle     :  0.453   6.543  10846  Z= 0.228
  Chirality :  0.038   0.151   1232
  Planarity :  0.004   0.048   1346
  Dihedral  :  3.809  19.279   1064
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.05 %
    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:  2.71 (0.26), residues: 970
  helix:  2.46 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.23 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 312 
 PHE   0.006   0.001   PHE B 498 
 TYR   0.006   0.001   TYR B 495 
 ARG   0.001   0.000   ARG B 232 

*********************** 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
  110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7766 (ptp)
REVERT: A   35 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.6637 (mpt180)
REVERT: A  135 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8259 (mtt)
REVERT: A  181 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6697 (mt)
REVERT: A  226 TYR cc_start: 0.7011 (m-80) cc_final: 0.6598 (m-80)
REVERT: A  284 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7116 (mmpt)
REVERT: A  363 MET cc_start: 0.9027 (mtp) cc_final: 0.8811 (mtp)
REVERT: A  385 ARG cc_start: 0.6438 (mtt90) cc_final: 0.6180 (mtm-85)
REVERT: B   20 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7732 (ptp)
REVERT: B   35 ARG cc_start: 0.7767 (mtt-85) cc_final: 0.6655 (mpt180)
REVERT: B  135 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8274 (mtt)
REVERT: B  181 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6706 (mt)
REVERT: B  226 TYR cc_start: 0.7008 (m-80) cc_final: 0.6603 (m-80)
REVERT: B  284 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7119 (mmpt)
REVERT: B  363 MET cc_start: 0.9050 (mtp) cc_final: 0.8828 (mtp)
REVERT: B  385 ARG cc_start: 0.6458 (mtt90) cc_final: 0.6188 (mtm-85)
  outliers start: 26
  outliers final: 7
  residues processed: 100
  average time/residue: 1.4946
  time to fit residues: 157.5839
Evaluate side-chains
  93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.147846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.104219 restraints weight = 8888.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.74
r_work: 0.2900 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7996  Z= 0.226
  Angle     :  0.510   6.044  10846  Z= 0.257
  Chirality :  0.040   0.160   1232
  Planarity :  0.004   0.046   1346
  Dihedral  :  3.912  17.709   1062
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.05 %
    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:  2.37 (0.26), residues: 970
  helix:  2.20 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.10 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 230 
 HIS   0.004   0.001   HIS A 312 
 PHE   0.007   0.001   PHE B 498 
 TYR   0.015   0.001   TYR B 405 
 ARG   0.002   0.000   ARG A 464 

*********************** 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
  111 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 81
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7795 (ptp)
REVERT: A  135 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8240 (mtt)
REVERT: A  226 TYR cc_start: 0.6958 (m-80) cc_final: 0.6551 (m-80)
REVERT: A  242 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: A  284 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7015 (mmpt)
REVERT: A  385 ARG cc_start: 0.6447 (mtt90) cc_final: 0.6106 (mtm-85)
REVERT: A  448 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5596 (tp)
REVERT: A  463 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7452 (pp30)
REVERT: B   20 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7735 (ptp)
REVERT: B  135 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8249 (mtt)
REVERT: B  191 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7551 (pt0)
REVERT: B  226 TYR cc_start: 0.6944 (m-80) cc_final: 0.6539 (m-80)
REVERT: B  242 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (tp)
REVERT: B  284 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7017 (mmpt)
REVERT: B  385 ARG cc_start: 0.6443 (mtt90) cc_final: 0.6118 (mtm-85)
REVERT: B  448 ILE cc_start: 0.5865 (OUTLIER) cc_final: 0.5560 (tp)
REVERT: B  463 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7473 (pp30)
  outliers start: 30
  outliers final: 7
  residues processed: 100
  average time/residue: 1.3389
  time to fit residues: 141.4325
Evaluate side-chains
  96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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  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  135 MET
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  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
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:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0070
   chunk 86 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0470
   overall best weight:    0.4296

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.154767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.112773 restraints weight = 8877.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.74
r_work: 0.3037 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1963

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= 0.135
  Angle     :  0.447   7.504  10846  Z= 0.224
  Chirality :  0.037   0.149   1232
  Planarity :  0.004   0.049   1346
  Dihedral  :  3.708  17.592   1062
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.13 %
    Favored  : 74.64 %
  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:  2.63 (0.27), residues: 970
  helix:  2.41 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.16 (0.36), residues: 290

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   0.005   0.001   PHE A 498 
 TYR   0.007   0.001   TYR A  22 
 ARG   0.001   0.000   ARG B 264 

*********************** 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
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7584 (ptp)
REVERT: A   30 PHE cc_start: 0.7863 (m-80) cc_final: 0.7592 (m-80)
REVERT: A  150 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6863 (mpp80)
REVERT: A  217 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7191 (mtt90)
REVERT: A  226 TYR cc_start: 0.6966 (m-80) cc_final: 0.6532 (m-80)
REVERT: A  284 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7006 (mmpt)
REVERT: A  385 ARG cc_start: 0.6443 (mtt90) cc_final: 0.6173 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6636 (m90) cc_final: 0.5891 (t70)
REVERT: A  448 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5642 (tp)
REVERT: A  463 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7288 (pp30)
REVERT: B   20 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7615 (ptp)
REVERT: B   30 PHE cc_start: 0.7880 (m-80) cc_final: 0.7606 (m-80)
REVERT: B   35 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.6644 (mpt180)
REVERT: B  150 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6856 (mpp80)
REVERT: B  217 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7167 (mtt90)
REVERT: B  226 TYR cc_start: 0.6943 (m-80) cc_final: 0.6512 (m-80)
REVERT: B  284 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7019 (mmpt)
REVERT: B  385 ARG cc_start: 0.6462 (mtt90) cc_final: 0.6162 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6641 (m90) cc_final: 0.5839 (t70)
REVERT: B  448 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5620 (tp)
REVERT: B  463 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7307 (pp30)
  outliers start: 27
  outliers final: 1
  residues processed: 99
  average time/residue: 1.4935
  time to fit residues: 155.5818
Evaluate side-chains
  92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
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  150 ARG
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 94 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0010
   chunk 17 optimal weight:    0.9980
   overall best weight:    2.7992

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 333 HIS
B  24 GLN
B 333 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.149017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.106302 restraints weight = 8844.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.75
r_work: 0.2944 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7996  Z= 0.346
  Angle     :  0.598   6.525  10846  Z= 0.304
  Chirality :  0.044   0.172   1232
  Planarity :  0.005   0.048   1346
  Dihedral  :  4.250  18.136   1062
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.29 %
    Favored  : 74.88 %
  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:  1.97 (0.26), residues: 970
  helix:  1.85 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop :  0.08 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 230 
 HIS   0.004   0.001   HIS B 312 
 PHE   0.011   0.001   PHE A  30 
 TYR   0.019   0.002   TYR A 405 
 ARG   0.002   0.001   ARG B 464 

*********************** 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
  114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7793 (ptp)
REVERT: A  135 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8236 (mtt)
REVERT: A  150 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6810 (mpp80)
REVERT: A  226 TYR cc_start: 0.6997 (m-80) cc_final: 0.6615 (m-80)
REVERT: A  242 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8376 (tp)
REVERT: A  284 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7029 (mmpt)
REVERT: A  385 ARG cc_start: 0.6598 (mtt90) cc_final: 0.6171 (mtm-85)
REVERT: A  448 ILE cc_start: 0.5979 (OUTLIER) cc_final: 0.5634 (tp)
REVERT: A  463 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7572 (pp30)
REVERT: B  135 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8237 (mtt)
REVERT: B  150 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6789 (mpp80)
REVERT: B  191 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7593 (pt0)
REVERT: B  226 TYR cc_start: 0.6985 (m-80) cc_final: 0.6625 (m-80)
REVERT: B  242 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8379 (tp)
REVERT: B  284 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7034 (mmpt)
REVERT: B  385 ARG cc_start: 0.6616 (mtt90) cc_final: 0.6191 (mtm-85)
REVERT: B  448 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5632 (tp)
REVERT: B  463 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7554 (pp30)
  outliers start: 32
  outliers final: 8
  residues processed: 100
  average time/residue: 1.2855
  time to fit residues: 136.6421
Evaluate side-chains
  99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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  150 ARG
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  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  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  234 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.151122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.108804 restraints weight = 8889.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.75
r_work: 0.2977 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7996  Z= 0.182
  Angle     :  0.491   6.953  10846  Z= 0.249
  Chirality :  0.039   0.157   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  4.041  18.113   1062
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.49 %
    Favored  : 74.16 %
  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:  2.27 (0.26), residues: 970
  helix:  2.12 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.06 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 247 
 HIS   0.003   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 217 

*********************** 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
  108 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8237 (mtt)
REVERT: A  150 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6823 (mpp80)
REVERT: A  226 TYR cc_start: 0.6999 (m-80) cc_final: 0.6618 (m-80)
REVERT: A  242 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8320 (tp)
REVERT: A  284 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7001 (mmpt)
REVERT: A  385 ARG cc_start: 0.6528 (mtt90) cc_final: 0.6211 (mtm-85)
REVERT: A  448 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5773 (tp)
REVERT: A  463 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7400 (pp30)
REVERT: B  135 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8243 (mtt)
REVERT: B  150 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6817 (mpp80)
REVERT: B  226 TYR cc_start: 0.6983 (m-80) cc_final: 0.6592 (m-80)
REVERT: B  242 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8315 (tp)
REVERT: B  284 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7020 (mmpt)
REVERT: B  385 ARG cc_start: 0.6612 (mtt90) cc_final: 0.6269 (mtm-85)
REVERT: B  448 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5772 (tp)
REVERT: B  463 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7417 (pp30)
  outliers start: 28
  outliers final: 7
  residues processed: 97
  average time/residue: 1.4189
  time to fit residues: 145.2706
Evaluate side-chains
  96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 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  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
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  228 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 67 optimal weight:    0.1980
   chunk 81 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 52 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.153346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.111433 restraints weight = 8914.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.74
r_work: 0.2957 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2227

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= 0.147
  Angle     :  0.459   8.492  10846  Z= 0.231
  Chirality :  0.038   0.152   1232
  Planarity :  0.004   0.051   1346
  Dihedral  :  3.842  17.388   1062
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.56 %
    Favored  : 74.16 %
  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:  2.42 (0.27), residues: 970
  helix:  2.23 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.03 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 364 
 PHE   0.006   0.001   PHE B  30 
 TYR   0.022   0.001   TYR A 405 
 ARG   0.001   0.000   ARG B 232 

*********************** 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
  101 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8261 (mtt)
REVERT: A  150 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6819 (mpp80)
REVERT: A  226 TYR cc_start: 0.6956 (m-80) cc_final: 0.6559 (m-80)
REVERT: A  284 LYS cc_start: 0.7509 (mmtt) cc_final: 0.6975 (mmpt)
REVERT: A  385 ARG cc_start: 0.6424 (mtt90) cc_final: 0.6136 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6740 (m90) cc_final: 0.5974 (t70)
REVERT: A  448 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5759 (tp)
REVERT: A  463 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7341 (pp30)
REVERT: B  135 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8284 (mtt)
REVERT: B  150 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6834 (mpp80)
REVERT: B  226 TYR cc_start: 0.6953 (m-80) cc_final: 0.6546 (m-80)
REVERT: B  284 LYS cc_start: 0.7516 (mmtt) cc_final: 0.6987 (mmpt)
REVERT: B  385 ARG cc_start: 0.6440 (mtt90) cc_final: 0.6136 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6736 (m90) cc_final: 0.5973 (t70)
REVERT: B  448 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5752 (tp)
REVERT: B  463 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7364 (pp30)
  outliers start: 19
  outliers final: 7
  residues processed: 95
  average time/residue: 1.4678
  time to fit residues: 146.6935
Evaluate side-chains
  96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  228 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 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  228 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0170
   chunk 88 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 82 optimal weight:    0.0870
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.155389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113848 restraints weight = 8874.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.74
r_work: 0.3057 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2274

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= 0.129
  Angle     :  0.441   7.123  10846  Z= 0.222
  Chirality :  0.037   0.147   1232
  Planarity :  0.004   0.051   1346
  Dihedral  :  3.681  17.126   1062
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 23.92 %
    Favored  : 74.16 %
  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:  2.70 (0.27), residues: 970
  helix:  2.43 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop :  0.17 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 247 
 HIS   0.002   0.001   HIS B 364 
 PHE   0.006   0.001   PHE B 341 
 TYR   0.008   0.001   TYR B  42 
 ARG   0.001   0.000   ARG A 232 

********************** 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: 16
    poor density    : 88
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8320 (mtt)
REVERT: A  150 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6796 (mtp85)
REVERT: A  226 TYR cc_start: 0.6874 (m-80) cc_final: 0.6547 (m-80)
REVERT: A  284 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7025 (mmpt)
REVERT: A  385 ARG cc_start: 0.6527 (mtt90) cc_final: 0.6230 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6683 (m90) cc_final: 0.5969 (t-90)
REVERT: A  448 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5868 (tp)
REVERT: A  463 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7289 (pp30)
REVERT: B  135 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8300 (mtt)
REVERT: B  150 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6788 (mtp85)
REVERT: B  226 TYR cc_start: 0.6844 (m-80) cc_final: 0.6515 (m-80)
REVERT: B  284 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7041 (mmpt)
REVERT: B  385 ARG cc_start: 0.6525 (mtt90) cc_final: 0.6223 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6680 (m90) cc_final: 0.5964 (t-90)
REVERT: B  463 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7307 (pp30)
  outliers start: 16
  outliers final: 5
  residues processed: 100
  average time/residue: 1.4668
  time to fit residues: 154.3950
Evaluate side-chains
  99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
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  228 THR
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.154047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.112114 restraints weight = 8876.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.73
r_work: 0.3011 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2379

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= 0.150
  Angle     :  0.470   8.551  10846  Z= 0.235
  Chirality :  0.038   0.149   1232
  Planarity :  0.004   0.051   1346
  Dihedral  :  3.705  16.487   1062
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 23.92 %
    Favored  : 74.16 %
  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:  2.37 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.22 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 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 386 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5814.17 seconds
wall clock time: 103 minutes 17.13 seconds (6197.13 seconds total)