Starting phenix.real_space_refine
on Tue Feb 11 05:19:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xrp_33416/02_2025/7xrp_33416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xrp_33416/02_2025/7xrp_33416.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xrp_33416/02_2025/7xrp_33416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xrp_33416/02_2025/7xrp_33416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xrp_33416/02_2025/7xrp_33416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xrp_33416/02_2025/7xrp_33416.cif"
  }
  resolution = 3.88
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2655      2.51       5
     N     674      2.21       5
     O     786      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4129
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1684
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 11, 'TRANS': 197}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 935
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "F"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1454
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 9, 'TRANS': 172}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.36, per 1000 atoms: 1.30
  Number of scatterers: 4129
  At special positions: 0
  Unit cell: (73.91, 77.8, 113.588, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     786      8.00
     N     674      7.00
     C    2655      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 336 " - pdb=" SG  CYS F 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.06

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 165 "
      " NAG A 402 " - " ASN A 282 "
      " NAG A 403 " - " ASN A 122 "
      " NAG F 601 " - " ASN F 343 "
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 501.5 milliseconds
  

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  952

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      5.4% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'B' and resid 62 through 65
      removed outlier: 3.510A  pdb=" N   LYS B  65 " --> pdb=" O   ASP B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 62 through 65'
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'F' and resid 338 through 343
      removed outlier: 3.959A  pdb=" N   PHE F 342 " --> pdb=" O   PHE F 338 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN F 343 " --> pdb=" O   GLY F 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 338 through 343'
    Processing helix  chain 'F' and resid 403 through 410
      removed outlier: 3.708A  pdb=" N   GLU F 406 " --> pdb=" O   ARG F 403 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 502 through 506
      removed outlier: 3.761A  pdb=" N   GLN F 506 " --> pdb=" O   VAL F 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 3.590A  pdb=" N   SER A  31 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR A  63 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   THR A 208 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL A 193 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ILE A 203 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
      removed outlier: 3.713A  pdb=" N   THR A  51 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ASP A  53 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A 271 " --> pdb=" O   PHE A  55 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.778A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS A 129 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 120 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6
      removed outlier: 3.562A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR B  69 " --> pdb=" O   GLN B  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.601A  pdb=" N   THR B 122 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   SER B 124 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B 121 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA B  92 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLN B  39 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B  35 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   PHE B  33 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.601A  pdb=" N   THR B 122 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   SER B 124 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B 121 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA B  92 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50
    Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 357
      removed outlier: 5.047A  pdb=" N   ASN F 394 " --> pdb=" O   GLU F 516 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   GLU F 516 " --> pdb=" O   ASN F 394 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU F 513 " --> pdb=" O   CYS F 432 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL F 433 " --> pdb=" O   LYS F 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454

    95 hydrogen bonds defined for protein.
    219 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 666
        1.30 -     1.44: 1271
        1.44 -     1.57: 2278
        1.57 -     1.70: 1
        1.70 -     1.83: 15
  Bond restraints: 4231
  Sorted by residual:
  bond pdb=" CA  ALA F 352 "
       pdb=" C   ALA F 352 "
    ideal  model  delta    sigma   weight residual
    1.528  1.442  0.086 1.04e-02 9.25e+03 6.82e+01
  bond pdb=" CA  SER F 349 "
       pdb=" C   SER F 349 "
    ideal  model  delta    sigma   weight residual
    1.526  1.425  0.100 1.36e-02 5.41e+03 5.46e+01
  bond pdb=" CA  ARG F 346 "
       pdb=" C   ARG F 346 "
    ideal  model  delta    sigma   weight residual
    1.522  1.446  0.076 1.23e-02 6.61e+03 3.81e+01
  bond pdb=" CA  PHE F 347 "
       pdb=" C   PHE F 347 "
    ideal  model  delta    sigma   weight residual
    1.522  1.449  0.074 1.23e-02 6.61e+03 3.58e+01
  bond pdb=" CA  ALA F 348 "
       pdb=" C   ALA F 348 "
    ideal  model  delta    sigma   weight residual
    1.528  1.456  0.072 1.38e-02 5.25e+03 2.71e+01
  ... (remaining 4226 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.09: 5709
        5.09 -    10.19: 34
       10.19 -    15.28: 4
       15.28 -    20.37: 0
       20.37 -    25.46: 1
  Bond angle restraints: 5748
  Sorted by residual:
  angle pdb=" N   ARG A 214 "
        pdb=" CA  ARG A 214 "
        pdb=" C   ARG A 214 "
      ideal   model   delta    sigma   weight residual
     109.76   84.30   25.46 1.59e+00 3.96e-01 2.56e+02
  angle pdb=" N   VAL F 350 "
        pdb=" CA  VAL F 350 "
        pdb=" C   VAL F 350 "
      ideal   model   delta    sigma   weight residual
     110.62  118.46   -7.84 1.02e+00 9.61e-01 5.90e+01
  angle pdb=" N   ASN A 122 "
        pdb=" CA  ASN A 122 "
        pdb=" C   ASN A 122 "
      ideal   model   delta    sigma   weight residual
     111.28  118.92   -7.64 1.09e+00 8.42e-01 4.91e+01
  angle pdb=" N   TYR F 473 "
        pdb=" CA  TYR F 473 "
        pdb=" C   TYR F 473 "
      ideal   model   delta    sigma   weight residual
     113.38  121.61   -8.23 1.23e+00 6.61e-01 4.47e+01
  angle pdb=" N   VAL A 130 "
        pdb=" CA  VAL A 130 "
        pdb=" C   VAL A 130 "
      ideal   model   delta    sigma   weight residual
     113.10  107.19    5.91 9.70e-01 1.06e+00 3.72e+01
  ... (remaining 5743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2217
       17.34 -    34.67: 241
       34.67 -    52.01: 47
       52.01 -    69.35: 5
       69.35 -    86.68: 4
  Dihedral angle restraints: 2514
    sinusoidal: 1022
      harmonic: 1492
  Sorted by residual:
  dihedral pdb=" CA  CYS F 336 "
           pdb=" C   CYS F 336 "
           pdb=" N   PRO F 337 "
           pdb=" CA  PRO F 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.94  -31.06     0      5.00e+00 4.00e-02 3.86e+01
  dihedral pdb=" CA  ASN F 360 "
           pdb=" C   ASN F 360 "
           pdb=" N   CYS F 361 "
           pdb=" CA  CYS F 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.27   25.73     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  PHE F 490 "
           pdb=" C   PHE F 490 "
           pdb=" N   PRO F 491 "
           pdb=" CA  PRO F 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2511 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 546
       0.095 -    0.190: 71
       0.190 -    0.284: 14
       0.284 -    0.379: 4
       0.379 -    0.474: 4
  Chirality restraints: 639
  Sorted by residual:
  chirality pdb=" CA  PRO A 217 "
            pdb=" N   PRO A 217 "
            pdb=" C   PRO A 217 "
            pdb=" CB  PRO A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.24    0.47 2.00e-01 2.50e+01 5.61e+00
  chirality pdb=" CA  PHE F 429 "
            pdb=" N   PHE F 429 "
            pdb=" C   PHE F 429 "
            pdb=" CB  PHE F 429 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.42e+00
  chirality pdb=" CA  VAL F 350 "
            pdb=" N   VAL F 350 "
            pdb=" C   VAL F 350 "
            pdb=" CB  VAL F 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.03    0.42 2.00e-01 2.50e+01 4.32e+00
  ... (remaining 636 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 403 "   -0.344 2.00e-02 2.50e+03   2.97e-01 1.10e+03
        pdb=" C7  NAG A 403 "    0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG A 403 "   -0.135 2.00e-02 2.50e+03
        pdb=" N2  NAG A 403 "    0.529 2.00e-02 2.50e+03
        pdb=" O7  NAG A 403 "   -0.132 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 401 "   -0.316 2.00e-02 2.50e+03   2.74e-01 9.36e+02
        pdb=" C7  NAG A 401 "    0.071 2.00e-02 2.50e+03
        pdb=" C8  NAG A 401 "   -0.148 2.00e-02 2.50e+03
        pdb=" N2  NAG A 401 "    0.488 2.00e-02 2.50e+03
        pdb=" O7  NAG A 401 "   -0.096 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F 601 "   -0.276 2.00e-02 2.50e+03   2.30e-01 6.61e+02
        pdb=" C7  NAG F 601 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG F 601 "   -0.185 2.00e-02 2.50e+03
        pdb=" N2  NAG F 601 "    0.385 2.00e-02 2.50e+03
        pdb=" O7  NAG F 601 "    0.000 2.00e-02 2.50e+03
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1059
        2.79 -     3.32: 3382
        3.32 -     3.84: 6407
        3.84 -     4.37: 6913
        4.37 -     4.90: 12570
  Nonbonded interactions: 30331
  Sorted by model distance:
  nonbonded pdb=" O   THR A  51 "
            pdb=" OG1 THR A 274 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" N   ARG A 214 "
            pdb=" O   ARG A 214 "
     model   vdw
     2.271 2.496
  nonbonded pdb=" O   ASP A 290 "
            pdb=" OG  SER A 297 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER F 383 "
            pdb=" O   THR F 385 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   SER B 103 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.286 3.040
  ... (remaining 30326 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.560
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
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      :  0.008   0.100   4231  Z= 0.501
  Angle     :  1.139  25.464   5748  Z= 0.701
  Chirality :  0.079   0.474    639
  Planarity :  0.019   0.297    735
  Dihedral  : 14.361  86.684   1547
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 12.87 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    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: -4.63 (0.29), residues: 499
  helix: -5.03 (0.29), residues: 24
  sheet: -3.31 (0.33), residues: 154
  loop : -2.90 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP F 436 
 HIS   0.004   0.001   HIS B  30 
 PHE   0.036   0.002   PHE F 400 
 TYR   0.020   0.002   TYR F 351 
 ARG   0.002   0.001   ARG F 457 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7900 (mttm) cc_final: 0.7665 (tmtt)
REVERT: B   39 GLN cc_start: 0.6561 (tt0) cc_final: 0.6258 (pp30)
REVERT: B  115 TRP cc_start: 0.7598 (m100) cc_final: 0.7101 (m100)
REVERT: F  355 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8178 (ttm-80)
REVERT: F  449 TYR cc_start: 0.8004 (m-80) cc_final: 0.7562 (m-80)
REVERT: F  456 PHE cc_start: 0.8398 (m-80) cc_final: 0.8031 (m-80)
REVERT: F  498 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7866 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2376
  time to fit residues: 35.5899
Evaluate side-chains
  90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.149540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.119101 restraints weight = 6389.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.122302 restraints weight = 4643.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123343 restraints weight = 3177.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4231  Z= 0.246
  Angle     :  0.690   8.331   5748  Z= 0.357
  Chirality :  0.046   0.165    639
  Planarity :  0.005   0.062    735
  Dihedral  :  6.689  59.868    646
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 18.96 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.03 (0.33), residues: 499
  helix: -4.51 (0.44), residues: 30
  sheet: -2.67 (0.34), residues: 186
  loop : -2.46 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 436 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.021   0.002   PHE A 168 
 TYR   0.015   0.001   TYR B  80 
 ARG   0.006   0.001   ARG B  67 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7965 (mttm) cc_final: 0.7668 (tmtt)
REVERT: A   91 TYR cc_start: 0.9069 (t80) cc_final: 0.8815 (t80)
REVERT: A  227 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8477 (m)
REVERT: A  275 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7652 (m-10)
REVERT: B   19 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6413 (mtt180)
REVERT: B   20 LEU cc_start: 0.8486 (mm) cc_final: 0.8173 (mm)
REVERT: B   38 ARG cc_start: 0.7867 (ptm160) cc_final: 0.7182 (tmm-80)
REVERT: B   39 GLN cc_start: 0.6326 (tt0) cc_final: 0.5506 (pp30)
REVERT: B   46 GLU cc_start: 0.6902 (tp30) cc_final: 0.6653 (tp30)
REVERT: B   95 TYR cc_start: 0.8244 (m-80) cc_final: 0.7868 (m-80)
REVERT: B  115 TRP cc_start: 0.7646 (m100) cc_final: 0.7341 (m100)
REVERT: F  338 PHE cc_start: 0.8156 (p90) cc_final: 0.7885 (p90)
REVERT: F  355 ARG cc_start: 0.8277 (ttt90) cc_final: 0.7900 (ttm-80)
REVERT: F  364 ASP cc_start: 0.7987 (p0) cc_final: 0.7621 (p0)
REVERT: F  417 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7960 (ttpp)
REVERT: F  444 LYS cc_start: 0.7216 (tptp) cc_final: 0.6881 (tptp)
REVERT: F  449 TYR cc_start: 0.7908 (m-80) cc_final: 0.7353 (m-80)
REVERT: F  456 PHE cc_start: 0.8420 (m-80) cc_final: 0.8094 (m-80)
REVERT: F  465 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8076 (mt-10)
REVERT: F  498 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7713 (mm-40)
  outliers start: 18
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2335
  time to fit residues: 33.3675
Evaluate side-chains
  100 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  510 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    0.5896

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.153379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124084 restraints weight = 6344.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126780 restraints weight = 3665.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.128889 restraints weight = 2992.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4231  Z= 0.205
  Angle     :  0.625   8.319   5748  Z= 0.322
  Chirality :  0.044   0.156    639
  Planarity :  0.004   0.043    735
  Dihedral  :  5.510  38.780    646
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 22.35 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.75 (0.33), residues: 499
  helix: -4.30 (0.48), residues: 30
  sheet: -2.40 (0.34), residues: 186
  loop : -2.34 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 436 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.015   0.001   PHE F 338 
 TYR   0.022   0.001   TYR A 170 
 ARG   0.007   0.001   ARG F 466 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.8033 (mttm) cc_final: 0.7692 (tmtt)
REVERT: A   91 TYR cc_start: 0.9016 (t80) cc_final: 0.8806 (t80)
REVERT: A  129 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6931 (tttm)
REVERT: A  170 TYR cc_start: 0.7374 (t80) cc_final: 0.7111 (t80)
REVERT: B   20 LEU cc_start: 0.8642 (mm) cc_final: 0.8381 (mm)
REVERT: B   38 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7319 (tmm-80)
REVERT: B   39 GLN cc_start: 0.6159 (tt0) cc_final: 0.5396 (pp30)
REVERT: B   46 GLU cc_start: 0.6849 (tp30) cc_final: 0.6621 (tp30)
REVERT: B   95 TYR cc_start: 0.8209 (m-80) cc_final: 0.7822 (m-80)
REVERT: B  115 TRP cc_start: 0.7638 (m100) cc_final: 0.7395 (m100)
REVERT: F  408 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7051 (ptp90)
REVERT: F  421 TYR cc_start: 0.8218 (m-80) cc_final: 0.8013 (m-80)
REVERT: F  444 LYS cc_start: 0.7246 (tptp) cc_final: 0.6900 (tptp)
REVERT: F  449 TYR cc_start: 0.7844 (m-80) cc_final: 0.7330 (m-80)
REVERT: F  498 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7723 (mm-40)
  outliers start: 19
  outliers final: 10
  residues processed: 104
  average time/residue: 0.2304
  time to fit residues: 28.2582
Evaluate side-chains
  95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  510 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0870
   chunk 14 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.154628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126053 restraints weight = 6406.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.128402 restraints weight = 3805.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.130173 restraints weight = 3236.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4231  Z= 0.183
  Angle     :  0.604  11.440   5748  Z= 0.304
  Chirality :  0.044   0.153    639
  Planarity :  0.004   0.037    735
  Dihedral  :  5.433  48.251    646
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 25.06 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.34), residues: 499
  helix: -4.14 (0.50), residues: 30
  sheet: -2.39 (0.34), residues: 192
  loop : -2.14 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 436 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.020   0.001   PHE F 338 
 TYR   0.018   0.001   TYR F 369 
 ARG   0.007   0.001   ARG F 466 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7996 (mttm) cc_final: 0.7747 (tmtt)
REVERT: A  129 LYS cc_start: 0.7519 (ttpt) cc_final: 0.7102 (tttm)
REVERT: B   20 LEU cc_start: 0.8570 (mm) cc_final: 0.8327 (mm)
REVERT: B   38 ARG cc_start: 0.7918 (ptm160) cc_final: 0.7206 (tmm-80)
REVERT: B   95 TYR cc_start: 0.8174 (m-80) cc_final: 0.7743 (m-80)
REVERT: F  417 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7828 (ttpp)
REVERT: F  444 LYS cc_start: 0.7229 (tptp) cc_final: 0.6936 (tptp)
REVERT: F  449 TYR cc_start: 0.7792 (m-80) cc_final: 0.7266 (m-80)
REVERT: F  498 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7763 (mm-40)
  outliers start: 14
  outliers final: 11
  residues processed: 95
  average time/residue: 0.2388
  time to fit residues: 26.7698
Evaluate side-chains
  87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  510 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0980
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.153016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123729 restraints weight = 6554.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126270 restraints weight = 3915.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128283 restraints weight = 3237.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4231  Z= 0.221
  Angle     :  0.588   9.307   5748  Z= 0.304
  Chirality :  0.044   0.150    639
  Planarity :  0.004   0.044    735
  Dihedral  :  5.401  43.284    646
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.38 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.34), residues: 499
  helix: -3.90 (0.57), residues: 30
  sheet: -2.31 (0.35), residues: 186
  loop : -2.09 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 436 
 HIS   0.001   0.000   HIS A  66 
 PHE   0.016   0.001   PHE F 338 
 TYR   0.026   0.002   TYR A 170 
 ARG   0.007   0.001   ARG F 466 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.8011 (mttm) cc_final: 0.7767 (tmtt)
REVERT: A  129 LYS cc_start: 0.7471 (ttpt) cc_final: 0.6995 (tttm)
REVERT: A  170 TYR cc_start: 0.7106 (t80) cc_final: 0.6872 (t80)
REVERT: A  275 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7641 (m-10)
REVERT: B   20 LEU cc_start: 0.8620 (mm) cc_final: 0.8272 (mm)
REVERT: B   38 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7343 (tmm-80)
REVERT: F  417 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7925 (ttpp)
REVERT: F  444 LYS cc_start: 0.7201 (tptp) cc_final: 0.6893 (tptp)
REVERT: F  449 TYR cc_start: 0.7769 (m-80) cc_final: 0.7250 (m-80)
REVERT: F  498 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7795 (mm-40)
  outliers start: 18
  outliers final: 13
  residues processed: 98
  average time/residue: 0.2280
  time to fit residues: 26.4281
Evaluate side-chains
  89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.151320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121995 restraints weight = 6480.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124590 restraints weight = 3969.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.126374 restraints weight = 3308.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4231  Z= 0.270
  Angle     :  0.612   8.848   5748  Z= 0.317
  Chirality :  0.045   0.146    639
  Planarity :  0.004   0.027    735
  Dihedral  :  5.091  22.192    646
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.73 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.42 (0.35), residues: 499
  helix: -3.86 (0.58), residues: 30
  sheet: -2.40 (0.35), residues: 186
  loop : -1.96 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 436 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.020   0.002   PHE F 400 
 TYR   0.021   0.002   TYR F 369 
 ARG   0.007   0.001   ARG A  34 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.8018 (mttm) cc_final: 0.7719 (tmtt)
REVERT: A   91 TYR cc_start: 0.9121 (t80) cc_final: 0.8828 (t80)
REVERT: A  275 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7707 (m-10)
REVERT: B   20 LEU cc_start: 0.8655 (mm) cc_final: 0.8321 (mm)
REVERT: B   38 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7350 (tmm-80)
REVERT: B   80 TYR cc_start: 0.5827 (m-80) cc_final: 0.5489 (m-80)
REVERT: F  417 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7931 (ttpp)
REVERT: F  444 LYS cc_start: 0.7249 (tptp) cc_final: 0.6901 (tptp)
REVERT: F  449 TYR cc_start: 0.7827 (m-80) cc_final: 0.7338 (m-80)
REVERT: F  498 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7760 (mm-40)
  outliers start: 21
  outliers final: 15
  residues processed: 97
  average time/residue: 0.2150
  time to fit residues: 25.2797
Evaluate side-chains
  90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.153353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.123926 restraints weight = 6389.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.126474 restraints weight = 3846.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.128159 restraints weight = 3280.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4231  Z= 0.212
  Angle     :  0.589   8.188   5748  Z= 0.306
  Chirality :  0.044   0.145    639
  Planarity :  0.004   0.041    735
  Dihedral  :  4.819  21.669    646
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 27.09 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.35), residues: 499
  helix: -3.68 (0.63), residues: 30
  sheet: -2.35 (0.35), residues: 186
  loop : -1.89 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 353 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.017   0.001   PHE F 400 
 TYR   0.019   0.001   TYR F 369 
 ARG   0.007   0.001   ARG A  34 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.425 
Fit side-chains
REVERT: B   20 LEU cc_start: 0.8618 (mm) cc_final: 0.8327 (mm)
REVERT: B   38 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7368 (tmm-80)
REVERT: B   80 TYR cc_start: 0.5768 (m-80) cc_final: 0.5426 (m-80)
REVERT: F  417 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7842 (ttpp)
REVERT: F  444 LYS cc_start: 0.7274 (tptp) cc_final: 0.6983 (tptp)
REVERT: F  449 TYR cc_start: 0.7900 (m-80) cc_final: 0.7403 (m-80)
REVERT: F  498 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7745 (mm-40)
  outliers start: 19
  outliers final: 17
  residues processed: 88
  average time/residue: 0.2151
  time to fit residues: 22.7497
Evaluate side-chains
  87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 13 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.153004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123949 restraints weight = 6423.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.126626 restraints weight = 3917.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.127957 restraints weight = 3310.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4231  Z= 0.232
  Angle     :  0.609   8.049   5748  Z= 0.315
  Chirality :  0.044   0.148    639
  Planarity :  0.004   0.031    735
  Dihedral  :  4.771  21.524    646
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 28.44 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.26 (0.35), residues: 499
  helix: -3.75 (0.59), residues: 30
  sheet: -2.28 (0.35), residues: 186
  loop : -1.84 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 436 
 HIS   0.001   0.000   HIS B  30 
 PHE   0.018   0.001   PHE F 338 
 TYR   0.026   0.001   TYR F 423 
 ARG   0.005   0.001   ARG F 466 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.7310 (tttt) cc_final: 0.7008 (tmtt)
REVERT: B   20 LEU cc_start: 0.8562 (mm) cc_final: 0.8283 (mm)
REVERT: B   38 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7458 (tmm-80)
REVERT: F  417 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7859 (ttpp)
REVERT: F  444 LYS cc_start: 0.7253 (tptp) cc_final: 0.6950 (tptp)
REVERT: F  449 TYR cc_start: 0.7872 (m-80) cc_final: 0.7389 (m-80)
REVERT: F  498 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7737 (mm-40)
  outliers start: 17
  outliers final: 16
  residues processed: 85
  average time/residue: 0.2210
  time to fit residues: 22.4153
Evaluate side-chains
  84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 9 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0050
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.154574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.125764 restraints weight = 6420.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128301 restraints weight = 3739.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.129467 restraints weight = 3278.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4231  Z= 0.195
  Angle     :  0.596   7.899   5748  Z= 0.307
  Chirality :  0.044   0.146    639
  Planarity :  0.004   0.032    735
  Dihedral  :  4.623  22.585    646
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 28.44 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.35), residues: 499
  helix: -3.62 (0.62), residues: 30
  sheet: -2.17 (0.36), residues: 181
  loop : -1.82 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 436 
 HIS   0.001   0.000   HIS B  30 
 PHE   0.018   0.001   PHE F 338 
 TYR   0.030   0.001   TYR F 423 
 ARG   0.009   0.001   ARG A  34 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.7219 (tttt) cc_final: 0.6915 (tmtt)
REVERT: B   20 LEU cc_start: 0.8574 (mm) cc_final: 0.8319 (mm)
REVERT: B   38 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7450 (tmm-80)
REVERT: F  417 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7924 (ttpp)
REVERT: F  444 LYS cc_start: 0.7252 (tptp) cc_final: 0.6962 (tptp)
REVERT: F  449 TYR cc_start: 0.7873 (m-80) cc_final: 0.7387 (m-80)
REVERT: F  498 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7720 (mm-40)
  outliers start: 16
  outliers final: 16
  residues processed: 88
  average time/residue: 0.2233
  time to fit residues: 23.4774
Evaluate side-chains
  84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.152375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123595 restraints weight = 6414.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.126001 restraints weight = 3816.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.127205 restraints weight = 3364.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4231  Z= 0.255
  Angle     :  0.629   7.499   5748  Z= 0.326
  Chirality :  0.045   0.162    639
  Planarity :  0.004   0.042    735
  Dihedral  :  4.771  22.829    646
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 27.99 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.36), residues: 499
  helix: -3.60 (0.63), residues: 30
  sheet: -2.16 (0.35), residues: 186
  loop : -1.79 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 436 
 HIS   0.007   0.001   HIS B  30 
 PHE   0.019   0.001   PHE F 400 
 TYR   0.037   0.002   TYR A 170 
 ARG   0.011   0.001   ARG A  34 

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   91 TYR cc_start: 0.9123 (t80) cc_final: 0.8806 (t80)
REVERT: A  129 LYS cc_start: 0.7300 (tttt) cc_final: 0.7037 (tmtt)
REVERT: B   20 LEU cc_start: 0.8570 (mm) cc_final: 0.8292 (mm)
REVERT: B   30 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7707 (m90)
REVERT: F  417 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7953 (ttpp)
REVERT: F  444 LYS cc_start: 0.7257 (tptp) cc_final: 0.6961 (tptp)
REVERT: F  456 PHE cc_start: 0.8095 (m-80) cc_final: 0.7834 (m-80)
REVERT: F  498 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7709 (mm-40)
  outliers start: 17
  outliers final: 16
  residues processed: 85
  average time/residue: 0.2063
  time to fit residues: 21.3114
Evaluate side-chains
  85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   30 HIS
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  467 ASP
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0970
   chunk 49 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0570
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.155230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127216 restraints weight = 6352.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.129139 restraints weight = 3880.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.130270 restraints weight = 3597.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.4137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4231  Z= 0.186
  Angle     :  0.603   7.654   5748  Z= 0.312
  Chirality :  0.044   0.159    639
  Planarity :  0.004   0.033    735
  Dihedral  :  4.586  21.496    646
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 28.89 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.35), residues: 499
  helix: -3.42 (0.67), residues: 30
  sheet: -2.09 (0.36), residues: 180
  loop : -1.83 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 436 
 HIS   0.007   0.001   HIS B  30 
 PHE   0.019   0.001   PHE F 338 
 TYR   0.040   0.002   TYR A 170 
 ARG   0.007   0.001   ARG F 357 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2057.82 seconds
wall clock time: 37 minutes 23.60 seconds (2243.60 seconds total)