Starting phenix.real_space_refine
on Wed Apr 30 23:20:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mgv_9112/04_2025/6mgv_9112.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mgv_9112/04_2025/6mgv_9112.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mgv_9112/04_2025/6mgv_9112.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mgv_9112/04_2025/6mgv_9112.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mgv_9112/04_2025/6mgv_9112.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mgv_9112/04_2025/6mgv_9112.cif"
  }
  resolution = 3.1
  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=   0.021
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      48      5.16       5
     C    6744      2.51       5
     N    1650      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5075
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.64, per 1000 atoms: 0.95
  Number of scatterers: 10150
  At special positions: 0
  Unit cell: (123.05, 129.95, 95.45, 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      48     16.00
     O    1708      8.00
     N    1650      7.00
     C    6744      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: 2.90
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      76.9% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 29
    Processing helix  chain 'A' and resid 30 through 33
      removed outlier: 6.322A  pdb=" N   PHE A  33 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 30 through 33'
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.557A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 4.048A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 314 through 317
      removed outlier: 6.347A  pdb=" N   LYS A 317 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 314 through 317'
    Processing helix  chain 'A' and resid 329 through 337
    Processing helix  chain 'A' and resid 360 through 366
      removed outlier: 3.710A  pdb=" N   ILE A 366 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 389 through 400
    Processing helix  chain 'A' and resid 422 through 438
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 476
    Processing helix  chain 'A' and resid 477 through 489
    Processing helix  chain 'A' and resid 504 through 512
      Proline residue:  A 510  - end of helix
    Processing helix  chain 'A' and resid 512 through 524
    Processing helix  chain 'A' and resid 524 through 532
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 587 through 589
      No H-bonds generated for 'chain 'A' and resid 587 through 589'
    Processing helix  chain 'A' and resid 590 through 612
    Processing helix  chain 'A' and resid 623 through 646
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.027A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
    Processing helix  chain 'B' and resid 30 through 33
      removed outlier: 6.323A  pdb=" N   PHE B  33 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.557A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 121
      removed outlier: 4.048A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 157 through 195
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 314 through 317
      removed outlier: 6.347A  pdb=" N   LYS B 317 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 314 through 317'
    Processing helix  chain 'B' and resid 329 through 337
    Processing helix  chain 'B' and resid 360 through 366
      removed outlier: 3.711A  pdb=" N   ILE B 366 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 389 through 400
    Processing helix  chain 'B' and resid 422 through 438
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 452
    Processing helix  chain 'B' and resid 456 through 476
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 504 through 512
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 512 through 524
    Processing helix  chain 'B' and resid 524 through 532
    Processing helix  chain 'B' and resid 534 through 548
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 584
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 587 through 589
      No H-bonds generated for 'chain 'B' and resid 587 through 589'
    Processing helix  chain 'B' and resid 590 through 612
    Processing helix  chain 'B' and resid 623 through 646
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.027A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.602A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240
      removed outlier: 5.602A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    2055 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: 3.00

  Time building geometry restraints manager: 3.25 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2294
        1.33 -     1.45: 2924
        1.45 -     1.58: 5128
        1.58 -     1.70: 6
        1.70 -     1.83: 88
  Bond restraints: 10440
  Sorted by residual:
  bond pdb=" N   PRO B 210 "
       pdb=" CD  PRO B 210 "
    ideal  model  delta    sigma   weight residual
    1.473  1.410  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" N   PRO A 210 "
       pdb=" CD  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.473  1.410  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" CB  GLN B 615 "
       pdb=" CG  GLN B 615 "
    ideal  model  delta    sigma   weight residual
    1.520  1.407  0.113 3.00e-02 1.11e+03 1.43e+01
  bond pdb=" CB  GLN A 615 "
       pdb=" CG  GLN A 615 "
    ideal  model  delta    sigma   weight residual
    1.520  1.407  0.113 3.00e-02 1.11e+03 1.43e+01
  bond pdb=" N   PRO A 715 "
       pdb=" CD  PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.473  1.424  0.049 1.40e-02 5.10e+03 1.21e+01
  ... (remaining 10435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 12698
        2.27 -     4.53: 1340
        4.53 -     6.80: 126
        6.80 -     9.06: 34
        9.06 -    11.33: 2
  Bond angle restraints: 14200
  Sorted by residual:
  angle pdb=" N   SER B 619 "
        pdb=" CA  SER B 619 "
        pdb=" C   SER B 619 "
      ideal   model   delta    sigma   weight residual
     110.17   98.84   11.33 1.61e+00 3.86e-01 4.95e+01
  angle pdb=" N   SER A 619 "
        pdb=" CA  SER A 619 "
        pdb=" C   SER A 619 "
      ideal   model   delta    sigma   weight residual
     110.17   98.86   11.31 1.61e+00 3.86e-01 4.94e+01
  angle pdb=" N   ASP A 554 "
        pdb=" CA  ASP A 554 "
        pdb=" C   ASP A 554 "
      ideal   model   delta    sigma   weight residual
     113.17  105.63    7.54 1.26e+00 6.30e-01 3.58e+01
  angle pdb=" N   ASP B 554 "
        pdb=" CA  ASP B 554 "
        pdb=" C   ASP B 554 "
      ideal   model   delta    sigma   weight residual
     113.17  105.68    7.49 1.26e+00 6.30e-01 3.54e+01
  angle pdb=" N   LYS A  41 "
        pdb=" CA  LYS A  41 "
        pdb=" C   LYS A  41 "
      ideal   model   delta    sigma   weight residual
     110.41  103.15    7.26 1.23e+00 6.61e-01 3.48e+01
  ... (remaining 14195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 5849
       14.74 -    29.49: 209
       29.49 -    44.23: 38
       44.23 -    58.98: 26
       58.98 -    73.72: 6
  Dihedral angle restraints: 6128
    sinusoidal: 2386
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CA  ASP A 212 "
           pdb=" CB  ASP A 212 "
           pdb=" CG  ASP A 212 "
           pdb=" OD1 ASP A 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.32   52.32     1      2.00e+01 2.50e-03 9.33e+00
  dihedral pdb=" CA  ASP B 212 "
           pdb=" CB  ASP B 212 "
           pdb=" CG  ASP B 212 "
           pdb=" OD1 ASP B 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.29   52.29     1      2.00e+01 2.50e-03 9.32e+00
  dihedral pdb=" N   TYR A 613 "
           pdb=" C   TYR A 613 "
           pdb=" CA  TYR A 613 "
           pdb=" CB  TYR A 613 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.19   -7.39     0      2.50e+00 1.60e-01 8.74e+00
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1089
       0.075 -    0.150: 401
       0.150 -    0.225: 81
       0.225 -    0.300: 28
       0.300 -    0.375: 5
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CA  PHE A 109 "
            pdb=" N   PHE A 109 "
            pdb=" C   PHE A 109 "
            pdb=" CB  PHE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" CA  PHE B 109 "
            pdb=" N   PHE B 109 "
            pdb=" C   PHE B 109 "
            pdb=" CB  PHE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.46e+00
  chirality pdb=" CA  TYR A 613 "
            pdb=" N   TYR A 613 "
            pdb=" C   TYR A 613 "
            pdb=" CB  TYR A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.84e+00
  ... (remaining 1601 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 352 "   -0.041 2.00e-02 2.50e+03   1.98e-02 9.81e+00
        pdb=" CG  TRP B 352 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 352 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 352 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 352 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 352 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 352 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 352 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 352 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 352 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 519 "    0.036 2.00e-02 2.50e+03   2.20e-02 9.64e+00
        pdb=" CG  TYR A 519 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 519 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 519 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR A 519 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 352 "    0.040 2.00e-02 2.50e+03   1.96e-02 9.62e+00
        pdb=" CG  TRP A 352 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 352 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 352 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 352 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 352 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 352 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 352 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 352 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 352 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 192
        2.65 -     3.21: 10310
        3.21 -     3.77: 16551
        3.77 -     4.34: 22521
        4.34 -     4.90: 36727
  Nonbonded interactions: 86301
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 330 "
            pdb=" OE1 GLU B 695 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" NH2 ARG A 330 "
            pdb=" OE1 GLU A 695 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" OH  TYR A 167 "
            pdb=" O   PHE A 657 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR B 167 "
            pdb=" O   PHE B 657 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" NH1 ARG A 330 "
            pdb=" OE1 GLU A 695 "
     model   vdw
     2.272 3.120
  ... (remaining 86296 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: 0.05
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:             0.330
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.000
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  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:   32.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
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      :  0.018   0.113  10440  Z= 0.908
  Angle     :  1.436  11.328  14200  Z= 0.968
  Chirality :  0.084   0.375   1604
  Planarity :  0.009   0.039   1762
  Dihedral  :  9.732  73.722   3696
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.37 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.22), residues: 1248
  helix:  0.35 (0.16), residues: 880
  sheet: -1.04 (0.73), residues: 46
  loop : -1.58 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.006   TRP B 352 
 HIS   0.011   0.003   HIS B 293 
 PHE   0.045   0.008   PHE A  72 
 TYR   0.045   0.009   TYR A  38 
 ARG   0.007   0.001   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15357 (  695)
  hydrogen bonds       : angle       6.99427 ( 2055)
  covalent geometry    : bond        0.01807 (10440)
  covalent geometry    : angle       1.43554 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A  320 MET cc_start: 0.8368 (mmm) cc_final: 0.8164 (mmp)
REVERT: A  638 SER cc_start: 0.8300 (t) cc_final: 0.8039 (p)
REVERT: A  689 MET cc_start: 0.9055 (tpp) cc_final: 0.8805 (tpt)
REVERT: B  320 MET cc_start: 0.8363 (mmm) cc_final: 0.8159 (mmp)
REVERT: B  638 SER cc_start: 0.8302 (t) cc_final: 0.8039 (p)
REVERT: B  689 MET cc_start: 0.9053 (tpp) cc_final: 0.8814 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2699
  time to fit residues: 82.4636
Evaluate side-chains
  163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 341 GLN
A 363 ASN
A 607 HIS
A 608 GLN
A 614 ASN
B 340 GLN
B 341 GLN
B 363 ASN
B 607 HIS
B 608 GLN
B 614 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.161207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130627 restraints weight = 11693.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.46
r_work: 0.3227 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10440  Z= 0.161
  Angle     :  0.632   6.709  14200  Z= 0.341
  Chirality :  0.044   0.178   1604
  Planarity :  0.005   0.046   1762
  Dihedral  :  4.667  21.704   1360
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  4.06 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.23), residues: 1248
  helix:  1.90 (0.17), residues: 858
  sheet: -1.20 (0.77), residues: 42
  loop : -1.33 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 624 
 HIS   0.004   0.001   HIS B 232 
 PHE   0.026   0.002   PHE B 428 
 TYR   0.013   0.002   TYR B  38 
 ARG   0.007   0.001   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05332 (  695)
  hydrogen bonds       : angle       5.11072 ( 2055)
  covalent geometry    : bond        0.00353 (10440)
  covalent geometry    : angle       0.63198 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 1.113 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6295 (mtp)
REVERT: A  299 ASP cc_start: 0.7251 (t70) cc_final: 0.7046 (t0)
REVERT: A  320 MET cc_start: 0.8844 (mmm) cc_final: 0.8607 (mmp)
REVERT: A  437 PHE cc_start: 0.8076 (m-80) cc_final: 0.7762 (m-80)
REVERT: A  531 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6949 (mt-10)
REVERT: A  559 MET cc_start: 0.7261 (ttp) cc_final: 0.6753 (ptm)
REVERT: A  638 SER cc_start: 0.8297 (t) cc_final: 0.7816 (p)
REVERT: A  689 MET cc_start: 0.9310 (tpp) cc_final: 0.9061 (tpt)
REVERT: B  165 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6286 (mtp)
REVERT: B  299 ASP cc_start: 0.7246 (t70) cc_final: 0.7044 (t0)
REVERT: B  320 MET cc_start: 0.8848 (mmm) cc_final: 0.8615 (mmp)
REVERT: B  437 PHE cc_start: 0.8085 (m-80) cc_final: 0.7746 (m-80)
REVERT: B  531 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6962 (mt-10)
REVERT: B  559 MET cc_start: 0.7263 (ttp) cc_final: 0.6753 (ptm)
REVERT: B  638 SER cc_start: 0.8285 (t) cc_final: 0.7803 (p)
REVERT: B  689 MET cc_start: 0.9311 (tpp) cc_final: 0.9065 (tpt)
  outliers start: 7
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1981
  time to fit residues: 54.5231
Evaluate side-chains
  154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  531 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 48 optimal weight:    0.1980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.161219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.130326 restraints weight = 11782.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.47
r_work: 0.3254 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10440  Z= 0.130
  Angle     :  0.562   6.547  14200  Z= 0.297
  Chirality :  0.041   0.140   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.467  23.521   1360
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.62 %
    Favored  : 92.72 %
  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:  1.52 (0.24), residues: 1248
  helix:  2.14 (0.17), residues: 848
  sheet: -1.18 (0.76), residues: 46
  loop : -1.57 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 624 
 HIS   0.003   0.001   HIS B 379 
 PHE   0.023   0.002   PHE B 428 
 TYR   0.007   0.001   TYR B  43 
 ARG   0.004   0.000   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04495 (  695)
  hydrogen bonds       : angle       4.80670 ( 2055)
  covalent geometry    : bond        0.00281 (10440)
  covalent geometry    : angle       0.56224 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 166
  time to evaluate  : 1.124 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6447 (mtp)
REVERT: A  320 MET cc_start: 0.8809 (mmm) cc_final: 0.8538 (mmp)
REVERT: A  390 ILE cc_start: 0.8320 (mm) cc_final: 0.7887 (mm)
REVERT: A  437 PHE cc_start: 0.8158 (m-80) cc_final: 0.7718 (m-80)
REVERT: A  531 GLU cc_start: 0.7388 (mp0) cc_final: 0.6573 (mm-30)
REVERT: A  559 MET cc_start: 0.7263 (ttp) cc_final: 0.7055 (ptm)
REVERT: A  564 ILE cc_start: 0.8455 (tp) cc_final: 0.8237 (tp)
REVERT: A  638 SER cc_start: 0.8271 (t) cc_final: 0.7822 (p)
REVERT: A  645 LEU cc_start: 0.6194 (tt) cc_final: 0.5903 (tp)
REVERT: A  670 HIS cc_start: 0.8163 (m-70) cc_final: 0.7359 (t-170)
REVERT: A  689 MET cc_start: 0.9313 (tpp) cc_final: 0.9073 (tpt)
REVERT: B  165 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6442 (mtp)
REVERT: B  320 MET cc_start: 0.8800 (mmm) cc_final: 0.8531 (mmp)
REVERT: B  390 ILE cc_start: 0.8326 (mm) cc_final: 0.7925 (mm)
REVERT: B  437 PHE cc_start: 0.8135 (m-80) cc_final: 0.7680 (m-80)
REVERT: B  531 GLU cc_start: 0.7391 (mp0) cc_final: 0.6576 (mm-30)
REVERT: B  559 MET cc_start: 0.7268 (ttp) cc_final: 0.7050 (ptm)
REVERT: B  638 SER cc_start: 0.8267 (t) cc_final: 0.7817 (p)
REVERT: B  645 LEU cc_start: 0.6197 (tt) cc_final: 0.5908 (tp)
REVERT: B  689 MET cc_start: 0.9315 (tpp) cc_final: 0.9080 (tpt)
  outliers start: 7
  outliers final: 2
  residues processed: 167
  average time/residue: 0.1932
  time to fit residues: 47.5267
Evaluate side-chains
  160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 156
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 28 optimal weight:    0.1980
   chunk 101 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 542 HIS
B 363 ASN
B 542 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.160488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.126272 restraints weight = 11759.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.38
r_work: 0.3196 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10440  Z= 0.128
  Angle     :  0.546   6.977  14200  Z= 0.286
  Chirality :  0.041   0.139   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.362  24.260   1360
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  7.84 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.24), residues: 1248
  helix:  2.20 (0.17), residues: 848
  sheet: -1.33 (0.76), residues: 46
  loop : -1.63 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 624 
 HIS   0.003   0.001   HIS A 379 
 PHE   0.025   0.002   PHE B 428 
 TYR   0.007   0.001   TYR A 181 
 ARG   0.004   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  695)
  hydrogen bonds       : angle       4.65423 ( 2055)
  covalent geometry    : bond        0.00288 (10440)
  covalent geometry    : angle       0.54557 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 1.111 
Fit side-chains
REVERT: A   47 LEU cc_start: 0.8270 (mp) cc_final: 0.8048 (mt)
REVERT: A  165 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6278 (mtp)
REVERT: A  320 MET cc_start: 0.8783 (mmm) cc_final: 0.8469 (mmp)
REVERT: A  448 MET cc_start: 0.8724 (mtm) cc_final: 0.8451 (mtp)
REVERT: A  531 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6521 (mt-10)
REVERT: A  559 MET cc_start: 0.7158 (ttp) cc_final: 0.6782 (ptm)
REVERT: A  564 ILE cc_start: 0.8396 (tp) cc_final: 0.8177 (tp)
REVERT: A  638 SER cc_start: 0.8277 (t) cc_final: 0.7788 (p)
REVERT: A  645 LEU cc_start: 0.6102 (tt) cc_final: 0.5782 (tp)
REVERT: A  689 MET cc_start: 0.9282 (tpp) cc_final: 0.9041 (tpt)
REVERT: B   47 LEU cc_start: 0.8292 (mp) cc_final: 0.8089 (mt)
REVERT: B  165 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6266 (mtp)
REVERT: B  320 MET cc_start: 0.8785 (mmm) cc_final: 0.8475 (mmp)
REVERT: B  448 MET cc_start: 0.8720 (mtm) cc_final: 0.8446 (mtp)
REVERT: B  531 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6511 (mt-10)
REVERT: B  559 MET cc_start: 0.7139 (ttp) cc_final: 0.6727 (ptm)
REVERT: B  564 ILE cc_start: 0.8433 (tp) cc_final: 0.8216 (tp)
REVERT: B  638 SER cc_start: 0.8267 (t) cc_final: 0.7777 (p)
REVERT: B  645 LEU cc_start: 0.6097 (tt) cc_final: 0.5778 (tp)
REVERT: B  689 MET cc_start: 0.9284 (tpp) cc_final: 0.9045 (tpt)
  outliers start: 13
  outliers final: 6
  residues processed: 174
  average time/residue: 0.1832
  time to fit residues: 47.6278
Evaluate side-chains
  171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 111 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.160554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.126233 restraints weight = 11736.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.38
r_work: 0.3266 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10440  Z= 0.121
  Angle     :  0.521   5.670  14200  Z= 0.275
  Chirality :  0.041   0.137   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.227  23.476   1360
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  8.60 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.24), residues: 1248
  helix:  2.36 (0.17), residues: 836
  sheet: -1.51 (0.75), residues: 46
  loop : -1.46 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 624 
 HIS   0.002   0.001   HIS A 607 
 PHE   0.023   0.002   PHE B 428 
 TYR   0.006   0.001   TYR A 181 
 ARG   0.003   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  695)
  hydrogen bonds       : angle       4.60703 ( 2055)
  covalent geometry    : bond        0.00273 (10440)
  covalent geometry    : angle       0.52129 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 1.162 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6537 (mtp)
REVERT: A  320 MET cc_start: 0.8785 (mmm) cc_final: 0.8475 (mmp)
REVERT: A  378 MET cc_start: 0.7938 (mmm) cc_final: 0.7064 (mmm)
REVERT: A  437 PHE cc_start: 0.8222 (m-80) cc_final: 0.7892 (m-80)
REVERT: A  531 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6485 (mt-10)
REVERT: A  540 MET cc_start: 0.7180 (mmt) cc_final: 0.6948 (mmt)
REVERT: A  559 MET cc_start: 0.7138 (ttp) cc_final: 0.6912 (ptm)
REVERT: A  564 ILE cc_start: 0.8499 (tp) cc_final: 0.8289 (tp)
REVERT: A  638 SER cc_start: 0.8319 (t) cc_final: 0.7821 (p)
REVERT: A  670 HIS cc_start: 0.8206 (m-70) cc_final: 0.7301 (t-170)
REVERT: A  689 MET cc_start: 0.9270 (tpp) cc_final: 0.9021 (tpt)
REVERT: B  165 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6525 (mtp)
REVERT: B  320 MET cc_start: 0.8783 (mmm) cc_final: 0.8477 (mmp)
REVERT: B  437 PHE cc_start: 0.8175 (m-80) cc_final: 0.7865 (m-80)
REVERT: B  531 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6484 (mt-10)
REVERT: B  559 MET cc_start: 0.7174 (ttp) cc_final: 0.6871 (ptm)
REVERT: B  564 ILE cc_start: 0.8485 (tp) cc_final: 0.8275 (tp)
REVERT: B  638 SER cc_start: 0.8310 (t) cc_final: 0.7811 (p)
REVERT: B  689 MET cc_start: 0.9279 (tpp) cc_final: 0.9031 (tpt)
  outliers start: 16
  outliers final: 6
  residues processed: 179
  average time/residue: 0.2611
  time to fit residues: 69.6362
Evaluate side-chains
  176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 166
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0970
   chunk 55 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.160406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.126511 restraints weight = 11796.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.35
r_work: 0.3225 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10440  Z= 0.118
  Angle     :  0.527   7.561  14200  Z= 0.272
  Chirality :  0.041   0.136   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.148  23.652   1360
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.26 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.24), residues: 1248
  helix:  2.33 (0.17), residues: 848
  sheet: -1.67 (0.75), residues: 46
  loop : -1.49 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 624 
 HIS   0.002   0.001   HIS A 542 
 PHE   0.023   0.001   PHE A 428 
 TYR   0.005   0.001   TYR B 469 
 ARG   0.003   0.000   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  695)
  hydrogen bonds       : angle       4.55358 ( 2055)
  covalent geometry    : bond        0.00265 (10440)
  covalent geometry    : angle       0.52717 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 178
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8441 (mtt) cc_final: 0.7949 (mtt)
REVERT: A  165 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6573 (mtp)
REVERT: A  320 MET cc_start: 0.8786 (mmm) cc_final: 0.8483 (mmp)
REVERT: A  531 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6315 (mm-30)
REVERT: A  540 MET cc_start: 0.7206 (mmt) cc_final: 0.6964 (mmt)
REVERT: A  559 MET cc_start: 0.7136 (ttp) cc_final: 0.6871 (ptm)
REVERT: A  638 SER cc_start: 0.8304 (t) cc_final: 0.7812 (p)
REVERT: A  670 HIS cc_start: 0.8260 (m-70) cc_final: 0.7396 (t-170)
REVERT: A  689 MET cc_start: 0.9272 (tpp) cc_final: 0.9029 (tpt)
REVERT: B   76 MET cc_start: 0.8359 (mtt) cc_final: 0.7873 (mtt)
REVERT: B  165 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6566 (mtp)
REVERT: B  320 MET cc_start: 0.8786 (mmm) cc_final: 0.8484 (mmp)
REVERT: B  437 PHE cc_start: 0.8183 (m-80) cc_final: 0.7804 (m-80)
REVERT: B  531 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6328 (mm-30)
REVERT: B  559 MET cc_start: 0.7270 (ttp) cc_final: 0.6868 (ptm)
REVERT: B  638 SER cc_start: 0.8294 (t) cc_final: 0.7800 (p)
REVERT: B  689 MET cc_start: 0.9278 (tpp) cc_final: 0.9037 (tpt)
  outliers start: 15
  outliers final: 8
  residues processed: 181
  average time/residue: 0.1961
  time to fit residues: 51.9635
Evaluate side-chains
  180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 168
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  531 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 120 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 114 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.154310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.122475 restraints weight = 12122.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.48
r_work: 0.3168 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10440  Z= 0.131
  Angle     :  0.541   8.347  14200  Z= 0.279
  Chirality :  0.042   0.260   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.136  23.088   1360
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.64 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.24), residues: 1248
  helix:  2.39 (0.17), residues: 848
  sheet: -1.79 (0.73), residues: 46
  loop : -1.58 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 669 
 PHE   0.023   0.001   PHE A 428 
 TYR   0.006   0.001   TYR A 181 
 ARG   0.017   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  695)
  hydrogen bonds       : angle       4.56964 ( 2055)
  covalent geometry    : bond        0.00305 (10440)
  covalent geometry    : angle       0.54061 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 182
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A   47 LEU cc_start: 0.8365 (mp) cc_final: 0.8164 (mt)
REVERT: A   76 MET cc_start: 0.8527 (mtt) cc_final: 0.8089 (mtt)
REVERT: A  165 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6941 (mtp)
REVERT: A  320 MET cc_start: 0.8776 (mmm) cc_final: 0.8557 (mmp)
REVERT: A  531 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6503 (mm-30)
REVERT: A  540 MET cc_start: 0.7436 (mmt) cc_final: 0.7229 (mmt)
REVERT: A  559 MET cc_start: 0.7409 (ttp) cc_final: 0.6995 (ptm)
REVERT: A  638 SER cc_start: 0.8463 (t) cc_final: 0.8002 (p)
REVERT: A  670 HIS cc_start: 0.8300 (m-70) cc_final: 0.7629 (t-170)
REVERT: A  689 MET cc_start: 0.9273 (tpp) cc_final: 0.9023 (tpt)
REVERT: B   76 MET cc_start: 0.8518 (mtt) cc_final: 0.8085 (mtt)
REVERT: B  165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6938 (mtp)
REVERT: B  531 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6511 (mm-30)
REVERT: B  559 MET cc_start: 0.7430 (ttp) cc_final: 0.6997 (ptm)
REVERT: B  638 SER cc_start: 0.8462 (t) cc_final: 0.7997 (p)
REVERT: B  689 MET cc_start: 0.9274 (tpp) cc_final: 0.9028 (tpt)
  outliers start: 15
  outliers final: 9
  residues processed: 185
  average time/residue: 0.2013
  time to fit residues: 54.2634
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  531 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 85 optimal weight:   30.0000
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9980
   chunk 120 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.154119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.124307 restraints weight = 12059.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.28
r_work: 0.3141 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10440  Z= 0.165
  Angle     :  0.582   9.433  14200  Z= 0.298
  Chirality :  0.044   0.326   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.258  23.259   1360
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.83 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1248
  helix:  2.34 (0.18), residues: 836
  sheet: -1.90 (0.68), residues: 46
  loop : -1.48 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 624 
 HIS   0.005   0.001   HIS B 542 
 PHE   0.024   0.002   PHE A 428 
 TYR   0.007   0.001   TYR B 294 
 ARG   0.010   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  695)
  hydrogen bonds       : angle       4.65797 ( 2055)
  covalent geometry    : bond        0.00398 (10440)
  covalent geometry    : angle       0.58245 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 189
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8545 (mtt) cc_final: 0.8097 (mtt)
REVERT: A  165 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7005 (mtp)
REVERT: A  395 PHE cc_start: 0.7110 (m-10) cc_final: 0.6672 (m-10)
REVERT: A  437 PHE cc_start: 0.8408 (m-80) cc_final: 0.8146 (m-80)
REVERT: A  531 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6552 (mm-30)
REVERT: A  559 MET cc_start: 0.7346 (ttp) cc_final: 0.6902 (ptm)
REVERT: A  638 SER cc_start: 0.8496 (t) cc_final: 0.8020 (p)
REVERT: A  670 HIS cc_start: 0.8325 (m-70) cc_final: 0.7659 (t-170)
REVERT: A  689 MET cc_start: 0.9245 (tpp) cc_final: 0.8993 (tpt)
REVERT: B   47 LEU cc_start: 0.8394 (mp) cc_final: 0.8192 (mt)
REVERT: B   48 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.7224 (mtp-110)
REVERT: B   76 MET cc_start: 0.8533 (mtt) cc_final: 0.8082 (mtt)
REVERT: B  165 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7005 (mtp)
REVERT: B  395 PHE cc_start: 0.7134 (m-10) cc_final: 0.6699 (m-10)
REVERT: B  437 PHE cc_start: 0.8499 (m-80) cc_final: 0.8277 (m-80)
REVERT: B  531 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6576 (mm-30)
REVERT: B  559 MET cc_start: 0.7350 (ttp) cc_final: 0.6894 (ptm)
REVERT: B  638 SER cc_start: 0.8485 (t) cc_final: 0.8009 (p)
REVERT: B  689 MET cc_start: 0.9245 (tpp) cc_final: 0.8999 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 191
  average time/residue: 0.2615
  time to fit residues: 73.7222
Evaluate side-chains
  202 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  531 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 113 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.158901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128361 restraints weight = 11877.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.46
r_work: 0.3178 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10440  Z= 0.118
  Angle     :  0.547  10.607  14200  Z= 0.278
  Chirality :  0.042   0.316   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.125  22.401   1360
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.68 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.24), residues: 1248
  helix:  2.41 (0.18), residues: 836
  sheet: -1.89 (0.71), residues: 46
  loop : -1.49 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 624 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.027   0.001   PHE B 428 
 TYR   0.005   0.001   TYR B 469 
 ARG   0.012   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  695)
  hydrogen bonds       : angle       4.57869 ( 2055)
  covalent geometry    : bond        0.00268 (10440)
  covalent geometry    : angle       0.54719 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 190
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8521 (mtt) cc_final: 0.8102 (mtt)
REVERT: A  165 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6683 (mtp)
REVERT: A  382 PHE cc_start: 0.8745 (t80) cc_final: 0.8464 (t80)
REVERT: A  395 PHE cc_start: 0.6917 (m-10) cc_final: 0.6442 (m-10)
REVERT: A  437 PHE cc_start: 0.8288 (m-80) cc_final: 0.7999 (m-80)
REVERT: A  531 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6444 (mm-30)
REVERT: A  559 MET cc_start: 0.7169 (ttp) cc_final: 0.6487 (ptm)
REVERT: A  638 SER cc_start: 0.8297 (t) cc_final: 0.7796 (p)
REVERT: A  689 MET cc_start: 0.9288 (tpp) cc_final: 0.9077 (tpp)
REVERT: B   48 ARG cc_start: 0.7313 (mtp-110) cc_final: 0.6997 (mtp-110)
REVERT: B   76 MET cc_start: 0.8509 (mtt) cc_final: 0.8085 (mtt)
REVERT: B  165 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6659 (mtp)
REVERT: B  382 PHE cc_start: 0.8737 (t80) cc_final: 0.8462 (t80)
REVERT: B  437 PHE cc_start: 0.8412 (m-80) cc_final: 0.8146 (m-80)
REVERT: B  531 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6458 (mm-30)
REVERT: B  559 MET cc_start: 0.7241 (ttp) cc_final: 0.6491 (ptm)
REVERT: B  638 SER cc_start: 0.8284 (t) cc_final: 0.7778 (p)
REVERT: B  689 MET cc_start: 0.9289 (tpp) cc_final: 0.9080 (tpp)
  outliers start: 13
  outliers final: 9
  residues processed: 192
  average time/residue: 0.1975
  time to fit residues: 55.0438
Evaluate side-chains
  197 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 184
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  531 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 110 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 111 optimal weight:    0.2980
   chunk 88 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.158304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127171 restraints weight = 11896.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.42
r_work: 0.3189 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10440  Z= 0.130
  Angle     :  0.565  11.204  14200  Z= 0.284
  Chirality :  0.043   0.328   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.125  22.241   1360
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.87 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.24), residues: 1248
  helix:  2.39 (0.18), residues: 836
  sheet: -1.93 (0.70), residues: 46
  loop : -1.49 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 624 
 HIS   0.007   0.001   HIS B 542 
 PHE   0.028   0.001   PHE A 428 
 TYR   0.005   0.001   TYR B 294 
 ARG   0.011   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  695)
  hydrogen bonds       : angle       4.57732 ( 2055)
  covalent geometry    : bond        0.00302 (10440)
  covalent geometry    : angle       0.56468 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 1.131 
Fit side-chains
REVERT: A   47 LEU cc_start: 0.8302 (mp) cc_final: 0.7990 (mt)
REVERT: A   76 MET cc_start: 0.8518 (mtt) cc_final: 0.8088 (mtt)
REVERT: A  165 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6652 (mtp)
REVERT: A  395 PHE cc_start: 0.6921 (m-10) cc_final: 0.6437 (m-10)
REVERT: A  437 PHE cc_start: 0.8278 (m-80) cc_final: 0.8010 (m-80)
REVERT: A  531 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6436 (mm-30)
REVERT: A  559 MET cc_start: 0.7106 (ttp) cc_final: 0.6519 (ptm)
REVERT: A  638 SER cc_start: 0.8295 (t) cc_final: 0.7786 (p)
REVERT: B   48 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6981 (mtp-110)
REVERT: B   76 MET cc_start: 0.8515 (mtt) cc_final: 0.8083 (mtt)
REVERT: B  165 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6637 (mtp)
REVERT: B  437 PHE cc_start: 0.8388 (m-80) cc_final: 0.8100 (m-80)
REVERT: B  531 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6443 (mm-30)
REVERT: B  559 MET cc_start: 0.7127 (ttp) cc_final: 0.6511 (ptm)
REVERT: B  638 SER cc_start: 0.8291 (t) cc_final: 0.7782 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 190
  average time/residue: 0.1881
  time to fit residues: 52.4429
Evaluate side-chains
  196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 183
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  589 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0980
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 109 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0570
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.161386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.130788 restraints weight = 11814.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.45
r_work: 0.3236 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10440  Z= 0.105
  Angle     :  0.543  10.444  14200  Z= 0.272
  Chirality :  0.042   0.305   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.017  21.317   1360
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.06 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.24), residues: 1248
  helix:  2.31 (0.17), residues: 860
  sheet: -1.80 (0.74), residues: 46
  loop : -1.81 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 624 
 HIS   0.004   0.001   HIS A 162 
 PHE   0.030   0.001   PHE A 428 
 TYR   0.005   0.001   TYR B 469 
 ARG   0.009   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03411 (  695)
  hydrogen bonds       : angle       4.50172 ( 2055)
  covalent geometry    : bond        0.00227 (10440)
  covalent geometry    : angle       0.54257 (14200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6200.61 seconds
wall clock time: 109 minutes 24.17 seconds (6564.17 seconds total)