Starting phenix.real_space_refine
on Wed Sep 17 17:14:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mgv_9112/09_2025/6mgv_9112.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mgv_9112/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mgv_9112/09_2025/6mgv_9112.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mgv_9112/09_2025/6mgv_9112.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mgv_9112/09_2025/6mgv_9112.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mgv_9112/09_2025/6mgv_9112.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.45, per 1000 atoms: 0.44
  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: 1.09
  Conformation dependent library (CDL) restraints added in 387.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.34
  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: 1.76

  Time building geometry restraints manager: 1.36 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: 0.02
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:             0.780
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.940
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.340
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG B 330 
 TYR   0.045   0.009   TYR A  38 
 PHE   0.045   0.008   PHE A  72 
 TRP   0.041   0.006   TRP B 352 
 HIS   0.011   0.003   HIS B 293 

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

*********************** 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  : 0.365 
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: 0.1299
  time to fit residues: 39.7608
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  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.161788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.131294 restraints weight = 11756.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.47
r_work: 0.3238 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2693

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= 0.156
  Angle     :  0.628   6.586  14200  Z= 0.336
  Chirality :  0.045   0.179   1604
  Planarity :  0.005   0.046   1762
  Dihedral  :  4.705  21.951   1360
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  3.78 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.23), residues: 1248
  helix:  1.92 (0.17), residues: 858
  sheet: -1.21 (0.78), residues: 42
  loop : -1.34 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 606 
 TYR   0.012   0.002   TYR B  38 
 PHE   0.027   0.002   PHE B 428 
 TRP   0.023   0.002   TRP B 624 
 HIS   0.004   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10440)
  covalent geometry    : angle       0.62757 (14200)
  hydrogen bonds       : bond        0.05118 (  695)
  hydrogen bonds       : angle       5.09567 ( 2055)

*********************** 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
  196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 188
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6441 (mtp)
REVERT: A  299 ASP cc_start: 0.7270 (t70) cc_final: 0.7064 (t0)
REVERT: A  320 MET cc_start: 0.8832 (mmm) cc_final: 0.8598 (mmp)
REVERT: A  437 PHE cc_start: 0.8058 (m-80) cc_final: 0.7739 (m-80)
REVERT: A  531 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6955 (mt-10)
REVERT: A  559 MET cc_start: 0.7257 (ttp) cc_final: 0.6770 (ptm)
REVERT: A  638 SER cc_start: 0.8307 (t) cc_final: 0.7842 (p)
REVERT: A  689 MET cc_start: 0.9311 (tpp) cc_final: 0.9067 (tpt)
REVERT: B  165 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6436 (mtp)
REVERT: B  299 ASP cc_start: 0.7265 (t70) cc_final: 0.7061 (t0)
REVERT: B  320 MET cc_start: 0.8836 (mmm) cc_final: 0.8606 (mmp)
REVERT: B  437 PHE cc_start: 0.8064 (m-80) cc_final: 0.7740 (m-80)
REVERT: B  531 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6882 (mt-10)
REVERT: B  559 MET cc_start: 0.7261 (ttp) cc_final: 0.6769 (ptm)
REVERT: B  638 SER cc_start: 0.8294 (t) cc_final: 0.7828 (p)
REVERT: B  689 MET cc_start: 0.9311 (tpp) cc_final: 0.9071 (tpt)
  outliers start: 8
  outliers final: 0
  residues processed: 190
  average time/residue: 0.0949
  time to fit residues: 26.5847
Evaluate side-chains
  155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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 125 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 78 optimal weight:    0.2980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.160836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.130218 restraints weight = 11752.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.47
r_work: 0.3248 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3189

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= 0.132
  Angle     :  0.559   6.496  14200  Z= 0.297
  Chirality :  0.042   0.145   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.420  24.082   1360
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  6.81 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.24), residues: 1248
  helix:  2.18 (0.17), residues: 846
  sheet: -1.23 (0.75), residues: 46
  loop : -1.61 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 606 
 TYR   0.008   0.001   TYR A  43 
 PHE   0.024   0.002   PHE A 428 
 TRP   0.021   0.001   TRP B 624 
 HIS   0.003   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10440)
  covalent geometry    : angle       0.55926 (14200)
  hydrogen bonds       : bond        0.04421 (  695)
  hydrogen bonds       : angle       4.75561 ( 2055)

*********************** 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
  176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6438 (mtp)
REVERT: A  320 MET cc_start: 0.8802 (mmm) cc_final: 0.8526 (mmp)
REVERT: A  390 ILE cc_start: 0.8317 (mm) cc_final: 0.7886 (mm)
REVERT: A  437 PHE cc_start: 0.8167 (m-80) cc_final: 0.7719 (m-80)
REVERT: A  531 GLU cc_start: 0.7158 (mp0) cc_final: 0.6406 (mm-30)
REVERT: A  564 ILE cc_start: 0.8455 (tp) cc_final: 0.8209 (tp)
REVERT: A  638 SER cc_start: 0.8356 (t) cc_final: 0.7910 (p)
REVERT: A  645 LEU cc_start: 0.6241 (tt) cc_final: 0.5948 (tp)
REVERT: A  670 HIS cc_start: 0.8223 (m-70) cc_final: 0.7346 (t-170)
REVERT: A  689 MET cc_start: 0.9331 (tpp) cc_final: 0.9082 (tpt)
REVERT: B  165 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6406 (mtp)
REVERT: B  320 MET cc_start: 0.8806 (mmm) cc_final: 0.8533 (mmp)
REVERT: B  390 ILE cc_start: 0.8328 (mm) cc_final: 0.7905 (mm)
REVERT: B  437 PHE cc_start: 0.8096 (m-80) cc_final: 0.7685 (m-80)
REVERT: B  531 GLU cc_start: 0.7170 (mp0) cc_final: 0.6418 (mm-30)
REVERT: B  559 MET cc_start: 0.7244 (ttp) cc_final: 0.7043 (ptm)
REVERT: B  564 ILE cc_start: 0.8450 (tp) cc_final: 0.8203 (tp)
REVERT: B  638 SER cc_start: 0.8339 (t) cc_final: 0.7892 (p)
REVERT: B  645 LEU cc_start: 0.6240 (tt) cc_final: 0.5950 (tp)
REVERT: B  670 HIS cc_start: 0.8259 (m-70) cc_final: 0.7354 (t-170)
REVERT: B  689 MET cc_start: 0.9330 (tpp) cc_final: 0.9089 (tpt)
  outliers start: 8
  outliers final: 2
  residues processed: 170
  average time/residue: 0.0909
  time to fit residues: 22.8117
Evaluate side-chains
  162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 158
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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 101 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 110 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0670
   chunk 108 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 542 HIS
A 615 GLN
B 363 ASN
B 542 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.160711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.126569 restraints weight = 11859.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.39
r_work: 0.3282 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3436

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= 0.123
  Angle     :  0.535   6.295  14200  Z= 0.281
  Chirality :  0.041   0.137   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  4.327  24.013   1360
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  8.60 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.24), residues: 1248
  helix:  2.23 (0.17), residues: 848
  sheet: -1.35 (0.76), residues: 46
  loop : -1.60 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 606 
 TYR   0.006   0.001   TYR B  43 
 PHE   0.024   0.002   PHE A 428 
 TRP   0.018   0.001   TRP B 624 
 HIS   0.002   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10440)
  covalent geometry    : angle       0.53538 (14200)
  hydrogen bonds       : bond        0.04084 (  695)
  hydrogen bonds       : angle       4.64572 ( 2055)

*********************** 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
  181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6390 (mtp)
REVERT: A  320 MET cc_start: 0.8778 (mmm) cc_final: 0.8491 (mmp)
REVERT: A  531 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6523 (mt-10)
REVERT: A  564 ILE cc_start: 0.8460 (tp) cc_final: 0.8246 (tp)
REVERT: A  638 SER cc_start: 0.8285 (t) cc_final: 0.7823 (p)
REVERT: A  645 LEU cc_start: 0.6225 (tt) cc_final: 0.5907 (tp)
REVERT: A  689 MET cc_start: 0.9290 (tpp) cc_final: 0.9061 (tpt)
REVERT: B   47 LEU cc_start: 0.8293 (mp) cc_final: 0.8084 (mt)
REVERT: B  165 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6386 (mtp)
REVERT: B  320 MET cc_start: 0.8769 (mmm) cc_final: 0.8483 (mmp)
REVERT: B  531 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6548 (mt-10)
REVERT: B  559 MET cc_start: 0.7192 (ttp) cc_final: 0.6763 (ptm)
REVERT: B  564 ILE cc_start: 0.8466 (tp) cc_final: 0.8248 (tp)
REVERT: B  638 SER cc_start: 0.8277 (t) cc_final: 0.7809 (p)
REVERT: B  645 LEU cc_start: 0.6222 (tt) cc_final: 0.5904 (tp)
REVERT: B  689 MET cc_start: 0.9295 (tpp) cc_final: 0.9068 (tpt)
  outliers start: 11
  outliers final: 6
  residues processed: 173
  average time/residue: 0.0822
  time to fit residues: 21.5933
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  : 0.383 
-------------------------------------------------------------------------------
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 125 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 108 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 121 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.160118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.125869 restraints weight = 11764.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.38
r_work: 0.3240 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3684

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= 0.124
  Angle     :  0.527   6.581  14200  Z= 0.276
  Chirality :  0.041   0.150   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.219  23.569   1360
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.03 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.24), residues: 1248
  helix:  2.28 (0.17), residues: 848
  sheet: -1.52 (0.75), residues: 46
  loop : -1.61 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 606 
 TYR   0.006   0.001   TYR A 368 
 PHE   0.024   0.001   PHE A 428 
 TRP   0.016   0.001   TRP B 624 
 HIS   0.002   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10440)
  covalent geometry    : angle       0.52742 (14200)
  hydrogen bonds       : bond        0.03971 (  695)
  hydrogen bonds       : angle       4.61369 ( 2055)

*********************** 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
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6533 (mtp)
REVERT: A  320 MET cc_start: 0.8784 (mmm) cc_final: 0.8478 (mmp)
REVERT: A  378 MET cc_start: 0.7937 (mmm) cc_final: 0.7051 (mmm)
REVERT: A  388 PHE cc_start: 0.7400 (m-10) cc_final: 0.7176 (m-10)
REVERT: A  437 PHE cc_start: 0.8228 (m-80) cc_final: 0.7903 (m-80)
REVERT: A  531 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6500 (mt-10)
REVERT: A  564 ILE cc_start: 0.8501 (tp) cc_final: 0.8295 (tp)
REVERT: A  638 SER cc_start: 0.8323 (t) cc_final: 0.7822 (p)
REVERT: A  689 MET cc_start: 0.9283 (tpp) cc_final: 0.9055 (tpt)
REVERT: B  165 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6524 (mtp)
REVERT: B  320 MET cc_start: 0.8779 (mmm) cc_final: 0.8470 (mmp)
REVERT: B  378 MET cc_start: 0.7933 (mmm) cc_final: 0.7055 (mmm)
REVERT: B  388 PHE cc_start: 0.7374 (m-10) cc_final: 0.7153 (m-10)
REVERT: B  437 PHE cc_start: 0.8217 (m-80) cc_final: 0.7920 (m-80)
REVERT: B  531 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6512 (mt-10)
REVERT: B  559 MET cc_start: 0.7190 (ttp) cc_final: 0.6944 (ptm)
REVERT: B  564 ILE cc_start: 0.8492 (tp) cc_final: 0.8284 (tp)
REVERT: B  638 SER cc_start: 0.8312 (t) cc_final: 0.7809 (p)
REVERT: B  689 MET cc_start: 0.9283 (tpp) cc_final: 0.9056 (tpt)
  outliers start: 17
  outliers final: 6
  residues processed: 174
  average time/residue: 0.0863
  time to fit residues: 22.5344
Evaluate side-chains
  175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 165
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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 74 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 109 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.160169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125631 restraints weight = 11907.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.39
r_work: 0.3200 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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      :  0.003   0.029  10440  Z= 0.121
  Angle     :  0.524   6.497  14200  Z= 0.272
  Chirality :  0.041   0.153   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.151  23.753   1360
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.79 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.24), residues: 1248
  helix:  2.35 (0.17), residues: 848
  sheet: -1.62 (0.75), residues: 46
  loop : -1.60 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 606 
 TYR   0.005   0.001   TYR B 469 
 PHE   0.025   0.002   PHE B 428 
 TRP   0.016   0.001   TRP B 624 
 HIS   0.004   0.001   HIS A 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10440)
  covalent geometry    : angle       0.52359 (14200)
  hydrogen bonds       : bond        0.03828 (  695)
  hydrogen bonds       : angle       4.56439 ( 2055)

*********************** 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
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6504 (mtp)
REVERT: A  320 MET cc_start: 0.8787 (mmm) cc_final: 0.8473 (mmp)
REVERT: A  388 PHE cc_start: 0.7213 (m-10) cc_final: 0.6996 (m-10)
REVERT: A  437 PHE cc_start: 0.8117 (m-80) cc_final: 0.7722 (m-80)
REVERT: A  531 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6326 (mm-30)
REVERT: A  540 MET cc_start: 0.7129 (mmt) cc_final: 0.6899 (mmt)
REVERT: A  638 SER cc_start: 0.8266 (t) cc_final: 0.7747 (p)
REVERT: A  670 HIS cc_start: 0.8239 (m-70) cc_final: 0.7346 (t-170)
REVERT: A  689 MET cc_start: 0.9268 (tpp) cc_final: 0.9022 (tpt)
REVERT: B  165 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6490 (mtp)
REVERT: B  320 MET cc_start: 0.8784 (mmm) cc_final: 0.8470 (mmp)
REVERT: B  388 PHE cc_start: 0.7220 (m-10) cc_final: 0.7002 (m-10)
REVERT: B  437 PHE cc_start: 0.8190 (m-80) cc_final: 0.7812 (m-80)
REVERT: B  531 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6335 (mm-30)
REVERT: B  559 MET cc_start: 0.7104 (ttp) cc_final: 0.6884 (ptm)
REVERT: B  638 SER cc_start: 0.8250 (t) cc_final: 0.7729 (p)
REVERT: B  670 HIS cc_start: 0.8281 (m-70) cc_final: 0.7351 (t-170)
REVERT: B  689 MET cc_start: 0.9266 (tpp) cc_final: 0.9022 (tpt)
  outliers start: 15
  outliers final: 9
  residues processed: 174
  average time/residue: 0.0819
  time to fit residues: 21.1793
Evaluate side-chains
  182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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  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  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.154507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.121295 restraints weight = 12015.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.28
r_work: 0.3191 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3924

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= 0.122
  Angle     :  0.534   7.932  14200  Z= 0.273
  Chirality :  0.042   0.247   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.095  23.092   1360
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.07 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.24), residues: 1248
  helix:  2.47 (0.18), residues: 836
  sheet: -1.67 (0.74), residues: 46
  loop : -1.48 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  48 
 TYR   0.005   0.001   TYR A 707 
 PHE   0.025   0.001   PHE B 428 
 TRP   0.015   0.001   TRP B 624 
 HIS   0.006   0.001   HIS A 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10440)
  covalent geometry    : angle       0.53379 (14200)
  hydrogen bonds       : bond        0.03793 (  695)
  hydrogen bonds       : angle       4.55926 ( 2055)

*********************** 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  : 0.404 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6760 (mtp)
REVERT: A  320 MET cc_start: 0.8744 (mmm) cc_final: 0.8481 (mmp)
REVERT: A  531 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6382 (mm-30)
REVERT: A  540 MET cc_start: 0.7250 (mmt) cc_final: 0.7027 (mmt)
REVERT: A  638 SER cc_start: 0.8336 (t) cc_final: 0.7842 (p)
REVERT: A  643 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6766 (ttm)
REVERT: A  670 HIS cc_start: 0.8254 (m-70) cc_final: 0.7537 (t-170)
REVERT: A  689 MET cc_start: 0.9276 (tpp) cc_final: 0.9016 (tpt)
REVERT: B  165 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6759 (mtp)
REVERT: B  320 MET cc_start: 0.8734 (mmm) cc_final: 0.8468 (mmp)
REVERT: B  395 PHE cc_start: 0.7060 (m-10) cc_final: 0.6579 (m-10)
REVERT: B  437 PHE cc_start: 0.8406 (m-80) cc_final: 0.8031 (m-80)
REVERT: B  531 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6403 (mm-30)
REVERT: B  559 MET cc_start: 0.7191 (ttp) cc_final: 0.6946 (ptm)
REVERT: B  638 SER cc_start: 0.8325 (t) cc_final: 0.7823 (p)
REVERT: B  643 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6754 (ttm)
REVERT: B  670 HIS cc_start: 0.8264 (m-70) cc_final: 0.7537 (t-170)
REVERT: B  689 MET cc_start: 0.9281 (tpp) cc_final: 0.9023 (tpt)
  outliers start: 15
  outliers final: 9
  residues processed: 183
  average time/residue: 0.0907
  time to fit residues: 24.2473
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
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 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  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  589 MET
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 122 optimal weight:    0.2980
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 112 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.159701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.125446 restraints weight = 11880.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.39
r_work: 0.3202 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4088

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= 0.115
  Angle     :  0.524   9.370  14200  Z= 0.269
  Chirality :  0.041   0.256   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.036  22.505   1360
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.45 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.24), residues: 1248
  helix:  2.45 (0.17), residues: 836
  sheet: -1.71 (0.74), residues: 46
  loop : -1.50 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  48 
 TYR   0.006   0.001   TYR B 469 
 PHE   0.028   0.001   PHE B 428 
 TRP   0.016   0.001   TRP B 624 
 HIS   0.002   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10440)
  covalent geometry    : angle       0.52375 (14200)
  hydrogen bonds       : bond        0.03651 (  695)
  hydrogen bonds       : angle       4.53067 ( 2055)

*********************** 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
  204 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6512 (mtp)
REVERT: A  320 MET cc_start: 0.8775 (mmm) cc_final: 0.8518 (mmp)
REVERT: A  395 PHE cc_start: 0.6901 (m-10) cc_final: 0.6468 (m-10)
REVERT: A  437 PHE cc_start: 0.8341 (m-80) cc_final: 0.8065 (m-80)
REVERT: A  531 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6152 (mm-30)
REVERT: A  540 MET cc_start: 0.7130 (mmt) cc_final: 0.6910 (mmt)
REVERT: A  564 ILE cc_start: 0.8586 (tp) cc_final: 0.7956 (pt)
REVERT: A  638 SER cc_start: 0.8170 (t) cc_final: 0.7647 (p)
REVERT: A  643 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6816 (ttm)
REVERT: A  670 HIS cc_start: 0.8227 (m-70) cc_final: 0.7350 (t-170)
REVERT: A  689 MET cc_start: 0.9230 (tpp) cc_final: 0.8994 (tpp)
REVERT: B  165 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6483 (mtp)
REVERT: B  320 MET cc_start: 0.8791 (mmm) cc_final: 0.8535 (mmp)
REVERT: B  531 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6240 (mm-30)
REVERT: B  559 MET cc_start: 0.6953 (ttp) cc_final: 0.6452 (ptm)
REVERT: B  564 ILE cc_start: 0.8576 (tp) cc_final: 0.7942 (pt)
REVERT: B  638 SER cc_start: 0.8156 (t) cc_final: 0.7631 (p)
REVERT: B  643 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6838 (ttm)
REVERT: B  670 HIS cc_start: 0.8231 (m-70) cc_final: 0.7355 (t-170)
REVERT: B  689 MET cc_start: 0.9228 (tpp) cc_final: 0.8999 (tpp)
  outliers start: 15
  outliers final: 8
  residues processed: 190
  average time/residue: 0.0919
  time to fit residues: 25.6362
Evaluate side-chains
  192 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 178
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  388 PHE
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  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  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.7980
   chunk 116 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 109 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 115 optimal weight:    0.3980
   chunk 59 optimal weight:    0.3980
   chunk 73 optimal weight:    5.9990
   chunk 85 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.160214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125935 restraints weight = 11809.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.38
r_work: 0.3205 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.4187

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= 0.113
  Angle     :  0.537  10.477  14200  Z= 0.271
  Chirality :  0.042   0.316   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.994  21.884   1360
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.40 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.24), residues: 1248
  helix:  2.47 (0.17), residues: 836
  sheet: -1.71 (0.74), residues: 46
  loop : -1.51 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  48 
 TYR   0.005   0.001   TYR B 469 
 PHE   0.028   0.001   PHE B 428 
 TRP   0.016   0.001   TRP A 624 
 HIS   0.007   0.001   HIS A 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10440)
  covalent geometry    : angle       0.53697 (14200)
  hydrogen bonds       : bond        0.03596 (  695)
  hydrogen bonds       : angle       4.51749 ( 2055)

*********************** 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
  195 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  165 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6469 (mtp)
REVERT: A  320 MET cc_start: 0.8768 (mmm) cc_final: 0.8513 (mmp)
REVERT: A  395 PHE cc_start: 0.6872 (m-10) cc_final: 0.6392 (m-10)
REVERT: A  531 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6130 (mm-30)
REVERT: A  564 ILE cc_start: 0.8569 (tp) cc_final: 0.7925 (pt)
REVERT: A  638 SER cc_start: 0.8151 (t) cc_final: 0.7610 (p)
REVERT: A  643 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6861 (ttm)
REVERT: A  689 MET cc_start: 0.9223 (tpp) cc_final: 0.8971 (tpt)
REVERT: B  165 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6465 (mtp)
REVERT: B  320 MET cc_start: 0.8780 (mmm) cc_final: 0.8526 (mmp)
REVERT: B  395 PHE cc_start: 0.6690 (m-10) cc_final: 0.6318 (m-10)
REVERT: B  437 PHE cc_start: 0.8225 (m-80) cc_final: 0.7977 (m-80)
REVERT: B  531 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6159 (mm-30)
REVERT: B  559 MET cc_start: 0.6944 (ttp) cc_final: 0.6431 (ptm)
REVERT: B  564 ILE cc_start: 0.8547 (tp) cc_final: 0.7883 (pt)
REVERT: B  638 SER cc_start: 0.8132 (t) cc_final: 0.7589 (p)
REVERT: B  643 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6833 (ttm)
REVERT: B  689 MET cc_start: 0.9216 (tpp) cc_final: 0.8968 (tpt)
  outliers start: 14
  outliers final: 8
  residues processed: 182
  average time/residue: 0.0901
  time to fit residues: 23.8086
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  388 PHE
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  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  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:    0.0770
   chunk 86 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 104 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.6940

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.160122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126109 restraints weight = 11732.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.36
r_work: 0.3236 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10440  Z= 0.114
  Angle     :  0.531  11.002  14200  Z= 0.271
  Chirality :  0.042   0.307   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.983  21.587   1360
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.21 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.24), residues: 1248
  helix:  2.47 (0.17), residues: 836
  sheet: -1.75 (0.74), residues: 46
  loop : -1.53 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  48 
 TYR   0.005   0.001   TYR A 469 
 PHE   0.029   0.002   PHE B 428 
 TRP   0.015   0.001   TRP A 624 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10440)
  covalent geometry    : angle       0.53055 (14200)
  hydrogen bonds       : bond        0.03591 (  695)
  hydrogen bonds       : angle       4.51542 ( 2055)

********************** 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
  194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6557 (mtp)
REVERT: A  320 MET cc_start: 0.8795 (mmm) cc_final: 0.8530 (mmp)
REVERT: A  395 PHE cc_start: 0.6901 (m-10) cc_final: 0.6412 (m-10)
REVERT: A  437 PHE cc_start: 0.8292 (m-80) cc_final: 0.7961 (m-80)
REVERT: A  531 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6165 (mm-30)
REVERT: A  564 ILE cc_start: 0.8464 (tp) cc_final: 0.7894 (pt)
REVERT: A  638 SER cc_start: 0.8185 (t) cc_final: 0.7651 (p)
REVERT: A  643 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6941 (ttm)
REVERT: A  689 MET cc_start: 0.9249 (tpp) cc_final: 0.9007 (tpt)
REVERT: B  165 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6539 (mtp)
REVERT: B  320 MET cc_start: 0.8803 (mmm) cc_final: 0.8540 (mmp)
REVERT: B  395 PHE cc_start: 0.6711 (m-10) cc_final: 0.6328 (m-10)
REVERT: B  437 PHE cc_start: 0.8361 (m-80) cc_final: 0.8110 (m-80)
REVERT: B  531 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6187 (mm-30)
REVERT: B  559 MET cc_start: 0.6964 (ttp) cc_final: 0.6441 (ptm)
REVERT: B  564 ILE cc_start: 0.8576 (tp) cc_final: 0.7906 (pt)
REVERT: B  638 SER cc_start: 0.8173 (t) cc_final: 0.7636 (p)
REVERT: B  643 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6930 (ttm)
REVERT: B  689 MET cc_start: 0.9249 (tpp) cc_final: 0.9010 (tpt)
  outliers start: 15
  outliers final: 9
  residues processed: 180
  average time/residue: 0.0862
  time to fit residues: 23.0956
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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 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  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  589 MET
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.4980
   chunk 79 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0050
   chunk 76 optimal weight:    0.9980
   chunk 87 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.160484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.129754 restraints weight = 11855.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.47
r_work: 0.3218 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10440  Z= 0.112
  Angle     :  0.534  10.722  14200  Z= 0.271
  Chirality :  0.042   0.297   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.985  21.161   1360
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.87 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.24), residues: 1248
  helix:  2.42 (0.17), residues: 848
  sheet: -1.74 (0.74), residues: 46
  loop : -1.72 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  48 
 TYR   0.005   0.001   TYR B 469 
 PHE   0.033   0.002   PHE A 382 
 TRP   0.015   0.001   TRP A 624 
 HIS   0.007   0.001   HIS B 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10440)
  covalent geometry    : angle       0.53444 (14200)
  hydrogen bonds       : bond        0.03559 (  695)
  hydrogen bonds       : angle       4.50654 ( 2055)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2869.79 seconds
wall clock time: 49 minutes 45.52 seconds (2985.52 seconds total)