Starting phenix.real_space_refine
on Thu Oct 22 21:32:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wuv_66272/10_2026/9wuv_66272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wuv_66272/10_2026/9wuv_66272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wuv_66272/10_2026/9wuv_66272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wuv_66272/10_2026/9wuv_66272.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wuv_66272/10_2026/9wuv_66272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wuv_66272/10_2026/9wuv_66272.map"
  }
  resolution = 2.81
  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=   0.087
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 192 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       2      5.49       5
     S      36      5.16       5
     C    3612      2.51       5
     N     962      2.21       5
     O    1012      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5626
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2811
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 350, 2796
          Classifications: {'peptide': 350}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 326}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 350, 2796
          Classifications: {'peptide': 350}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 326}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 2847
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Restraints were copied for chains:
    A
  Time building chain proxies: 2.40, per 1000 atoms: 0.43
  Number of scatterers: 5626
  At special positions: 0
  Unit cell: (88.844, 96.86, 68.136, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      2     19.99
     S      36     16.00
     P       2     15.00
     O    1012      8.00
     N     962      7.00
     C    3612      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: 0.38
  Conformation dependent library (CDL) restraints added in 475.9 milliseconds
  

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1348

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      45.7% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 211 through 218
      removed outlier: 3.557A  pdb=" N   ARG B 216 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 240
      removed outlier: 3.659A  pdb=" N   GLU B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   LEU B 237 " --> pdb=" O   TRP B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 305
    Processing helix  chain 'B' and resid 310 through 330
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 4.034A  pdb=" N   MET B 389 " --> pdb=" O   THR B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 395
    Processing helix  chain 'B' and resid 408 through 422
      removed outlier: 3.702A  pdb=" N   TRP B 412 " --> pdb=" O   LYS B 408 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR B 419 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLU B 420 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 444
      removed outlier: 3.620A  pdb=" N   LEU B 444 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 463
      removed outlier: 3.535A  pdb=" N   LEU B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 470
    Processing helix  chain 'B' and resid 472 through 486
      removed outlier: 3.806A  pdb=" N   CYS B 480 " --> pdb=" O   ALA B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 492
      removed outlier: 3.665A  pdb=" N   LYS B 492 " --> pdb=" O   THR B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 517
    Processing helix  chain 'B' and resid 536 through 549
      removed outlier: 3.634A  pdb=" N   ARG B 549 " --> pdb=" O   SER B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 564
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 3.556A  pdb=" N   ARG A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 240
      removed outlier: 3.659A  pdb=" N   GLU A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   LEU A 237 " --> pdb=" O   TRP A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 310 through 330
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 4.034A  pdb=" N   MET A 389 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 395
    Processing helix  chain 'A' and resid 408 through 422
      removed outlier: 3.701A  pdb=" N   TRP A 412 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.620A  pdb=" N   LEU A 444 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 463
      removed outlier: 3.535A  pdb=" N   LEU A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 472 through 486
      removed outlier: 3.805A  pdb=" N   CYS A 480 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 492
      removed outlier: 3.665A  pdb=" N   LYS A 492 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 517
    Processing helix  chain 'A' and resid 536 through 549
      removed outlier: 3.633A  pdb=" N   ARG A 549 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 564
    Processing sheet with id=AA1, first strand: chain 'B' and resid 175 through 177
    Processing sheet with id=AA2, first strand: chain 'B' and resid 299 through 300
    Processing sheet with id=AA3, first strand: chain 'B' and resid 333 through 334
    Processing sheet with id=AA4, first strand: chain 'B' and resid 372 through 374
    Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 334
    Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374

    238 hydrogen bonds defined for protein.
    650 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: 0.75

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1788
        1.34 -     1.46: 1220
        1.46 -     1.58: 2696
        1.58 -     1.69: 6
        1.69 -     1.81: 56
  Bond restraints: 5766
  Sorted by residual:
  bond pdb=" OG1 TPO A 530 "
       pdb=" P   TPO A 530 "
    ideal  model  delta    sigma   weight residual
    1.717  1.612  0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" OG1 TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.717  1.613  0.104 2.00e-02 2.50e+03 2.72e+01
  bond pdb=" O1P TPO A 530 "
       pdb=" P   TPO A 530 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" O1P TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" O2P TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.63e+01
  ... (remaining 5761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 7764
        2.34 -     4.67: 62
        4.67 -     7.01: 12
        7.01 -     9.35: 2
        9.35 -    11.69: 4
  Bond angle restraints: 7844
  Sorted by residual:
  angle pdb=" CB  TPO B 530 "
        pdb=" OG1 TPO B 530 "
        pdb=" P   TPO B 530 "
      ideal   model   delta    sigma   weight residual
     119.31  107.62   11.69 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" CB  TPO A 530 "
        pdb=" OG1 TPO A 530 "
        pdb=" P   TPO A 530 "
      ideal   model   delta    sigma   weight residual
     119.31  107.70   11.61 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" OG1 TPO A 530 "
        pdb=" P   TPO A 530 "
        pdb=" O1P TPO A 530 "
      ideal   model   delta    sigma   weight residual
     100.43  109.91   -9.48 3.00e+00 1.11e-01 9.99e+00
  angle pdb=" OG1 TPO B 530 "
        pdb=" P   TPO B 530 "
        pdb=" O1P TPO B 530 "
      ideal   model   delta    sigma   weight residual
     100.43  109.90   -9.47 3.00e+00 1.11e-01 9.97e+00
  angle pdb=" C   LYS B 190 "
        pdb=" N   TYR B 191 "
        pdb=" CA  TYR B 191 "
      ideal   model   delta    sigma   weight residual
     121.80  128.95   -7.15 2.44e+00 1.68e-01 8.60e+00
  ... (remaining 7839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.15: 3223
       16.15 -    32.30: 217
       32.30 -    48.46: 36
       48.46 -    64.61: 6
       64.61 -    80.76: 6
  Dihedral angle restraints: 3488
    sinusoidal: 1410
      harmonic: 2078
  Sorted by residual:
  dihedral pdb=" CA BARG B 240 "
           pdb=" CB BARG B 240 "
           pdb=" CG BARG B 240 "
           pdb=" CD BARG B 240 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.78   57.78     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CA BARG A 240 "
           pdb=" CB BARG A 240 "
           pdb=" CG BARG A 240 "
           pdb=" CD BARG A 240 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.49   57.49     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CA  LEU B 355 "
           pdb=" CB  LEU B 355 "
           pdb=" CG  LEU B 355 "
           pdb=" CD1 LEU B 355 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.65   43.35     3      1.50e+01 4.44e-03 7.79e+00
  ... (remaining 3485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 597
       0.034 -    0.067: 207
       0.067 -    0.101: 47
       0.101 -    0.134: 23
       0.134 -    0.168: 2
  Chirality restraints: 876
  Sorted by residual:
  chirality pdb=" CB  THR B 400 "
            pdb=" CA  THR B 400 "
            pdb=" OG1 THR B 400 "
            pdb=" CG2 THR B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.03e-01
  chirality pdb=" CB  THR A 400 "
            pdb=" CA  THR A 400 "
            pdb=" OG1 THR A 400 "
            pdb=" CG2 THR A 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CA  ILE A 250 "
            pdb=" N   ILE A 250 "
            pdb=" C   ILE A 250 "
            pdb=" CB  ILE A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 873 not shown)

  Planarity restraints: 994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 247 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO A 248 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 247 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO B 248 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B 248 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 248 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 191 "   -0.007 2.00e-02 2.50e+03   7.26e-03 1.05e+00
        pdb=" CG  TYR B 191 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 191 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 191 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 191 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 191 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 191 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 191 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 991 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 775
        2.76 -     3.29: 5105
        3.29 -     3.83: 8405
        3.83 -     4.36: 10848
        4.36 -     4.90: 18779
  Nonbonded interactions: 43912
  Sorted by model distance:
  nonbonded pdb=" OG1 TPO B 530 "
            pdb=" N   ARG B 531 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OG1 TPO A 530 "
            pdb=" N   ARG A 531 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OD1 ASP A 359 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OD1 ASP B 359 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OE2 GLU B 217 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.327 3.040
  ... (remaining 43907 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.590
  Find NCS groups from input model:        0.040
  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:6.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   5766  Z= 0.177
  Angle     :  0.582  11.687   7844  Z= 0.261
  Chirality :  0.040   0.168    876
  Planarity :  0.004   0.038    994
  Dihedral  : 11.521  80.762   2140
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.05 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole: -0.37 (0.32), residues: 686
  helix:  0.14 (0.29), residues: 286
  sheet:  0.47 (0.55), residues: 100
  loop : -0.78 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 470 
 TYR   0.018   0.001   TYR B 191 
 PHE   0.013   0.001   PHE A 291 
 TRP   0.006   0.001   TRP B 233 
 HIS   0.003   0.001   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.18 ( 5766)
  covalent geometry    : angle       0.58195 /  0.26 ( 7844)
  hydrogen bonds       : bond        0.27436 / 16.73 (  238)
  hydrogen bonds       : angle       6.91695 /  4.85 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.216 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.5585
  time to fit residues: 42.6622
Evaluate side-chains
  61 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27]
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 342 ASN
A 228 HIS
A 342 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.181872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.156351 restraints weight = 12350.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.61
r_work: 0.3376 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5766  Z= 0.128
  Angle     :  0.604   8.805   7844  Z= 0.294
  Chirality :  0.042   0.142    876
  Planarity :  0.005   0.037    994
  Dihedral  :  3.842  13.309    768
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.93 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.61 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.53 (0.33), residues: 686
  helix:  1.54 (0.32), residues: 276
  sheet:  0.87 (0.57), residues: 100
  loop : -0.93 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 433 
 TYR   0.019   0.002   TYR A 191 
 PHE   0.019   0.001   PHE B 291 
 TRP   0.006   0.001   TRP B 412 
 HIS   0.004   0.001   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 5766)
  covalent geometry    : angle       0.60435 /  0.29 ( 7844)
  hydrogen bonds       : bond        0.05144 /  3.23 (  238)
  hydrogen bonds       : angle       4.60978 /  3.23 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.260 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 74
  average time/residue: 0.6259
  time to fit residues: 48.2926
Evaluate side-chains
  66 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [0, 13, 42, 25, 2, 39, 59, 14, 66, 63, 30]
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    0.2980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.178865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.139086 restraints weight = 18088.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 5.90
r_work: 0.3194 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3254
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3254
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5766  Z= 0.130
  Angle     :  0.586   7.036   7844  Z= 0.284
  Chirality :  0.041   0.138    876
  Planarity :  0.005   0.039    994
  Dihedral  :  3.996  13.582    768
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.49 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.87 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.66 (0.34), residues: 686
  helix:  1.77 (0.33), residues: 280
  sheet:  1.00 (0.57), residues: 100
  loop : -1.06 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.018   0.002   TYR A 191 
 PHE   0.016   0.001   PHE A 291 
 TRP   0.007   0.001   TRP A 561 
 HIS   0.002   0.001   HIS B 335 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 5766)
  covalent geometry    : angle       0.58575 /  0.28 ( 7844)
  hydrogen bonds       : bond        0.04916 /  3.10 (  238)
  hydrogen bonds       : angle       4.25870 /  2.95 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.254 
Fit side-chains
REVERT: B  208 MET cc_start: 0.6012 (mtp) cc_final: 0.5735 (mtt)
REVERT: A  208 MET cc_start: 0.6022 (mtp) cc_final: 0.5770 (mtt)
REVERT: A  214 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7026 (mmt)
  outliers start: 5
  outliers final: 1
  residues processed: 70
  average time/residue: 0.6182
  time to fit residues: 45.1193
Evaluate side-chains
  68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  512 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [65, 43, 52, 56, 23, 44, 10, 31, 46, 25, 4]
   chunk 65 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.178021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.140904 restraints weight = 15871.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 5.11
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5766  Z= 0.127
  Angle     :  0.570   6.937   7844  Z= 0.277
  Chirality :  0.041   0.136    876
  Planarity :  0.005   0.042    994
  Dihedral  :  4.118  18.574    768
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.64 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.19 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.69 (0.34), residues: 686
  helix:  1.72 (0.33), residues: 288
  sheet:  1.02 (0.58), residues: 100
  loop : -1.04 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 470 
 TYR   0.019   0.002   TYR A 191 
 PHE   0.013   0.001   PHE A 291 
 TRP   0.009   0.001   TRP A 561 
 HIS   0.002   0.001   HIS A 335 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 5766)
  covalent geometry    : angle       0.56980 /  0.28 ( 7844)
  hydrogen bonds       : bond        0.04363 /  2.76 (  238)
  hydrogen bonds       : angle       4.01155 /  2.76 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.206 
Fit side-chains
REVERT: B  197 MET cc_start: 0.6682 (mtp) cc_final: 0.6405 (ptp)
REVERT: B  208 MET cc_start: 0.6018 (mtp) cc_final: 0.5734 (mtt)
REVERT: B  214 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6791 (mmt)
REVERT: B  292 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7738 (tp)
REVERT: A  197 MET cc_start: 0.6770 (mtp) cc_final: 0.6301 (ptp)
REVERT: A  208 MET cc_start: 0.6010 (mtp) cc_final: 0.5732 (mtt)
REVERT: A  214 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6743 (mmt)
  outliers start: 11
  outliers final: 2
  residues processed: 70
  average time/residue: 0.6259
  time to fit residues: 45.6394
Evaluate side-chains
  70 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  512 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [65, 52, 21, 51, 8, 35, 29, 18, 26, 58, 23]
   chunk 65 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0970
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0370
   chunk 18 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4456

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.179623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.148012 restraints weight = 7727.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.80
r_work: 0.3395 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5766  Z= 0.102
  Angle     :  0.519   6.756   7844  Z= 0.256
  Chirality :  0.040   0.132    876
  Planarity :  0.005   0.039    994
  Dihedral  :  4.030  23.724    768
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.35 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.97 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.85 (0.34), residues: 686
  helix:  1.90 (0.34), residues: 288
  sheet:  1.07 (0.57), residues: 100
  loop : -1.00 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 549 
 TYR   0.018   0.001   TYR B 191 
 PHE   0.015   0.001   PHE A 291 
 TRP   0.011   0.001   TRP A 561 
 HIS   0.003   0.001   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.10 ( 5766)
  covalent geometry    : angle       0.51947 /  0.26 ( 7844)
  hydrogen bonds       : bond        0.03671 /  2.30 (  238)
  hydrogen bonds       : angle       3.88424 /  2.66 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  208 MET cc_start: 0.6070 (mtp) cc_final: 0.5752 (mtt)
REVERT: B  214 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7210 (mmt)
REVERT: A  197 MET cc_start: 0.7069 (mtp) cc_final: 0.6661 (ptp)
REVERT: A  208 MET cc_start: 0.6093 (mtp) cc_final: 0.5764 (mtt)
REVERT: A  214 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7234 (mmt)
  outliers start: 7
  outliers final: 1
  residues processed: 69
  average time/residue: 0.6510
  time to fit residues: 46.6706
Evaluate side-chains
  69 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain A residue  214 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [47, 8, 17, 33, 51, 16, 64, 36, 52, 23, 20]
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0670
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0770
   chunk 64 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 23 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4076

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 478 ASN
A 228 HIS
A 478 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.179553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.140921 restraints weight = 18326.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 5.79
r_work: 0.3223 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5766  Z= 0.098
  Angle     :  0.509   6.657   7844  Z= 0.252
  Chirality :  0.040   0.131    876
  Planarity :  0.005   0.039    994
  Dihedral  :  4.009  27.434    768
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.79 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.29 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.88 (0.34), residues: 686
  helix:  2.02 (0.34), residues: 282
  sheet:  1.08 (0.57), residues: 100
  loop : -1.02 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 549 
 TYR   0.020   0.001   TYR A 540 
 PHE   0.014   0.001   PHE B 193 
 TRP   0.013   0.001   TRP A 561 
 HIS   0.003   0.000   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00223 /  0.10 ( 5766)
  covalent geometry    : angle       0.50855 /  0.25 ( 7844)
  hydrogen bonds       : bond        0.03475 /  2.18 (  238)
  hydrogen bonds       : angle       3.82279 /  2.61 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  208 MET cc_start: 0.6047 (mtp) cc_final: 0.5701 (mtt)
REVERT: B  214 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7192 (mmt)
REVERT: A  197 MET cc_start: 0.6936 (mtp) cc_final: 0.6648 (ptp)
REVERT: A  208 MET cc_start: 0.6077 (mtp) cc_final: 0.5752 (mtt)
REVERT: A  214 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7235 (mmt)
  outliers start: 6
  outliers final: 2
  residues processed: 62
  average time/residue: 0.6680
  time to fit residues: 42.9266
Evaluate side-chains
  64 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  214 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [48, 9, 19, 23, 27, 32, 67, 22, 34, 11, 46]
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0570
   chunk 23 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0010
   chunk 34 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.4104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 228 HIS
A 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.179868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.142943 restraints weight = 17897.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 5.23
r_work: 0.3220 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5766  Z= 0.098
  Angle     :  0.508   6.656   7844  Z= 0.252
  Chirality :  0.040   0.130    876
  Planarity :  0.004   0.040    994
  Dihedral  :  4.034  30.462    768
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.49 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.77 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.90 (0.34), residues: 686
  helix:  2.05 (0.34), residues: 282
  sheet:  1.09 (0.56), residues: 100
  loop : -1.03 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 549 
 TYR   0.020   0.001   TYR A 540 
 PHE   0.016   0.001   PHE B 291 
 TRP   0.016   0.001   TRP A 561 
 HIS   0.002   0.000   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.10 ( 5766)
  covalent geometry    : angle       0.50830 /  0.25 ( 7844)
  hydrogen bonds       : bond        0.03398 /  2.12 (  238)
  hydrogen bonds       : angle       3.79200 /  2.59 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B  208 MET cc_start: 0.5983 (mtp) cc_final: 0.5647 (mtt)
REVERT: B  214 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7080 (mmt)
REVERT: A  197 MET cc_start: 0.6893 (mtp) cc_final: 0.6673 (ptp)
REVERT: A  208 MET cc_start: 0.6036 (mtp) cc_final: 0.5710 (mtt)
REVERT: A  214 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7156 (mmt)
  outliers start: 8
  outliers final: 4
  residues processed: 69
  average time/residue: 0.6612
  time to fit residues: 47.3782
Evaluate side-chains
  68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  212 LYS
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  376 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [67, 0, 17, 22, 61, 21, 37, 19, 8, 34, 48]
   chunk 67 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0970
   chunk 61 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0020
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 478 ASN
A 228 HIS
A 369 ASN
A 478 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.181557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.156305 restraints weight = 13835.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 1.69
r_work: 0.3396 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5766  Z= 0.091
  Angle     :  0.491   6.553   7844  Z= 0.245
  Chirality :  0.039   0.129    876
  Planarity :  0.004   0.040    994
  Dihedral  :  3.993  32.280    768
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.64 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.58 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.95 (0.34), residues: 686
  helix:  2.10 (0.34), residues: 282
  sheet:  1.13 (0.56), residues: 100
  loop : -1.02 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 549 
 TYR   0.021   0.001   TYR A 540 
 PHE   0.013   0.001   PHE B 291 
 TRP   0.017   0.001   TRP A 561 
 HIS   0.002   0.000   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00203 /  0.09 ( 5766)
  covalent geometry    : angle       0.49089 /  0.25 ( 7844)
  hydrogen bonds       : bond        0.03148 /  1.95 (  238)
  hydrogen bonds       : angle       3.78107 /  2.58 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B  208 MET cc_start: 0.5858 (mtp) cc_final: 0.5414 (mpt)
REVERT: A  208 MET cc_start: 0.5909 (mtp) cc_final: 0.5606 (mtt)
  outliers start: 5
  outliers final: 3
  residues processed: 73
  average time/residue: 0.6073
  time to fit residues: 46.2300
Evaluate side-chains
  70 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain A residue  376 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [21, 2, 20, 18, 26, 67, 35, 19, 32, 46, 15]
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 342 ASN
A 342 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.175466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.140487 restraints weight = 14705.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 3.46
r_work: 0.3166 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5766  Z= 0.130
  Angle     :  0.575   6.879   7844  Z= 0.281
  Chirality :  0.041   0.136    876
  Planarity :  0.005   0.042    994
  Dihedral  :  4.322  33.871    768
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.23 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.94 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.78 (0.33), residues: 686
  helix:  1.94 (0.33), residues: 282
  sheet:  1.09 (0.56), residues: 100
  loop : -1.10 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.019   0.002   TYR A 540 
 PHE   0.015   0.001   PHE B 291 
 TRP   0.021   0.001   TRP A 561 
 HIS   0.002   0.001   HIS A 335 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.13 ( 5766)
  covalent geometry    : angle       0.57514 /  0.28 ( 7844)
  hydrogen bonds       : bond        0.04357 /  2.73 (  238)
  hydrogen bonds       : angle       3.85106 /  2.63 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.261 
Fit side-chains
REVERT: B  208 MET cc_start: 0.5990 (mtp) cc_final: 0.5366 (mpt)
REVERT: A  208 MET cc_start: 0.6016 (mtp) cc_final: 0.5649 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 66
  average time/residue: 0.6546
  time to fit residues: 45.0009
Evaluate side-chains
  67 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  212 LYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  376 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [21, 52, 35, 26, 24, 58, 19, 12, 25, 50, 59]
   chunk 21 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.176793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.143684 restraints weight = 15658.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 4.23
r_work: 0.3174 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5766  Z= 0.119
  Angle     :  0.554   6.732   7844  Z= 0.273
  Chirality :  0.041   0.133    876
  Planarity :  0.005   0.040    994
  Dihedral  :  4.326  34.987    768
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.64 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.74 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.77 (0.33), residues: 686
  helix:  1.93 (0.33), residues: 282
  sheet:  1.04 (0.56), residues: 100
  loop : -1.09 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 470 
 TYR   0.020   0.001   TYR A 540 
 PHE   0.015   0.001   PHE B 291 
 TRP   0.024   0.001   TRP A 561 
 HIS   0.002   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 5766)
  covalent geometry    : angle       0.55443 /  0.27 ( 7844)
  hydrogen bonds       : bond        0.04079 /  2.54 (  238)
  hydrogen bonds       : angle       3.83660 /  2.62 (  650)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B  208 MET cc_start: 0.5938 (mtp) cc_final: 0.5296 (mpt)
REVERT: A  208 MET cc_start: 0.5948 (mtp) cc_final: 0.5560 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 64
  average time/residue: 0.6449
  time to fit residues: 42.8358
Evaluate side-chains
  64 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  212 LYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  376 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [4, 32, 60, 27, 23, 61, 24, 36, 25, 40, 20]
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.2784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.173115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.146893 restraints weight = 13287.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.70
r_work: 0.3288 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5766  Z= 0.184
  Angle     :  0.669   7.908   7844  Z= 0.323
  Chirality :  0.044   0.140    876
  Planarity :  0.006   0.054    994
  Dihedral  :  4.723  36.002    768
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.67 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.26 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 are not related in a simple way.
  whole:  0.48 (0.33), residues: 686
  helix:  1.64 (0.33), residues: 284
  sheet:  0.86 (0.56), residues: 100
  loop : -1.20 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 470 
 TYR   0.020   0.002   TYR B 191 
 PHE   0.017   0.002   PHE A 193 
 TRP   0.029   0.002   TRP A 561 
 HIS   0.003   0.001   HIS A 335 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.18 ( 5766)
  covalent geometry    : angle       0.66922 /  0.32 ( 7844)
  hydrogen bonds       : bond        0.05471 /  3.45 (  238)
  hydrogen bonds       : angle       3.98162 /  2.72 (  650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1997.51 seconds
wall clock time: 34 minutes 43.62 seconds (2083.62 seconds total)