Starting phenix.real_space_refine
on Tue Mar 11 16:42:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erp_28557/03_2025/8erp_28557_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erp_28557/03_2025/8erp_28557.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8erp_28557/03_2025/8erp_28557.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erp_28557/03_2025/8erp_28557.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erp_28557/03_2025/8erp_28557_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erp_28557/03_2025/8erp_28557_neut.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.023 sd=   0.179
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      4      5.21       5
     S      50      5.16       5
     C    4074      2.51       5
     N     894      2.21       5
     O    1028      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6056
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2836
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 15, 'TRANS': 348}
    Chain: "A"
      Number of atoms: 2836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2836
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 15, 'TRANS': 348}
    Chain: "B"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 192
          Unusual residues: {' MG': 2, 'CDC': 1, 'LBN': 10}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 361
          Unresolved non-hydrogen angles: 442
          Unresolved non-hydrogen dihedrals: 334
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'LBN:plan-2': 9, 'LBN:plan-3': 9, 'LBN:plan-1': 9}
          Unresolved non-hydrogen planarities: 93
    Chain: "A"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 192
          Unusual residues: {' MG': 2, 'CDC': 1, 'LBN': 10}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 361
          Unresolved non-hydrogen angles: 442
          Unresolved non-hydrogen dihedrals: 334
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'LBN:plan-2': 9, 'LBN:plan-3': 9, 'LBN:plan-1': 9}
          Unresolved non-hydrogen planarities: 93
  Time building chain proxies: 4.61, per 1000 atoms: 0.76
  Number of scatterers: 6056
  At special positions: 0
  Unit cell: (73.7, 115.5, 70.4, 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)
     S      50     16.00
     P       6     15.00
     Mg      4     11.99
     O    1028      8.00
     N     894      7.00
     C    4074      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: 1.87
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      76.4% alpha, 1.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'B' and resid 22 through 30
      removed outlier: 4.011A  pdb=" N   GLU B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 55
      removed outlier: 3.592A  pdb=" N   MET B  46 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 85
      removed outlier: 3.524A  pdb=" N   ILE B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 89
      removed outlier: 4.113A  pdb=" N   THR B  89 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 86 through 89'
    Processing helix  chain 'B' and resid 93 through 120
      removed outlier: 3.696A  pdb=" N   TYR B  97 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 152
      removed outlier: 3.979A  pdb=" N   GLU B 129 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   MET B 130 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 159
    Processing helix  chain 'B' and resid 160 through 180
      removed outlier: 4.234A  pdb=" N   CYS B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 209
    Processing helix  chain 'B' and resid 210 through 215
      removed outlier: 3.948A  pdb=" N   TRP B 213 " --> pdb=" O   PRO B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 249
      removed outlier: 3.657A  pdb=" N   GLY B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 284
      removed outlier: 3.816A  pdb=" N   HIS B 270 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 293
      removed outlier: 3.680A  pdb=" N   GLN B 292 " --> pdb=" O   ASN B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 318
      removed outlier: 3.686A  pdb=" N   LEU B 312 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 341
      removed outlier: 3.718A  pdb=" N   PHE B 341 " --> pdb=" O   PHE B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 378
      removed outlier: 3.878A  pdb=" N   TRP B 352 " --> pdb=" O   TYR B 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 30
      removed outlier: 4.011A  pdb=" N   GLU A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 55
      removed outlier: 3.592A  pdb=" N   MET A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 85
      removed outlier: 3.524A  pdb=" N   ILE A  66 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 89
      removed outlier: 4.113A  pdb=" N   THR A  89 " --> pdb=" O   PRO A  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 86 through 89'
    Processing helix  chain 'A' and resid 93 through 120
      removed outlier: 3.696A  pdb=" N   TYR A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 152
      removed outlier: 3.979A  pdb=" N   GLU A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   MET A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 151 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 159
    Processing helix  chain 'A' and resid 160 through 180
      removed outlier: 4.234A  pdb=" N   CYS A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 209
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 3.948A  pdb=" N   TRP A 213 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 249
      removed outlier: 3.657A  pdb=" N   GLY A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 284
      removed outlier: 3.816A  pdb=" N   HIS A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 293
      removed outlier: 3.680A  pdb=" N   GLN A 292 " --> pdb=" O   ASN A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 318
      removed outlier: 3.686A  pdb=" N   LEU A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 341
      removed outlier: 3.718A  pdb=" N   PHE A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 378
      removed outlier: 3.878A  pdb=" N   TRP A 352 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 38
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38

    406 hydrogen bonds defined for protein.
    1200 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: 1.79

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 900
        1.32 -     1.44: 1620
        1.44 -     1.57: 3576
        1.57 -     1.69: 12
        1.69 -     1.81: 74
  Bond restraints: 6182
  Sorted by residual:
  bond pdb=" O3A CDC A 507 "
       pdb=" PA  CDC A 507 "
    ideal  model  delta    sigma   weight residual
    1.653  1.592  0.061 2.00e-02 2.50e+03 9.28e+00
  bond pdb=" O3A CDC B 505 "
       pdb=" PA  CDC B 505 "
    ideal  model  delta    sigma   weight residual
    1.653  1.592  0.061 2.00e-02 2.50e+03 9.28e+00
  bond pdb=" O1B CDC B 505 "
       pdb=" PB  CDC B 505 "
    ideal  model  delta    sigma   weight residual
    1.654  1.596  0.058 2.00e-02 2.50e+03 8.47e+00
  bond pdb=" O1B CDC A 507 "
       pdb=" PB  CDC A 507 "
    ideal  model  delta    sigma   weight residual
    1.654  1.596  0.058 2.00e-02 2.50e+03 8.47e+00
  bond pdb=" O2  LBN B 506 "
       pdb=" P1  LBN B 506 "
    ideal  model  delta    sigma   weight residual
    1.650  1.596  0.054 2.00e-02 2.50e+03 7.27e+00
  ... (remaining 6177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 8092
        2.29 -     4.59: 192
        4.59 -     6.88: 30
        6.88 -     9.17: 4
        9.17 -    11.46: 6
  Bond angle restraints: 8324
  Sorted by residual:
  angle pdb=" O3A CDC A 507 "
        pdb=" PA  CDC A 507 "
        pdb=" O5' CDC A 507 "
      ideal   model   delta    sigma   weight residual
      94.32  105.78  -11.46 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" O3A CDC B 505 "
        pdb=" PA  CDC B 505 "
        pdb=" O5' CDC B 505 "
      ideal   model   delta    sigma   weight residual
      94.32  105.78  -11.46 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" C   TYR A 215 "
        pdb=" N   GLU A 216 "
        pdb=" CA  GLU A 216 "
      ideal   model   delta    sigma   weight residual
     121.31  126.84   -5.53 1.49e+00 4.50e-01 1.38e+01
  angle pdb=" C   TYR B 215 "
        pdb=" N   GLU B 216 "
        pdb=" CA  GLU B 216 "
      ideal   model   delta    sigma   weight residual
     121.31  126.84   -5.53 1.49e+00 4.50e-01 1.38e+01
  angle pdb=" O1  LBN A 508 "
        pdb=" P1  LBN A 508 "
        pdb=" O2  LBN A 508 "
      ideal   model   delta    sigma   weight residual
      93.45  104.32  -10.87 3.00e+00 1.11e-01 1.31e+01
  ... (remaining 8319 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.95: 3456
       28.95 -    57.91: 184
       57.91 -    86.86: 36
       86.86 -   115.82: 4
      115.82 -   144.77: 12
  Dihedral angle restraints: 3692
    sinusoidal: 1590
      harmonic: 2102
  Sorted by residual:
  dihedral pdb=" C32 LBN A 513 "
           pdb=" C33 LBN A 513 "
           pdb=" C4  LBN A 513 "
           pdb=" C7  LBN A 513 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.89  -35.34 -144.77     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" C32 LBN B 511 "
           pdb=" C33 LBN B 511 "
           pdb=" C4  LBN B 511 "
           pdb=" C7  LBN B 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.89  -35.34 -144.77     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" O5  LBN B 506 "
           pdb=" C2  LBN B 506 "
           pdb=" C3  LBN B 506 "
           pdb=" O7  LBN B 506 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67  -66.11  128.78     1      3.00e+01 1.11e-03 1.73e+01
  ... (remaining 3689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 716
       0.046 -    0.091: 196
       0.091 -    0.137: 28
       0.137 -    0.183: 2
       0.183 -    0.228: 6
  Chirality restraints: 948
  Sorted by residual:
  chirality pdb=" CB  ILE B 189 "
            pdb=" CA  ILE B 189 "
            pdb=" CG1 ILE B 189 "
            pdb=" CG2 ILE B 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  ILE A 189 "
            pdb=" CA  ILE A 189 "
            pdb=" CG1 ILE A 189 "
            pdb=" CG2 ILE A 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C1' CDC B 505 "
            pdb=" C2' CDC B 505 "
            pdb=" N1  CDC B 505 "
            pdb=" O4' CDC B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.42   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 945 not shown)

  Planarity restraints: 968
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN A 508 "    0.249 2.00e-02 2.50e+03   2.47e-01 6.08e+02
        pdb=" C42 LBN A 508 "   -0.255 2.00e-02 2.50e+03
        pdb=" C5  LBN A 508 "   -0.238 2.00e-02 2.50e+03
        pdb=" C8  LBN A 508 "    0.244 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN B 506 "   -0.249 2.00e-02 2.50e+03   2.47e-01 6.08e+02
        pdb=" C42 LBN B 506 "    0.255 2.00e-02 2.50e+03
        pdb=" C5  LBN B 506 "    0.238 2.00e-02 2.50e+03
        pdb=" C8  LBN B 506 "   -0.244 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 176 "    0.022 2.00e-02 2.50e+03   1.72e-02 7.44e+00
        pdb=" CG  TRP A 176 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 176 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 176 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 176 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 176 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 176 "    0.003 2.00e-02 2.50e+03
  ... (remaining 965 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 54
        2.59 -     3.17: 5196
        3.17 -     3.75: 8712
        3.75 -     4.32: 11424
        4.32 -     4.90: 19471
  Nonbonded interactions: 44857
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 136 "
            pdb="MG    MG A 503 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" OD1 ASP B 136 "
            pdb="MG    MG B 501 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" OD1 ASP B 111 "
            pdb="MG    MG B 501 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OD1 ASP A 111 "
            pdb="MG    MG A 503 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OD1 ASP B 132 "
            pdb="MG    MG B 501 "
     model   vdw
     2.067 2.170
  ... (remaining 44852 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 20 through 383 or (resid 506 and (name C29 or name C30 or  \ 
name C31 or name C32)) or (resid 508 and (name C25 or name C26 or name C27 or na \ 
me C28 or name C29 or name C30 or name C31 or name C32)) or (resid 509 and (name \ 
 C10 or name C13 or name C26 or name C27 or name C28 or name C29 or name C30 or  \ 
name C31 or name C32 or name C33 or name C4 or name C7 )) or resid 510 through 5 \ 
12 or (resid 513 and (name C10 or name C13 or name C25 or name C26 or name C27 o \ 
r name C28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C \ 
4 or name C7 ))))
  selection = (chain 'B' and (resid 20 through 383 or (resid 506 and (name C29 or name C30 or  \ 
name C31 or name C32)) or (resid 508 and (name C25 or name C26 or name C27 or na \ 
me C28 or name C29 or name C30 or name C31 or name C32)) or resid 509 through 51 \ 
0 or (resid 511 and (name C10 or name C13 or name C26 or name C27 or name C28 or \ 
 name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7  \ 
)) or resid 512 through 513))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.090
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
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   0.061   6182  Z= 0.276
  Angle     :  0.855  11.462   8324  Z= 0.452
  Chirality :  0.044   0.228    948
  Planarity :  0.013   0.247    968
  Dihedral  : 19.420 144.771   2348
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.32), residues: 724
  helix:  1.54 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.07 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP B 176 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.015   0.002   PHE A 171 
 TYR   0.007   0.001   TYR A 282 
 ARG   0.002   0.000   ARG A 378 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.672 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8097 (ttp) cc_final: 0.7738 (ttm)
REVERT: A  201 MET cc_start: 0.8083 (ttp) cc_final: 0.7733 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1509
  time to fit residues: 24.3687
Evaluate side-chains
  100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
B 177 GLN
B 293 ASN
A  74 ASN
A 177 GLN
A 293 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.154343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.129950 restraints weight = 6765.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.127586 restraints weight = 10778.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.127991 restraints weight = 12227.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6182  Z= 0.326
  Angle     :  0.747   7.079   8324  Z= 0.396
  Chirality :  0.045   0.188    948
  Planarity :  0.005   0.043    968
  Dihedral  : 16.565 116.112   1090
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.70 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.32), residues: 724
  helix:  1.72 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.71 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 176 
 HIS   0.005   0.002   HIS A 270 
 PHE   0.018   0.002   PHE B 171 
 TYR   0.022   0.002   TYR A 282 
 ARG   0.003   0.001   ARG B 120 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.668 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8231 (ttp) cc_final: 0.7762 (ttm)
REVERT: A  201 MET cc_start: 0.8231 (ttp) cc_final: 0.7761 (ttm)
  outliers start: 14
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1686
  time to fit residues: 25.2247
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   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 = 0.3809 r_free = 0.3809 target = 0.165898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.141199 restraints weight = 6642.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.139818 restraints weight = 9705.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.140641 restraints weight = 9778.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6182  Z= 0.198
  Angle     :  0.642   7.824   8324  Z= 0.342
  Chirality :  0.041   0.189    948
  Planarity :  0.005   0.040    968
  Dihedral  : 14.791  99.477   1090
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.24 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.33), residues: 724
  helix:  2.29 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.86 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.013   0.002   PHE B 171 
 TYR   0.010   0.001   TYR A 243 
 ARG   0.002   0.000   ARG A 245 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.745 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8096 (ttp) cc_final: 0.7461 (ttm)
REVERT: A  201 MET cc_start: 0.8093 (ttp) cc_final: 0.7466 (ttm)
  outliers start: 20
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1957
  time to fit residues: 28.8801
Evaluate side-chains
  100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 56 optimal weight:    0.2980
   chunk 55 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.160833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.133707 restraints weight = 6870.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.132143 restraints weight = 11207.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.133176 restraints weight = 10377.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6182  Z= 0.243
  Angle     :  0.644   6.250   8324  Z= 0.346
  Chirality :  0.042   0.157    948
  Planarity :  0.004   0.040    968
  Dihedral  : 13.952  96.199   1090
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.14 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.33), residues: 724
  helix:  2.34 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.81 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 176 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.016   0.002   PHE B 171 
 TYR   0.014   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 119 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.627 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8081 (ttp) cc_final: 0.7489 (ttm)
REVERT: A  201 MET cc_start: 0.8077 (ttp) cc_final: 0.7486 (ttm)
  outliers start: 20
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1679
  time to fit residues: 22.7863
Evaluate side-chains
  96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.163917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.140426 restraints weight = 6693.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.138890 restraints weight = 10508.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.140132 restraints weight = 10002.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6182  Z= 0.200
  Angle     :  0.626   8.364   8324  Z= 0.331
  Chirality :  0.041   0.187    948
  Planarity :  0.004   0.039    968
  Dihedral  : 13.270  90.982   1090
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.37 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.33), residues: 724
  helix:  2.54 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.91 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 270 
 PHE   0.032   0.002   PHE B  94 
 TYR   0.008   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A  39 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.641 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8053 (ttp) cc_final: 0.7545 (ttm)
REVERT: A  201 MET cc_start: 0.8045 (ttp) cc_final: 0.7538 (ttm)
  outliers start: 20
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1849
  time to fit residues: 28.0500
Evaluate side-chains
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.156878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.131015 restraints weight = 6670.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129966 restraints weight = 11201.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.130199 restraints weight = 11272.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6182  Z= 0.317
  Angle     :  0.693   6.449   8324  Z= 0.368
  Chirality :  0.044   0.174    948
  Planarity :  0.004   0.039    968
  Dihedral  : 13.479  86.738   1090
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.59 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.33), residues: 724
  helix:  2.36 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -2.69 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 176 
 HIS   0.005   0.001   HIS A 270 
 PHE   0.026   0.002   PHE B  94 
 TYR   0.018   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 119 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.572 
Fit side-chains
REVERT: B  131 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7983 (m-10)
REVERT: B  201 MET cc_start: 0.8211 (ttp) cc_final: 0.7489 (ttm)
REVERT: A  131 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7980 (m-10)
REVERT: A  201 MET cc_start: 0.8213 (ttp) cc_final: 0.7495 (ttm)
  outliers start: 22
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1715
  time to fit residues: 24.4719
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  131 PHE
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0060
   chunk 58 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.160343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.136434 restraints weight = 6739.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.135588 restraints weight = 8447.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.136533 restraints weight = 7821.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6182  Z= 0.240
  Angle     :  0.651   7.459   8324  Z= 0.345
  Chirality :  0.042   0.211    948
  Planarity :  0.004   0.037    968
  Dihedral  : 13.089  82.135   1090
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 20.95 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.33), residues: 724
  helix:  2.45 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.77 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  95 
 HIS   0.005   0.001   HIS A 270 
 PHE   0.025   0.002   PHE B  94 
 TYR   0.011   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 120 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.729 
Fit side-chains
REVERT: B   55 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: B  201 MET cc_start: 0.8100 (ttp) cc_final: 0.7702 (ttm)
REVERT: A   55 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: A  201 MET cc_start: 0.8090 (ttp) cc_final: 0.7695 (ttm)
  outliers start: 26
  outliers final: 20
  residues processed: 102
  average time/residue: 0.1858
  time to fit residues: 25.7654
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 69 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.163772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.141544 restraints weight = 6688.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141050 restraints weight = 10355.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.141145 restraints weight = 9176.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6182  Z= 0.190
  Angle     :  0.625   6.978   8324  Z= 0.331
  Chirality :  0.041   0.202    948
  Planarity :  0.004   0.038    968
  Dihedral  : 12.595  79.203   1090
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.54 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.33), residues: 724
  helix:  2.60 (0.22), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.79 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  95 
 HIS   0.004   0.001   HIS A 270 
 PHE   0.025   0.002   PHE A  94 
 TYR   0.008   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 120 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.645 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8050 (ttp) cc_final: 0.7397 (ttm)
REVERT: A  201 MET cc_start: 0.8048 (ttp) cc_final: 0.7398 (ttm)
  outliers start: 20
  outliers final: 18
  residues processed: 100
  average time/residue: 0.1699
  time to fit residues: 23.0925
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   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 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.163278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.135499 restraints weight = 6676.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.135004 restraints weight = 5523.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.135288 restraints weight = 5234.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6182  Z= 0.204
  Angle     :  0.631   6.631   8324  Z= 0.333
  Chirality :  0.041   0.198    948
  Planarity :  0.004   0.039    968
  Dihedral  : 12.278  76.591   1090
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 22.86 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.33), residues: 724
  helix:  2.59 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.79 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 176 
 HIS   0.004   0.001   HIS A 270 
 PHE   0.024   0.002   PHE A  94 
 TYR   0.009   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 120 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.626 
Fit side-chains
REVERT: B  120 ARG cc_start: 0.8090 (ptt-90) cc_final: 0.7797 (ptt180)
REVERT: B  201 MET cc_start: 0.7964 (ttp) cc_final: 0.7619 (ttm)
REVERT: A  120 ARG cc_start: 0.8096 (ptt-90) cc_final: 0.7805 (ptt180)
REVERT: A  201 MET cc_start: 0.7954 (ttp) cc_final: 0.7606 (ttm)
  outliers start: 18
  outliers final: 16
  residues processed: 98
  average time/residue: 0.1917
  time to fit residues: 24.6805
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.154503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.130560 restraints weight = 6940.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.129165 restraints weight = 12517.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.128133 restraints weight = 13383.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6182  Z= 0.318
  Angle     :  0.698   6.608   8324  Z= 0.368
  Chirality :  0.044   0.198    948
  Planarity :  0.004   0.038    968
  Dihedral  : 12.673  80.570   1090
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.49 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.32), residues: 724
  helix:  2.62 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.82 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 176 
 HIS   0.006   0.001   HIS A 270 
 PHE   0.025   0.002   PHE A  94 
 TYR   0.017   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B  39 

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.658 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8189 (ttp) cc_final: 0.7640 (ttm)
REVERT: A  201 MET cc_start: 0.8188 (ttp) cc_final: 0.7642 (ttm)
  outliers start: 18
  outliers final: 18
  residues processed: 100
  average time/residue: 0.1686
  time to fit residues: 22.9839
Evaluate side-chains
  104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 66 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.159732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.138651 restraints weight = 6917.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.136427 restraints weight = 11544.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.136450 restraints weight = 12203.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6182  Z= 0.193
  Angle     :  0.664   9.336   8324  Z= 0.348
  Chirality :  0.042   0.234    948
  Planarity :  0.004   0.037    968
  Dihedral  : 12.333  79.641   1090
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 24.13 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.32), residues: 724
  helix:  2.56 (0.23), residues: 500
  sheet:  None (None), residues: 0
  loop : -2.73 (0.39), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 176 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.026   0.002   PHE A  94 
 TYR   0.008   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 152 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1972.52 seconds
wall clock time: 35 minutes 4.64 seconds (2104.64 seconds total)