Starting phenix.real_space_refine
on Sat May 10 13:29:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erp_28557/05_2025/8erp_28557_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erp_28557/05_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_28557/05_2025/8erp_28557.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erp_28557/05_2025/8erp_28557.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erp_28557/05_2025/8erp_28557_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erp_28557/05_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-5687/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: 3.97, per 1000 atoms: 0.66
  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: 1.52
  Conformation dependent library (CDL) restraints added in 778.1 milliseconds
  

  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: 0.49
  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: 1.42

  Time building geometry restraints manager: 1.76 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:             0.390
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     16.670
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.110
-------------------------------------------------------------------------------
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= 0.237
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14403 (  406)
  hydrogen bonds       : angle       5.64852 ( 1200)
  covalent geometry    : bond        0.00448 ( 6182)
  covalent geometry    : angle       0.85501 ( 8324)

*********************** 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  : 0.700 
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: 0.1476
  time to fit residues: 23.8550
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  : 0.603 
-------------------------------------------------------------------------------
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 = 0.154338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.129416 restraints weight = 6765.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.127299 restraints weight = 11547.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.126761 restraints weight = 10882.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1825

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= 0.225
  Angle     :  0.747   7.080   8324  Z= 0.396
  Chirality :  0.045   0.188    948
  Planarity :  0.005   0.043    968
  Dihedral  : 16.564 116.103   1090
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.08
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08484 (  406)
  hydrogen bonds       : angle       4.29800 ( 1200)
  covalent geometry    : bond        0.00513 ( 6182)
  covalent geometry    : angle       0.74718 ( 8324)

*********************** 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  : 0.654 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8232 (ttp) cc_final: 0.7762 (ttm)
REVERT: A  201 MET cc_start: 0.8231 (ttp) cc_final: 0.7766 (ttm)
  outliers start: 14
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1632
  time to fit residues: 24.5861
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  : 0.643 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8760

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.164426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.139425 restraints weight = 6657.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137691 restraints weight = 9884.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.138442 restraints weight = 10039.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2056

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= 0.161
  Angle     :  0.650   7.845   8324  Z= 0.346
  Chirality :  0.041   0.185    948
  Planarity :  0.005   0.041    968
  Dihedral  : 14.898  99.936   1090
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.56 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.33), residues: 724
  helix:  2.24 (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   0.011   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.014   0.002   PHE A 171 
 TYR   0.010   0.001   TYR A 282 
 ARG   0.002   0.000   ARG B 245 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06941 (  406)
  hydrogen bonds       : angle       3.97533 ( 1200)
  covalent geometry    : bond        0.00336 ( 6182)
  covalent geometry    : angle       0.65044 ( 8324)

*********************** 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
  122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.655 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8110 (ttp) cc_final: 0.7495 (ttm)
REVERT: A  201 MET cc_start: 0.8110 (ttp) cc_final: 0.7495 (ttm)
  outliers start: 20
  outliers final: 14
  residues processed: 114
  average time/residue: 0.1765
  time to fit residues: 26.6572
Evaluate side-chains
  104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 43 optimal weight:    0.2980
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.157385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.127814 restraints weight = 6910.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.126506 restraints weight = 7054.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126734 restraints weight = 6645.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6182  Z= 0.196
  Angle     :  0.676   6.520   8324  Z= 0.362
  Chirality :  0.043   0.194    948
  Planarity :  0.005   0.040    968
  Dihedral  : 14.327  97.002   1090
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.46 %
    Favored  : 79.05 %
  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:  1.17 (0.33), residues: 724
  helix:  2.15 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.69 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.017   0.002   PHE B 171 
 TYR   0.015   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07715 (  406)
  hydrogen bonds       : angle       4.06542 ( 1200)
  covalent geometry    : bond        0.00441 ( 6182)
  covalent geometry    : angle       0.67574 ( 8324)

*********************** 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
  114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.645 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8082 (ttp) cc_final: 0.7462 (ttm)
REVERT: B  292 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6919 (mt0)
REVERT: A  201 MET cc_start: 0.8080 (ttp) cc_final: 0.7464 (ttm)
REVERT: A  292 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.6913 (mt0)
  outliers start: 22
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1718
  time to fit residues: 23.9264
Evaluate side-chains
  100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
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  248 LEU
Chi-restraints excluded: chain B residue  292 GLN
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  248 LEU
Chi-restraints excluded: chain A residue  292 GLN
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:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.164063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.143707 restraints weight = 6689.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142116 restraints weight = 9410.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142181 restraints weight = 9757.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2509

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= 0.148
  Angle     :  0.633   8.571   8324  Z= 0.334
  Chirality :  0.041   0.202    948
  Planarity :  0.004   0.039    968
  Dihedral  : 13.485  91.296   1090
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.37 %
    Favored  : 77.14 %
  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:  1.37 (0.33), residues: 724
  helix:  2.51 (0.23), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.94 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 213 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.013   0.001   PHE B 171 
 TYR   0.008   0.001   TYR A 297 
 ARG   0.001   0.000   ARG A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06343 (  406)
  hydrogen bonds       : angle       3.79571 ( 1200)
  covalent geometry    : bond        0.00300 ( 6182)
  covalent geometry    : angle       0.63340 ( 8324)

*********************** 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
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.541 
Fit side-chains
REVERT: B   55 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7521 (tm-30)
REVERT: B  201 MET cc_start: 0.8028 (ttp) cc_final: 0.7477 (ttm)
REVERT: A   55 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7513 (tm-30)
REVERT: A  201 MET cc_start: 0.8024 (ttp) cc_final: 0.7475 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1841
  time to fit residues: 27.3207
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   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 = 0.3707 r_free = 0.3707 target = 0.155493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.130108 restraints weight = 6697.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.128590 restraints weight = 10241.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.129011 restraints weight = 11029.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6182  Z= 0.212
  Angle     :  0.686   6.876   8324  Z= 0.364
  Chirality :  0.043   0.187    948
  Planarity :  0.004   0.040    968
  Dihedral  : 13.628  87.647   1090
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.22 %
    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:  1.27 (0.33), residues: 724
  helix:  2.27 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.76 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 176 
 HIS   0.005   0.001   HIS A 270 
 PHE   0.016   0.002   PHE B 171 
 TYR   0.017   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07875 (  406)
  hydrogen bonds       : angle       4.03722 ( 1200)
  covalent geometry    : bond        0.00481 ( 6182)
  covalent geometry    : angle       0.68638 ( 8324)

*********************** 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
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.645 
Fit side-chains
REVERT: B   55 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: B  131 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7980 (m-10)
REVERT: B  201 MET cc_start: 0.8212 (ttp) cc_final: 0.7569 (ttm)
REVERT: A   55 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7621 (tm-30)
REVERT: A  131 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7981 (m-10)
REVERT: A  201 MET cc_start: 0.8214 (ttp) cc_final: 0.7569 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 100
  average time/residue: 0.1680
  time to fit residues: 22.5634
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  : 0.639 
-------------------------------------------------------------------------------
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  178 THR
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  131 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  178 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   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:    0.0040
   chunk 58 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8994

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.157606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.133602 restraints weight = 6758.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.131571 restraints weight = 10880.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.132361 restraints weight = 10669.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6182  Z= 0.158
  Angle     :  0.640   8.948   8324  Z= 0.338
  Chirality :  0.042   0.232    948
  Planarity :  0.004   0.039    968
  Dihedral  : 13.119  83.595   1090
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 22.54 %
    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 (0.33), residues: 724
  helix:  2.45 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.73 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.015   0.001   PHE B 171 
 TYR   0.009   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06794 (  406)
  hydrogen bonds       : angle       3.84986 ( 1200)
  covalent geometry    : bond        0.00329 ( 6182)
  covalent geometry    : angle       0.64037 ( 8324)

*********************** 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: 24
    poor density    : 86
  time to evaluate  : 0.667 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8100 (ttp) cc_final: 0.7451 (ttm)
REVERT: A  201 MET cc_start: 0.8094 (ttp) cc_final: 0.7451 (ttm)
  outliers start: 24
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1596
  time to fit residues: 22.9721
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
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  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  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:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.157905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.134914 restraints weight = 6749.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.133771 restraints weight = 11097.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.132182 restraints weight = 11478.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6182  Z= 0.181
  Angle     :  0.676   8.346   8324  Z= 0.357
  Chirality :  0.043   0.230    948
  Planarity :  0.004   0.039    968
  Dihedral  : 12.963  79.780   1090
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.86 %
    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:  1.42 (0.33), residues: 724
  helix:  2.42 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.81 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  95 
 HIS   0.005   0.001   HIS A 270 
 PHE   0.015   0.002   PHE A 171 
 TYR   0.014   0.001   TYR B 282 
 ARG   0.001   0.000   ARG B 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07198 (  406)
  hydrogen bonds       : angle       3.91091 ( 1200)
  covalent geometry    : bond        0.00400 ( 6182)
  covalent geometry    : angle       0.67627 ( 8324)

*********************** 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
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.639 
Fit side-chains
REVERT: B  131 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7976 (m-10)
REVERT: B  201 MET cc_start: 0.8143 (ttp) cc_final: 0.7728 (ttm)
REVERT: A  131 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7981 (m-10)
REVERT: A  201 MET cc_start: 0.8145 (ttp) cc_final: 0.7727 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 104
  average time/residue: 0.1596
  time to fit residues: 22.4855
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
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  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  131 PHE
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:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.159145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131065 restraints weight = 6717.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.129194 restraints weight = 7044.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.129641 restraints weight = 7269.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6182  Z= 0.159
  Angle     :  0.653   8.104   8324  Z= 0.345
  Chirality :  0.042   0.219    948
  Planarity :  0.004   0.038    968
  Dihedral  : 12.527  77.053   1090
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.86 %
    Favored  : 73.97 %
  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:  1.54 (0.32), residues: 724
  helix:  2.49 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.78 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  95 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.014   0.001   PHE A 171 
 TYR   0.010   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06717 (  406)
  hydrogen bonds       : angle       3.83192 ( 1200)
  covalent geometry    : bond        0.00335 ( 6182)
  covalent geometry    : angle       0.65311 ( 8324)

*********************** 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
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.651 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8049 (ttp) cc_final: 0.7656 (ttm)
REVERT: A  201 MET cc_start: 0.8042 (ttp) cc_final: 0.7652 (ttm)
  outliers start: 20
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1578
  time to fit residues: 21.7850
Evaluate side-chains
  100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0970
   chunk 36 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.161927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.141674 restraints weight = 6847.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.138833 restraints weight = 11003.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.138279 restraints weight = 11475.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6182  Z= 0.151
  Angle     :  0.649   7.790   8324  Z= 0.341
  Chirality :  0.041   0.216    948
  Planarity :  0.004   0.038    968
  Dihedral  : 12.111  74.684   1090
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  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:  1.61 (0.33), residues: 724
  helix:  2.58 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.82 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 270 
 PHE   0.014   0.001   PHE A 171 
 TYR   0.008   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06394 (  406)
  hydrogen bonds       : angle       3.78494 ( 1200)
  covalent geometry    : bond        0.00307 ( 6182)
  covalent geometry    : angle       0.64912 ( 8324)

********************** 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
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.599 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8043 (ttp) cc_final: 0.7664 (ttm)
REVERT: A  201 MET cc_start: 0.8043 (ttp) cc_final: 0.7662 (ttm)
  outliers start: 18
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1775
  time to fit residues: 24.7201
Evaluate side-chains
  104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.161802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.142178 restraints weight = 6920.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.140105 restraints weight = 12716.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.140134 restraints weight = 12063.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6182  Z= 0.152
  Angle     :  0.651   7.725   8324  Z= 0.342
  Chirality :  0.041   0.214    948
  Planarity :  0.004   0.038    968
  Dihedral  : 11.899  76.690   1090
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.81 %
    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:  1.62 (0.33), residues: 724
  helix:  2.62 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.87 (0.39), residues: 222

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   0.013   0.001   PHE B 171 
 TYR   0.009   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06376 (  406)
  hydrogen bonds       : angle       3.78337 ( 1200)
  covalent geometry    : bond        0.00315 ( 6182)
  covalent geometry    : angle       0.65113 ( 8324)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1850.64 seconds
wall clock time: 33 minutes 12.34 seconds (1992.34 seconds total)