Starting phenix.real_space_refine
on Fri Aug 22 17:13:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erp_28557/08_2025/8erp_28557_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erp_28557/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erp_28557/08_2025/8erp_28557_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erp_28557/08_2025/8erp_28557_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8erp_28557/08_2025/8erp_28557.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erp_28557/08_2025/8erp_28557.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.023 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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-1': 9, 'LBN:plan-2': 9, 'LBN:plan-3': 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-1': 9, 'LBN:plan-2': 9, 'LBN:plan-3': 9}
          Unresolved non-hydrogen planarities: 93
  Time building chain proxies: 1.73, per 1000 atoms: 0.29
  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: 0.62
  Conformation dependent library (CDL) restraints added in 353.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.19
  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: 1.00

  Time building geometry restraints manager: 0.80 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: 0.01
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:             0.750
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.160
  Find NCS groups from input model:        0.120
  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:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.710
-------------------------------------------------------------------------------
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 : 7.41
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (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
 ARG   0.002   0.000   ARG A 378 
 TYR   0.007   0.001   TYR A 282 
 PHE   0.015   0.002   PHE A 171 
 TRP   0.047   0.003   TRP B 176 
 HIS   0.004   0.001   HIS B 270 

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

*********************** 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  : 0.264 
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: 0.0658
  time to fit residues: 10.7797
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  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.167327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.146753 restraints weight = 6577.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.144558 restraints weight = 10829.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.143933 restraints weight = 10934.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.143144 restraints weight = 10055.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.143556 restraints weight = 8932.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6182  Z= 0.158
  Angle     :  0.652   6.231   8324  Z= 0.347
  Chirality :  0.041   0.181    948
  Planarity :  0.005   0.041    968
  Dihedral  : 16.976 115.100   1090
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.79 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.33), residues: 724
  helix:  2.13 (0.23), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.98 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.013   0.001   TYR B 243 
 PHE   0.015   0.002   PHE B 165 
 TRP   0.028   0.002   TRP A 176 
 HIS   0.005   0.002   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6182)
  covalent geometry    : angle       0.65224 ( 8324)
  hydrogen bonds       : bond        0.06697 (  406)
  hydrogen bonds       : angle       4.03685 ( 1200)

*********************** 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: 6
    poor density    : 112
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8128 (ttp) cc_final: 0.7762 (ttm)
REVERT: A  201 MET cc_start: 0.8132 (ttp) cc_final: 0.7762 (ttm)
  outliers start: 6
  outliers final: 6
  residues processed: 114
  average time/residue: 0.0791
  time to fit residues: 11.9050
Evaluate side-chains
  104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  316 HIS
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   84 TYR
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 36 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0000
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.170881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.145411 restraints weight = 6657.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.143781 restraints weight = 8879.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.144179 restraints weight = 9298.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.144373 restraints weight = 8204.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.144634 restraints weight = 7348.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6182  Z= 0.147
  Angle     :  0.626   7.275   8324  Z= 0.334
  Chirality :  0.041   0.179    948
  Planarity :  0.005   0.039    968
  Dihedral  : 14.544  98.536   1090
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.65 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.33), residues: 724
  helix:  2.39 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -2.99 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 120 
 TYR   0.012   0.001   TYR B 243 
 PHE   0.013   0.002   PHE A 165 
 TRP   0.009   0.001   TRP B  95 
 HIS   0.003   0.001   HIS B 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6182)
  covalent geometry    : angle       0.62633 ( 8324)
  hydrogen bonds       : bond        0.06258 (  406)
  hydrogen bonds       : angle       3.84595 ( 1200)

*********************** 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
  116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B  122 ASN cc_start: 0.8672 (p0) cc_final: 0.8456 (p0)
REVERT: B  201 MET cc_start: 0.8057 (ttp) cc_final: 0.7550 (ttm)
REVERT: A  122 ASN cc_start: 0.8675 (p0) cc_final: 0.8458 (p0)
REVERT: A  201 MET cc_start: 0.8052 (ttp) cc_final: 0.7548 (ttm)
  outliers start: 16
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0824
  time to fit residues: 11.8949
Evaluate side-chains
  100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  180 VAL
Chi-restraints excluded: chain B residue  188 ILE
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  180 VAL
Chi-restraints excluded: chain A residue  188 ILE
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 20 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0070
   chunk 13 optimal weight:    0.0970
   chunk 53 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8198

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

Flipped N/Q/H residues before XYZ refinement:
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.166397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 103)---------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136360 restraints weight = 6753.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.136009 restraints weight = 8303.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.138085 restraints weight = 6801.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.137961 restraints weight = 5529.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.137933 restraints weight = 5412.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2003

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= 0.151
  Angle     :  0.614   6.213   8324  Z= 0.330
  Chirality :  0.041   0.148    948
  Planarity :  0.004   0.040    968
  Dihedral  : 13.427  95.104   1090
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.24 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.33), residues: 724
  helix:  2.49 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.82 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 245 
 TYR   0.012   0.001   TYR A 282 
 PHE   0.015   0.002   PHE B 171 
 TRP   0.013   0.001   TRP B 176 
 HIS   0.004   0.001   HIS B 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6182)
  covalent geometry    : angle       0.61361 ( 8324)
  hydrogen bonds       : bond        0.06439 (  406)
  hydrogen bonds       : angle       3.84984 ( 1200)

*********************** 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
  118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B   55 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: B   56 LYS cc_start: 0.7766 (mttt) cc_final: 0.7484 (mtpt)
REVERT: B  201 MET cc_start: 0.8002 (ttp) cc_final: 0.7616 (ttm)
REVERT: A   55 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: A   56 LYS cc_start: 0.7765 (mttt) cc_final: 0.7486 (mtpt)
REVERT: A  201 MET cc_start: 0.7996 (ttp) cc_final: 0.7612 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0731
  time to fit residues: 10.7866
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  : 0.252 
-------------------------------------------------------------------------------
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 B residue  317 MET
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
Chi-restraints excluded: chain A residue  317 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.166927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.137994 restraints weight = 6766.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.137238 restraints weight = 5896.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137984 restraints weight = 6045.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.138294 restraints weight = 5512.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.138455 restraints weight = 5137.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6182  Z= 0.152
  Angle     :  0.601   6.208   8324  Z= 0.323
  Chirality :  0.040   0.147    948
  Planarity :  0.004   0.039    968
  Dihedral  : 12.738  91.648   1090
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.19 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.33), residues: 724
  helix:  2.60 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -2.89 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 119 
 TYR   0.011   0.001   TYR A 282 
 PHE   0.014   0.001   PHE B 171 
 TRP   0.016   0.001   TRP B 176 
 HIS   0.005   0.001   HIS B 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6182)
  covalent geometry    : angle       0.60108 ( 8324)
  hydrogen bonds       : bond        0.06459 (  406)
  hydrogen bonds       : angle       3.81711 ( 1200)

*********************** 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
  118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.221 
Fit side-chains
REVERT: B   55 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: B   56 LYS cc_start: 0.7843 (mttt) cc_final: 0.7554 (mtpt)
REVERT: B  201 MET cc_start: 0.7995 (ttp) cc_final: 0.7625 (ttm)
REVERT: A   55 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: A   56 LYS cc_start: 0.7846 (mttt) cc_final: 0.7557 (mtpt)
REVERT: A  201 MET cc_start: 0.7989 (ttp) cc_final: 0.7624 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0747
  time to fit residues: 10.9905
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  : 0.229 
-------------------------------------------------------------------------------
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  220 THR
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  220 THR
Chi-restraints excluded: chain A residue  229 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 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0010
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.168716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.146574 restraints weight = 6662.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.146059 restraints weight = 10118.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.144975 restraints weight = 10205.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.144202 restraints weight = 9322.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.144708 restraints weight = 7402.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2492

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= 0.141
  Angle     :  0.584   6.191   8324  Z= 0.313
  Chirality :  0.040   0.147    948
  Planarity :  0.004   0.039    968
  Dihedral  : 12.253  86.787   1090
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.33), residues: 724
  helix:  2.67 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -3.07 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.009   0.001   TYR A 282 
 PHE   0.030   0.002   PHE A  94 
 TRP   0.018   0.001   TRP B 176 
 HIS   0.005   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6182)
  covalent geometry    : angle       0.58428 ( 8324)
  hydrogen bonds       : bond        0.06069 (  406)
  hydrogen bonds       : angle       3.73347 ( 1200)

*********************** 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
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.218 
Fit side-chains
REVERT: B   56 LYS cc_start: 0.7700 (mttt) cc_final: 0.7483 (mtpt)
REVERT: B  201 MET cc_start: 0.8001 (ttp) cc_final: 0.7636 (ttm)
REVERT: A   56 LYS cc_start: 0.7702 (mttt) cc_final: 0.7482 (mtpt)
REVERT: A  201 MET cc_start: 0.8004 (ttp) cc_final: 0.7638 (ttm)
  outliers start: 24
  outliers final: 22
  residues processed: 112
  average time/residue: 0.0720
  time to fit residues: 11.0984
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  : 0.210 
-------------------------------------------------------------------------------
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  180 VAL
Chi-restraints excluded: chain B residue  188 ILE
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  180 VAL
Chi-restraints excluded: chain A residue  188 ILE
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 2 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 36 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0010
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.170933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.144545 restraints weight = 6664.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.142007 restraints weight = 8698.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.142560 restraints weight = 9192.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.142978 restraints weight = 8005.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.143191 restraints weight = 6734.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2563

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= 0.135
  Angle     :  0.591   6.178   8324  Z= 0.316
  Chirality :  0.039   0.148    948
  Planarity :  0.004   0.039    968
  Dihedral  : 11.800  84.059   1090
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.10 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.33), residues: 724
  helix:  2.72 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -3.03 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 120 
 TYR   0.007   0.001   TYR A 243 
 PHE   0.026   0.002   PHE A  94 
 TRP   0.018   0.001   TRP A 176 
 HIS   0.005   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6182)
  covalent geometry    : angle       0.59052 ( 8324)
  hydrogen bonds       : bond        0.05787 (  406)
  hydrogen bonds       : angle       3.68475 ( 1200)

*********************** 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
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B  201 MET cc_start: 0.7968 (ttp) cc_final: 0.7550 (ttm)
REVERT: A  201 MET cc_start: 0.7964 (ttp) cc_final: 0.7546 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0737
  time to fit residues: 11.3251
Evaluate side-chains
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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  188 ILE
Chi-restraints excluded: chain B residue  220 THR
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  188 ILE
Chi-restraints excluded: chain A residue  220 THR
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 0 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 46 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.160404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.129459 restraints weight = 6719.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.128728 restraints weight = 8143.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.130736 restraints weight = 7043.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.130950 restraints weight = 5903.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.130964 restraints weight = 5462.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6182  Z= 0.194
  Angle     :  0.665   6.298   8324  Z= 0.356
  Chirality :  0.042   0.164    948
  Planarity :  0.004   0.038    968
  Dihedral  : 12.255  78.868   1090
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.41 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.33), residues: 724
  helix:  2.42 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.75 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  39 
 TYR   0.017   0.001   TYR B 282 
 PHE   0.024   0.002   PHE B  94 
 TRP   0.027   0.002   TRP A 176 
 HIS   0.006   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6182)
  covalent geometry    : angle       0.66528 ( 8324)
  hydrogen bonds       : bond        0.07544 (  406)
  hydrogen bonds       : angle       3.94649 ( 1200)

*********************** 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
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.215 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8118 (ttp) cc_final: 0.7747 (ttm)
REVERT: A  201 MET cc_start: 0.8120 (ttp) cc_final: 0.7747 (ttm)
  outliers start: 20
  outliers final: 16
  residues processed: 106
  average time/residue: 0.0755
  time to fit residues: 10.8698
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  : 0.233 
-------------------------------------------------------------------------------
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  248 LEU
Chi-restraints excluded: chain B residue  316 HIS
Chi-restraints excluded: chain B residue  317 MET
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  248 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  317 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 70 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.163981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.145449 restraints weight = 6820.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.142645 restraints weight = 11355.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.142254 restraints weight = 11612.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141240 restraints weight = 10497.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.141350 restraints weight = 9689.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2848

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= 0.148
  Angle     :  0.654  10.472   8324  Z= 0.340
  Chirality :  0.041   0.175    948
  Planarity :  0.004   0.038    968
  Dihedral  : 11.771  77.025   1090
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.32), residues: 724
  helix:  2.59 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -3.07 (0.37), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.007   0.001   TYR B 297 
 PHE   0.024   0.002   PHE B  94 
 TRP   0.027   0.002   TRP A 176 
 HIS   0.004   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6182)
  covalent geometry    : angle       0.65435 ( 8324)
  hydrogen bonds       : bond        0.06306 (  406)
  hydrogen bonds       : angle       3.77113 ( 1200)

*********************** 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: 16
    poor density    : 88
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8033 (ttp) cc_final: 0.7481 (ttm)
REVERT: A  201 MET cc_start: 0.8030 (ttp) cc_final: 0.7481 (ttm)
  outliers start: 16
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0725
  time to fit residues: 9.9023
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  : 0.216 
-------------------------------------------------------------------------------
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  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  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 6 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 20 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   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 = 0.3779 r_free = 0.3779 target = 0.163216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.144745 restraints weight = 6837.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.141655 restraints weight = 11044.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.141052 restraints weight = 11502.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.139818 restraints weight = 11930.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.139978 restraints weight = 9976.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6182  Z= 0.155
  Angle     :  0.646   6.913   8324  Z= 0.338
  Chirality :  0.042   0.182    948
  Planarity :  0.004   0.038    968
  Dihedral  : 11.636  74.919   1090
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.33), residues: 724
  helix:  2.62 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.91 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 152 
 TYR   0.010   0.001   TYR B 282 
 PHE   0.024   0.002   PHE B  94 
 TRP   0.025   0.002   TRP A 176 
 HIS   0.005   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6182)
  covalent geometry    : angle       0.64645 ( 8324)
  hydrogen bonds       : bond        0.06411 (  406)
  hydrogen bonds       : angle       3.77679 ( 1200)

********************** 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
  98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8058 (ttp) cc_final: 0.7722 (ttm)
REVERT: A  201 MET cc_start: 0.8054 (ttp) cc_final: 0.7714 (ttm)
  outliers start: 14
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0762
  time to fit residues: 9.9163
Evaluate side-chains
  98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  220 THR
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  166 VAL
Chi-restraints excluded: chain A residue  220 THR
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 13 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0670
   chunk 57 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.166724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.145081 restraints weight = 6828.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.142766 restraints weight = 10868.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.143018 restraints weight = 11850.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.143161 restraints weight = 9103.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.143217 restraints weight = 8328.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2946

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= 0.143
  Angle     :  0.627   7.966   8324  Z= 0.328
  Chirality :  0.041   0.182    948
  Planarity :  0.005   0.040    968
  Dihedral  : 11.116  73.048   1090
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.27 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.33), residues: 724
  helix:  2.65 (0.23), residues: 500
  sheet:  None (None), residues: 0
  loop : -3.04 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.008   0.001   TYR B 282 
 PHE   0.021   0.002   PHE B  94 
 TRP   0.024   0.001   TRP B 176 
 HIS   0.005   0.001   HIS A 270 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6182)
  covalent geometry    : angle       0.62687 ( 8324)
  hydrogen bonds       : bond        0.05866 (  406)
  hydrogen bonds       : angle       3.69793 ( 1200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1055.71 seconds
wall clock time: 19 minutes 0.43 seconds (1140.43 seconds total)