Starting phenix.real_space_refine
on Fri Jul 25 15:28:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbi_61315/07_2025/9jbi_61315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbi_61315/07_2025/9jbi_61315.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbi_61315/07_2025/9jbi_61315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbi_61315/07_2025/9jbi_61315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbi_61315/07_2025/9jbi_61315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbi_61315/07_2025/9jbi_61315.cif"
  }
  resolution = 4.49
  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=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4920      2.51       5
     N    1188      2.21       5
     O    1324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7472
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 3736
          Classifications: {'peptide': 517}
          Incomplete info: {'truncation_to_alanine': 77}
          Link IDs: {'PTRANS': 19, 'TRANS': 497}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 337
          Unresolved non-hydrogen angles: 431
          Unresolved non-hydrogen dihedrals: 298
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 15, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 169
    Chain: "B"
      Number of atoms: 3736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 3736
          Classifications: {'peptide': 517}
          Incomplete info: {'truncation_to_alanine': 77}
          Link IDs: {'PTRANS': 19, 'TRANS': 497}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 337
          Unresolved non-hydrogen angles: 431
          Unresolved non-hydrogen dihedrals: 298
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 15, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 169
  Time building chain proxies: 7.39, per 1000 atoms: 0.99
  Number of scatterers: 7472
  At special positions: 0
  Unit cell: (70.296, 175.336, 66.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1324      8.00
     N    1188      7.00
     C    4920      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: 1.96
  Conformation dependent library (CDL) restraints added in 991.3 milliseconds
  

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      84.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 63
      Proline residue:  A  44  - end of helix
    Processing helix  chain 'A' and resid 66 through 79
    Processing helix  chain 'A' and resid 80 through 93
    Processing helix  chain 'A' and resid 99 through 125
    Processing helix  chain 'A' and resid 126 through 134
      removed outlier: 3.936A  pdb=" N   PHE A 131 " --> pdb=" O   PRO A 127 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   SER A 132 " --> pdb=" O   ASP A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 141
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 164 through 180
      removed outlier: 4.459A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
    Processing helix  chain 'A' and resid 180 through 195
      removed outlier: 3.586A  pdb=" N   GLY A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 233
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 4.452A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
    Processing helix  chain 'A' and resid 274 through 288
      removed outlier: 3.856A  pdb=" N   VAL A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 302
      removed outlier: 3.502A  pdb=" N   GLU A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 3.958A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 365
      removed outlier: 3.527A  pdb=" N   ILE A 343 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A 351 " --> pdb=" O   MET A 347 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 373 through 404
    Processing helix  chain 'A' and resid 410 through 430
      removed outlier: 4.067A  pdb=" N   LEU A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 472
      removed outlier: 3.865A  pdb=" N   LEU A 450 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR A 458 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 491
      removed outlier: 3.802A  pdb=" N   ILE A 491 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 487 through 491'
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 519 through 537
    Processing helix  chain 'A' and resid 655 through 682
      removed outlier: 3.771A  pdb=" N   GLY A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 701
    Processing helix  chain 'A' and resid 702 through 710
      removed outlier: 3.588A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 63
      Proline residue:  B  44  - end of helix
    Processing helix  chain 'B' and resid 66 through 79
    Processing helix  chain 'B' and resid 80 through 93
    Processing helix  chain 'B' and resid 99 through 125
    Processing helix  chain 'B' and resid 126 through 134
      removed outlier: 3.935A  pdb=" N   PHE B 131 " --> pdb=" O   PRO B 127 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   SER B 132 " --> pdb=" O   ASP B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 141
    Processing helix  chain 'B' and resid 149 through 159
    Processing helix  chain 'B' and resid 164 through 180
      removed outlier: 4.458A  pdb=" N   TYR B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
    Processing helix  chain 'B' and resid 180 through 195
      removed outlier: 3.585A  pdb=" N   GLY B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 233
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 4.452A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 263
    Processing helix  chain 'B' and resid 274 through 288
      removed outlier: 3.856A  pdb=" N   VAL B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 302
      removed outlier: 3.502A  pdb=" N   GLU B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 320
    Processing helix  chain 'B' and resid 326 through 337
      removed outlier: 3.958A  pdb=" N   ALA B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 365
      removed outlier: 3.527A  pdb=" N   ILE B 343 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR B 351 " --> pdb=" O   MET B 347 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 373 through 404
    Processing helix  chain 'B' and resid 410 through 430
      removed outlier: 4.067A  pdb=" N   LEU B 414 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 472
      removed outlier: 3.865A  pdb=" N   LEU B 450 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR B 458 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 491
      removed outlier: 3.802A  pdb=" N   ILE B 491 " --> pdb=" O   SER B 487 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 487 through 491'
    Processing helix  chain 'B' and resid 492 through 503
    Processing helix  chain 'B' and resid 519 through 537
    Processing helix  chain 'B' and resid 655 through 682
      removed outlier: 3.771A  pdb=" N   GLY B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 701
    Processing helix  chain 'B' and resid 702 through 710
      removed outlier: 3.587A  pdb=" N   ILE B 706 " --> pdb=" O   GLY B 702 " (cutoff:3.500A)

    604 hydrogen bonds defined for protein.
    1800 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: 2.25

  Time building geometry restraints manager: 2.31 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: 1182
        1.32 -     1.44: 1962
        1.44 -     1.57: 4410
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 7614
  Sorted by residual:
  bond pdb=" C   ALA A 173 "
       pdb=" O   ALA A 173 "
    ideal  model  delta    sigma   weight residual
    1.238  1.199  0.039 1.28e-02 6.10e+03 9.23e+00
  bond pdb=" C   ALA B 173 "
       pdb=" O   ALA B 173 "
    ideal  model  delta    sigma   weight residual
    1.238  1.199  0.039 1.28e-02 6.10e+03 9.21e+00
  bond pdb=" N   ILE B 532 "
       pdb=" CA  ILE B 532 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.037 1.30e-02 5.92e+03 8.30e+00
  bond pdb=" N   ILE A 706 "
       pdb=" CA  ILE A 706 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.14e+00
  bond pdb=" N   ILE B 706 "
       pdb=" CA  ILE B 706 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  ... (remaining 7609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 8727
        1.34 -     2.68: 1218
        2.68 -     4.02: 328
        4.02 -     5.36: 89
        5.36 -     6.70: 26
  Bond angle restraints: 10388
  Sorted by residual:
  angle pdb=" N   ASN A 315 "
        pdb=" CA  ASN A 315 "
        pdb=" C   ASN A 315 "
      ideal   model   delta    sigma   weight residual
     111.36  105.79    5.57 1.09e+00 8.42e-01 2.61e+01
  angle pdb=" N   ASN B 315 "
        pdb=" CA  ASN B 315 "
        pdb=" C   ASN B 315 "
      ideal   model   delta    sigma   weight residual
     111.36  105.79    5.57 1.09e+00 8.42e-01 2.61e+01
  angle pdb=" N   ALA B 134 "
        pdb=" CA  ALA B 134 "
        pdb=" C   ALA B 134 "
      ideal   model   delta    sigma   weight residual
     112.92  106.83    6.09 1.23e+00 6.61e-01 2.45e+01
  angle pdb=" N   ALA A 134 "
        pdb=" CA  ALA A 134 "
        pdb=" C   ALA A 134 "
      ideal   model   delta    sigma   weight residual
     112.92  106.86    6.06 1.23e+00 6.61e-01 2.42e+01
  angle pdb=" N   ILE A 522 "
        pdb=" CA  ILE A 522 "
        pdb=" C   ILE A 522 "
      ideal   model   delta    sigma   weight residual
     110.74  106.54    4.20 9.10e-01 1.21e+00 2.13e+01
  ... (remaining 10383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 4076
       17.44 -    34.87: 292
       34.87 -    52.31: 52
       52.31 -    69.74: 16
       69.74 -    87.18: 6
  Dihedral angle restraints: 4442
    sinusoidal: 1460
      harmonic: 2982
  Sorted by residual:
  dihedral pdb=" CA  MET B 179 "
           pdb=" C   MET B 179 "
           pdb=" N   LEU B 180 "
           pdb=" CA  LEU B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  MET A 179 "
           pdb=" C   MET A 179 "
           pdb=" N   LEU A 180 "
           pdb=" CA  LEU A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.90  -19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ILE B 431 "
           pdb=" C   ILE B 431 "
           pdb=" N   TRP B 432 "
           pdb=" CA  TRP B 432 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.99  -19.01     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 4439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 792
       0.044 -    0.088: 317
       0.088 -    0.133: 123
       0.133 -    0.177: 40
       0.177 -    0.221: 26
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" CA  ILE B 534 "
            pdb=" N   ILE B 534 "
            pdb=" C   ILE B 534 "
            pdb=" CB  ILE B 534 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  ILE A 534 "
            pdb=" N   ILE A 534 "
            pdb=" C   ILE A 534 "
            pdb=" CB  ILE A 534 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE A 392 "
            pdb=" N   ILE A 392 "
            pdb=" C   ILE A 392 "
            pdb=" CB  ILE A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1295 not shown)

  Planarity restraints: 1274
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 149 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.51e+00
        pdb=" C   LEU B 149 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   LEU B 149 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY B 150 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 149 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.47e+00
        pdb=" C   LEU A 149 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LEU A 149 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLY A 150 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  77 "    0.010 2.00e-02 2.50e+03   2.08e-02 4.34e+00
        pdb=" C   VAL A  77 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A  77 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER A  78 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1271 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1117
        2.76 -     3.29: 8965
        3.29 -     3.83: 12649
        3.83 -     4.36: 15552
        4.36 -     4.90: 22939
  Nonbonded interactions: 61222
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 384 "
            pdb=" OG  SER B 387 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   PHE A 384 "
            pdb=" OG  SER A 387 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   MET A 347 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   MET B 347 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ALA A 173 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.327 3.040
  ... (remaining 61217 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.340
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
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      :  0.006   0.050   7614  Z= 0.438
  Angle     :  1.114   6.704  10388  Z= 0.785
  Chirality :  0.062   0.221   1298
  Planarity :  0.006   0.050   1274
  Dihedral  : 13.693  87.177   2506
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  2.70 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.25), residues: 994
  helix: -1.14 (0.17), residues: 800
  sheet:  None (None), residues: 0
  loop : -2.51 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 193 
 HIS   0.003   0.001   HIS B 412 
 PHE   0.014   0.002   PHE B 114 
 TYR   0.030   0.003   TYR A 451 
 ARG   0.001   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18272 (  604)
  hydrogen bonds       : angle       7.80076 ( 1800)
  covalent geometry    : bond        0.00627 ( 7614)
  covalent geometry    : angle       1.11447 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.9065 (pt0) cc_final: 0.8822 (pp20)
REVERT: A   75 ASN cc_start: 0.9669 (m-40) cc_final: 0.9458 (m-40)
REVERT: A  185 PHE cc_start: 0.8481 (m-10) cc_final: 0.7487 (m-80)
REVERT: A  188 CYS cc_start: 0.9343 (t) cc_final: 0.9063 (t)
REVERT: A  234 ASP cc_start: 0.8992 (m-30) cc_final: 0.8774 (m-30)
REVERT: A  264 MET cc_start: 0.8638 (mmp) cc_final: 0.8410 (mmp)
REVERT: A  295 ARG cc_start: 0.8018 (ttt180) cc_final: 0.6983 (tmt170)
REVERT: A  451 TYR cc_start: 0.7567 (t80) cc_final: 0.7347 (t80)
REVERT: B   46 LEU cc_start: 0.9299 (mt) cc_final: 0.9013 (mt)
REVERT: B   48 GLU cc_start: 0.9075 (pt0) cc_final: 0.8834 (pp20)
REVERT: B  188 CYS cc_start: 0.9421 (t) cc_final: 0.9172 (t)
REVERT: B  234 ASP cc_start: 0.9019 (m-30) cc_final: 0.8792 (m-30)
REVERT: B  264 MET cc_start: 0.8710 (mmp) cc_final: 0.8400 (mmp)
REVERT: B  295 ARG cc_start: 0.7964 (ttt180) cc_final: 0.6951 (tmt170)
REVERT: B  451 TYR cc_start: 0.7727 (t80) cc_final: 0.7488 (t80)
REVERT: B  521 MET cc_start: 0.8525 (pmm) cc_final: 0.8007 (pmm)
  outliers start: 20
  outliers final: 3
  residues processed: 204
  average time/residue: 0.1377
  time to fit residues: 41.2710
Evaluate side-chains
  160 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 157
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 92 optimal weight:    6.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 191 GLN
A 315 ASN
A 654 GLN
A 683 GLN
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 GLN
B 315 ASN
** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.110165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.085575 restraints weight = 28733.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.087610 restraints weight = 22713.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.089011 restraints weight = 18926.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7614  Z= 0.148
  Angle     :  0.658   7.057  10388  Z= 0.336
  Chirality :  0.040   0.132   1298
  Planarity :  0.005   0.055   1274
  Dihedral  :  4.750  20.939   1058
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  2.97 %
    Favored  : 96.49 %
  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: -0.35 (0.26), residues: 994
  helix:  0.16 (0.18), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.50 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 193 
 HIS   0.001   0.001   HIS B 412 
 PHE   0.021   0.002   PHE A 114 
 TYR   0.011   0.001   TYR B 451 
 ARG   0.001   0.000   ARG B 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  604)
  hydrogen bonds       : angle       5.29344 ( 1800)
  covalent geometry    : bond        0.00303 ( 7614)
  covalent geometry    : angle       0.65799 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 186
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9118 (mm) cc_final: 0.8899 (mm)
REVERT: A   75 ASN cc_start: 0.9654 (m-40) cc_final: 0.9445 (m-40)
REVERT: A  165 TYR cc_start: 0.9180 (m-10) cc_final: 0.8905 (m-80)
REVERT: A  234 ASP cc_start: 0.9025 (m-30) cc_final: 0.8808 (m-30)
REVERT: A  295 ARG cc_start: 0.8202 (ttt180) cc_final: 0.7202 (tmt170)
REVERT: B   46 LEU cc_start: 0.9349 (mt) cc_final: 0.9108 (mt)
REVERT: B   54 LEU cc_start: 0.9096 (mm) cc_final: 0.8885 (mm)
REVERT: B   75 ASN cc_start: 0.9676 (m-40) cc_final: 0.9464 (m-40)
REVERT: B  151 TYR cc_start: 0.8685 (t80) cc_final: 0.8117 (t80)
REVERT: B  179 MET cc_start: 0.6145 (mmt) cc_final: 0.5934 (mmt)
REVERT: B  188 CYS cc_start: 0.9309 (t) cc_final: 0.9039 (t)
REVERT: B  234 ASP cc_start: 0.9087 (m-30) cc_final: 0.8871 (m-30)
REVERT: B  264 MET cc_start: 0.8768 (mmp) cc_final: 0.8537 (mmp)
REVERT: B  295 ARG cc_start: 0.8115 (ttt180) cc_final: 0.7128 (tmt170)
REVERT: B  358 MET cc_start: 0.9051 (ptp) cc_final: 0.8823 (ptp)
REVERT: B  521 MET cc_start: 0.8462 (pmm) cc_final: 0.8025 (pmm)
  outliers start: 4
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1324
  time to fit residues: 36.9509
Evaluate side-chains
  148 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 96 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0570
   chunk 9 optimal weight:    0.0670
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.111799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.086437 restraints weight = 28496.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.088468 restraints weight = 23082.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.089890 restraints weight = 19456.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7614  Z= 0.128
  Angle     :  0.611   6.583  10388  Z= 0.308
  Chirality :  0.039   0.131   1298
  Planarity :  0.005   0.058   1274
  Dihedral  :  4.451  18.026   1058
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.05 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.27), residues: 994
  helix:  0.73 (0.18), residues: 808
  sheet:  None (None), residues: 0
  loop : -1.17 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 679 
 HIS   0.001   0.000   HIS A 310 
 PHE   0.017   0.001   PHE A 384 
 TYR   0.014   0.001   TYR B 168 
 ARG   0.000   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04165 (  604)
  hydrogen bonds       : angle       4.91655 ( 1800)
  covalent geometry    : bond        0.00271 ( 7614)
  covalent geometry    : angle       0.61097 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 174
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9023 (mm) cc_final: 0.8799 (mm)
REVERT: A   75 ASN cc_start: 0.9635 (m-40) cc_final: 0.9427 (m-40)
REVERT: A   85 LEU cc_start: 0.9572 (pp) cc_final: 0.9337 (pp)
REVERT: A  234 ASP cc_start: 0.8939 (m-30) cc_final: 0.8735 (m-30)
REVERT: A  264 MET cc_start: 0.8730 (mmp) cc_final: 0.8490 (mmp)
REVERT: A  295 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7140 (tmt170)
REVERT: B   46 LEU cc_start: 0.9274 (mt) cc_final: 0.9057 (mt)
REVERT: B   54 LEU cc_start: 0.9008 (mm) cc_final: 0.8798 (mm)
REVERT: B   75 ASN cc_start: 0.9657 (m-40) cc_final: 0.9400 (m-40)
REVERT: B   85 LEU cc_start: 0.9549 (pp) cc_final: 0.9290 (pp)
REVERT: B  151 TYR cc_start: 0.8587 (t80) cc_final: 0.8184 (t80)
REVERT: B  178 MET cc_start: 0.5439 (tmm) cc_final: 0.4974 (ppp)
REVERT: B  234 ASP cc_start: 0.9001 (m-30) cc_final: 0.8778 (m-30)
REVERT: B  264 MET cc_start: 0.8851 (mmp) cc_final: 0.8553 (mmp)
REVERT: B  295 ARG cc_start: 0.8188 (ttt180) cc_final: 0.7163 (tmt170)
  outliers start: 2
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1394
  time to fit residues: 36.0902
Evaluate side-chains
  148 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 95 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    0.3980
   chunk 22 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 654 GLN
B 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.111344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.086707 restraints weight = 28509.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.088524 restraints weight = 23195.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.089992 restraints weight = 19806.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7614  Z= 0.127
  Angle     :  0.601   6.629  10388  Z= 0.300
  Chirality :  0.039   0.129   1298
  Planarity :  0.005   0.062   1274
  Dihedral  :  4.282  16.410   1058
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.57 %
    Favored  : 97.16 %
  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:  0.90 (0.27), residues: 994
  helix:  1.05 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop : -1.21 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 193 
 HIS   0.001   0.000   HIS A 310 
 PHE   0.015   0.001   PHE A 114 
 TYR   0.016   0.001   TYR A 320 
 ARG   0.001   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  604)
  hydrogen bonds       : angle       4.71521 ( 1800)
  covalent geometry    : bond        0.00269 ( 7614)
  covalent geometry    : angle       0.60143 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 170
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8991 (mm) cc_final: 0.8774 (mm)
REVERT: A   75 ASN cc_start: 0.9605 (m-40) cc_final: 0.9389 (m-40)
REVERT: A   85 LEU cc_start: 0.9593 (pp) cc_final: 0.9360 (pp)
REVERT: A  179 MET cc_start: 0.5678 (mmt) cc_final: 0.5472 (mmt)
REVERT: A  264 MET cc_start: 0.8712 (mmp) cc_final: 0.8460 (mmp)
REVERT: A  295 ARG cc_start: 0.8311 (ttt180) cc_final: 0.7416 (tmt170)
REVERT: A  320 TYR cc_start: 0.8169 (m-80) cc_final: 0.7949 (m-80)
REVERT: B   85 LEU cc_start: 0.9575 (pp) cc_final: 0.9339 (pp)
REVERT: B  151 TYR cc_start: 0.8562 (t80) cc_final: 0.8154 (t80)
REVERT: B  179 MET cc_start: 0.6635 (tpp) cc_final: 0.6204 (tpp)
REVERT: B  234 ASP cc_start: 0.8990 (m-30) cc_final: 0.8785 (m-30)
REVERT: B  264 MET cc_start: 0.8848 (mmp) cc_final: 0.8556 (mmp)
REVERT: B  295 ARG cc_start: 0.8325 (ttt180) cc_final: 0.7445 (tmt170)
REVERT: B  429 MET cc_start: 0.9128 (mmp) cc_final: 0.8917 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1684
  time to fit residues: 43.7551
Evaluate side-chains
  149 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 55 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:
A 654 GLN
B 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.110229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.085613 restraints weight = 27881.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.087197 restraints weight = 22804.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.088762 restraints weight = 19808.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7614  Z= 0.138
  Angle     :  0.621   6.920  10388  Z= 0.307
  Chirality :  0.039   0.125   1298
  Planarity :  0.005   0.062   1274
  Dihedral  :  4.257  18.690   1058
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.89 %
    Favored  : 97.84 %
  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:  1.00 (0.27), residues: 994
  helix:  1.11 (0.19), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.18 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 193 
 HIS   0.000   0.000   HIS A 412 
 PHE   0.018   0.001   PHE A 114 
 TYR   0.021   0.001   TYR A 458 
 ARG   0.001   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  604)
  hydrogen bonds       : angle       4.63739 ( 1800)
  covalent geometry    : bond        0.00286 ( 7614)
  covalent geometry    : angle       0.62070 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9603 (pp) cc_final: 0.9387 (pp)
REVERT: A  234 ASP cc_start: 0.8872 (m-30) cc_final: 0.8645 (m-30)
REVERT: A  264 MET cc_start: 0.8774 (mmp) cc_final: 0.8486 (mmp)
REVERT: A  295 ARG cc_start: 0.8308 (ttt180) cc_final: 0.7385 (tmt170)
REVERT: A  320 TYR cc_start: 0.8176 (m-80) cc_final: 0.7934 (m-80)
REVERT: A  429 MET cc_start: 0.9251 (mmp) cc_final: 0.9034 (mmm)
REVERT: A  521 MET cc_start: 0.8206 (pmm) cc_final: 0.7995 (pmm)
REVERT: B  151 TYR cc_start: 0.8504 (t80) cc_final: 0.8131 (t80)
REVERT: B  158 TYR cc_start: 0.8886 (m-80) cc_final: 0.8196 (m-80)
REVERT: B  234 ASP cc_start: 0.8882 (m-30) cc_final: 0.8655 (m-30)
REVERT: B  264 MET cc_start: 0.8850 (mmp) cc_final: 0.8545 (mmp)
REVERT: B  295 ARG cc_start: 0.8276 (ttt180) cc_final: 0.7369 (tmt170)
REVERT: B  358 MET cc_start: 0.8995 (ptp) cc_final: 0.8743 (ptp)
REVERT: B  429 MET cc_start: 0.9195 (mmp) cc_final: 0.8974 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2313
  time to fit residues: 57.7064
Evaluate side-chains
  145 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 35 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 654 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.110142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.085679 restraints weight = 28556.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.087406 restraints weight = 23780.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.088676 restraints weight = 20525.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7614  Z= 0.145
  Angle     :  0.618   6.798  10388  Z= 0.310
  Chirality :  0.040   0.153   1298
  Planarity :  0.005   0.062   1274
  Dihedral  :  4.207  18.307   1058
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  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:  1.03 (0.28), residues: 994
  helix:  1.13 (0.19), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.15 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 193 
 HIS   0.001   0.000   HIS B 412 
 PHE   0.020   0.001   PHE B 384 
 TYR   0.015   0.001   TYR B 158 
 ARG   0.001   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  604)
  hydrogen bonds       : angle       4.52514 ( 1800)
  covalent geometry    : bond        0.00308 ( 7614)
  covalent geometry    : angle       0.61812 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9598 (pp) cc_final: 0.9392 (pp)
REVERT: A  234 ASP cc_start: 0.8879 (m-30) cc_final: 0.8656 (m-30)
REVERT: A  264 MET cc_start: 0.8839 (mmp) cc_final: 0.8535 (mmp)
REVERT: A  295 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7333 (tmt170)
REVERT: B  158 TYR cc_start: 0.8905 (m-80) cc_final: 0.8158 (m-80)
REVERT: B  234 ASP cc_start: 0.8899 (m-30) cc_final: 0.8680 (m-30)
REVERT: B  264 MET cc_start: 0.8880 (mmp) cc_final: 0.8571 (mmp)
REVERT: B  295 ARG cc_start: 0.8287 (ttt180) cc_final: 0.7395 (tmt170)
REVERT: B  358 MET cc_start: 0.8893 (ptp) cc_final: 0.8669 (ptp)
REVERT: B  429 MET cc_start: 0.9212 (mmp) cc_final: 0.8989 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2375
  time to fit residues: 60.5119
Evaluate side-chains
  152 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.109885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.084604 restraints weight = 28114.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.086456 restraints weight = 23027.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.087854 restraints weight = 19712.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7614  Z= 0.134
  Angle     :  0.616   6.683  10388  Z= 0.305
  Chirality :  0.040   0.128   1298
  Planarity :  0.005   0.063   1274
  Dihedral  :  4.141  17.547   1058
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.08 (0.28), residues: 994
  helix:  1.23 (0.19), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.51 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 489 
 HIS   0.001   0.000   HIS B 412 
 PHE   0.015   0.001   PHE B 384 
 TYR   0.013   0.001   TYR B 158 
 ARG   0.001   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  604)
  hydrogen bonds       : angle       4.44964 ( 1800)
  covalent geometry    : bond        0.00284 ( 7614)
  covalent geometry    : angle       0.61640 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9641 (pp) cc_final: 0.9436 (pp)
REVERT: A  179 MET cc_start: 0.6250 (mmm) cc_final: 0.6007 (mmt)
REVERT: A  234 ASP cc_start: 0.8991 (m-30) cc_final: 0.8693 (m-30)
REVERT: A  264 MET cc_start: 0.8834 (mmp) cc_final: 0.8543 (mmp)
REVERT: A  295 ARG cc_start: 0.8128 (ttt180) cc_final: 0.7236 (tmt170)
REVERT: A  320 TYR cc_start: 0.8518 (m-10) cc_final: 0.8313 (m-80)
REVERT: A  429 MET cc_start: 0.9345 (mmp) cc_final: 0.9078 (mmm)
REVERT: B  102 PHE cc_start: 0.9136 (t80) cc_final: 0.8875 (t80)
REVERT: B  158 TYR cc_start: 0.9006 (m-80) cc_final: 0.8244 (m-80)
REVERT: B  234 ASP cc_start: 0.8960 (m-30) cc_final: 0.8692 (m-30)
REVERT: B  264 MET cc_start: 0.8878 (mmp) cc_final: 0.8585 (mmp)
REVERT: B  295 ARG cc_start: 0.8126 (ttt180) cc_final: 0.7239 (tmt170)
REVERT: B  358 MET cc_start: 0.9043 (ptp) cc_final: 0.8718 (ptp)
REVERT: B  429 MET cc_start: 0.9299 (mmp) cc_final: 0.8976 (mmm)
REVERT: B  521 MET cc_start: 0.8044 (pmm) cc_final: 0.7836 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1720
  time to fit residues: 44.7695
Evaluate side-chains
  148 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    0.3980
   chunk 92 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 20 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
B 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.111016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.085666 restraints weight = 28559.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.087554 restraints weight = 23308.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.088747 restraints weight = 19874.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   7614  Z= 0.129
  Angle     :  0.626   6.858  10388  Z= 0.306
  Chirality :  0.040   0.133   1298
  Planarity :  0.005   0.063   1274
  Dihedral  :  4.078  17.677   1058
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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:  1.09 (0.27), residues: 994
  helix:  1.23 (0.18), residues: 814
  sheet:  None (None), residues: 0
  loop : -1.47 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 193 
 HIS   0.000   0.000   HIS A 412 
 PHE   0.021   0.001   PHE B 102 
 TYR   0.014   0.001   TYR B 320 
 ARG   0.001   0.000   ARG B 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  604)
  hydrogen bonds       : angle       4.39524 ( 1800)
  covalent geometry    : bond        0.00285 ( 7614)
  covalent geometry    : angle       0.62573 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9642 (pp) cc_final: 0.9439 (pp)
REVERT: A  234 ASP cc_start: 0.8857 (m-30) cc_final: 0.8362 (p0)
REVERT: A  264 MET cc_start: 0.8835 (mmp) cc_final: 0.8553 (mmp)
REVERT: A  295 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7261 (tmt170)
REVERT: B  102 PHE cc_start: 0.9075 (t80) cc_final: 0.8843 (t80)
REVERT: B  158 TYR cc_start: 0.8972 (m-80) cc_final: 0.8195 (m-80)
REVERT: B  234 ASP cc_start: 0.8780 (m-30) cc_final: 0.8337 (p0)
REVERT: B  264 MET cc_start: 0.8878 (mmp) cc_final: 0.8579 (mmp)
REVERT: B  295 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7180 (tmt170)
REVERT: B  338 MET cc_start: 0.8159 (ttt) cc_final: 0.7958 (ttm)
REVERT: B  358 MET cc_start: 0.8973 (ptp) cc_final: 0.8686 (ptp)
REVERT: B  429 MET cc_start: 0.9271 (mmp) cc_final: 0.8950 (mmm)
REVERT: B  521 MET cc_start: 0.8012 (pmm) cc_final: 0.7800 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1386
  time to fit residues: 35.8356
Evaluate side-chains
  144 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0670
   chunk 46 optimal weight:    8.9990
   chunk 58 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 22 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0270
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
B 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.113096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.087375 restraints weight = 28745.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.089354 restraints weight = 23357.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.090620 restraints weight = 19877.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7614  Z= 0.121
  Angle     :  0.638   7.709  10388  Z= 0.303
  Chirality :  0.040   0.148   1298
  Planarity :  0.005   0.064   1274
  Dihedral  :  4.033  17.418   1058
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  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 (0.28), residues: 994
  helix:  1.32 (0.19), residues: 814
  sheet:  None (None), residues: 0
  loop : -1.61 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 412 
 PHE   0.022   0.001   PHE B 102 
 TYR   0.015   0.001   TYR A 320 
 ARG   0.001   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 (  604)
  hydrogen bonds       : angle       4.33153 ( 1800)
  covalent geometry    : bond        0.00258 ( 7614)
  covalent geometry    : angle       0.63780 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9656 (pp) cc_final: 0.9449 (pp)
REVERT: A  234 ASP cc_start: 0.8873 (m-30) cc_final: 0.8403 (p0)
REVERT: A  264 MET cc_start: 0.8821 (mmp) cc_final: 0.8537 (mmp)
REVERT: A  295 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7044 (tmt170)
REVERT: A  320 TYR cc_start: 0.8263 (m-80) cc_final: 0.7977 (m-80)
REVERT: B  102 PHE cc_start: 0.9056 (t80) cc_final: 0.8843 (t80)
REVERT: B  178 MET cc_start: 0.5792 (ppp) cc_final: 0.5077 (tpt)
REVERT: B  234 ASP cc_start: 0.8799 (m-30) cc_final: 0.8339 (p0)
REVERT: B  264 MET cc_start: 0.8873 (mmp) cc_final: 0.8556 (mmp)
REVERT: B  295 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7105 (tmt170)
REVERT: B  358 MET cc_start: 0.8866 (ptp) cc_final: 0.8650 (ptp)
REVERT: B  521 MET cc_start: 0.7935 (pmm) cc_final: 0.7733 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1297
  time to fit residues: 33.3959
Evaluate side-chains
  140 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0050
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.109603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.085873 restraints weight = 29235.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.087363 restraints weight = 24267.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.088742 restraints weight = 21191.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   7614  Z= 0.131
  Angle     :  0.648   7.186  10388  Z= 0.314
  Chirality :  0.040   0.133   1298
  Planarity :  0.004   0.063   1274
  Dihedral  :  3.980  17.847   1058
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 994
  helix:  1.33 (0.18), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.65 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 193 
 HIS   0.001   0.000   HIS B 310 
 PHE   0.022   0.001   PHE B 102 
 TYR   0.015   0.001   TYR A 320 
 ARG   0.001   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03855 (  604)
  hydrogen bonds       : angle       4.31270 ( 1800)
  covalent geometry    : bond        0.00294 ( 7614)
  covalent geometry    : angle       0.64802 (10388)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A  234 ASP cc_start: 0.8794 (m-30) cc_final: 0.8340 (p0)
REVERT: A  264 MET cc_start: 0.8835 (mmp) cc_final: 0.8513 (mmp)
REVERT: A  295 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7101 (tmt170)
REVERT: B  178 MET cc_start: 0.6620 (ppp) cc_final: 0.5917 (tpt)
REVERT: B  234 ASP cc_start: 0.8715 (m-30) cc_final: 0.8282 (p0)
REVERT: B  264 MET cc_start: 0.8890 (mmp) cc_final: 0.8542 (mmp)
REVERT: B  295 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7082 (tmt170)
REVERT: B  358 MET cc_start: 0.8897 (ptp) cc_final: 0.8636 (ptp)
REVERT: B  429 MET cc_start: 0.9301 (mmp) cc_final: 0.9013 (mmm)
REVERT: B  521 MET cc_start: 0.7923 (pmm) cc_final: 0.7702 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1388
  time to fit residues: 35.0585
Evaluate side-chains
  138 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0570
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.110834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.086746 restraints weight = 28694.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.088106 restraints weight = 23859.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.089657 restraints weight = 20992.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7614  Z= 0.121
  Angle     :  0.643   7.354  10388  Z= 0.306
  Chirality :  0.040   0.153   1298
  Planarity :  0.004   0.064   1274
  Dihedral  :  4.053  24.742   1058
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  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:  1.26 (0.27), residues: 994
  helix:  1.41 (0.19), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.68 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 193 
 HIS   0.001   0.000   HIS B 412 
 PHE   0.022   0.001   PHE A 102 
 TYR   0.013   0.001   TYR A 158 
 ARG   0.001   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03675 (  604)
  hydrogen bonds       : angle       4.21540 ( 1800)
  covalent geometry    : bond        0.00263 ( 7614)
  covalent geometry    : angle       0.64341 (10388)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3586.80 seconds
wall clock time: 65 minutes 53.91 seconds (3953.91 seconds total)