Starting phenix.real_space_refine
on Tue Mar 11 14:30:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dxi_30910/03_2025/7dxi_30910.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dxi_30910/03_2025/7dxi_30910.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2025/7dxi_30910.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2025/7dxi_30910.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2025/7dxi_30910.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dxi_30910/03_2025/7dxi_30910.cif"
  }
  resolution = 3.53
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      24      5.16       5
     C    3920      2.51       5
     N    1064      2.21       5
     O    1120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6130
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 3064
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 20, 'TRANS': 350}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.33, per 1000 atoms: 0.87
  Number of scatterers: 6130
  At special positions: 0
  Unit cell: (115.333, 115.333, 59.9472, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      24     16.00
     O    1120      8.00
     N    1064      7.00
     C    3920      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 515 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 476 " - pdb=" SG  CYS B 515 " distance=2.03

  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: 1.42
  Conformation dependent library (CDL) restraints added in 777.3 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      45.8% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 85
      removed outlier: 3.560A  pdb=" N   ILE A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASP A  81 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 102
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.727A  pdb=" N   LEU A 107 " --> pdb=" O   SER A 103 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLU A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
    Processing helix  chain 'A' and resid 155 through 160
      removed outlier: 3.715A  pdb=" N   ILE A 159 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 166
      removed outlier: 5.833A  pdb=" N   HIS A 164 " --> pdb=" O   THR A 161 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A 165 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE A 166 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 161 through 166'
    Processing helix  chain 'A' and resid 187 through 191
    Processing helix  chain 'A' and resid 349 through 364
      removed outlier: 3.750A  pdb=" N   SER A 353 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ALA A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 390
    Processing helix  chain 'A' and resid 392 through 401
      removed outlier: 3.592A  pdb=" N   LEU A 397 " --> pdb=" O   HIS A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 417
    Processing helix  chain 'A' and resid 428 through 435
    Processing helix  chain 'A' and resid 445 through 455
      removed outlier: 3.561A  pdb=" N   ARG A 455 " --> pdb=" O   THR A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 476
      removed outlier: 3.615A  pdb=" N   MET A 466 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   CYS A 476 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
      removed outlier: 3.504A  pdb=" N   VAL A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 524
    Processing helix  chain 'A' and resid 552 through 566
      removed outlier: 3.534A  pdb=" N   ARG A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN A 566 " --> pdb=" O   ARG A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 600
      removed outlier: 3.932A  pdb=" N   MET A 587 " --> pdb=" O   GLU A 583 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ARG A 589 " --> pdb=" O   ASN A 585 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE A 599 " --> pdb=" O   PHE A 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 85
      removed outlier: 3.560A  pdb=" N   ILE B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ASP B  81 " --> pdb=" O   ASN B  77 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 102
    Processing helix  chain 'B' and resid 103 through 111
      removed outlier: 3.727A  pdb=" N   LEU B 107 " --> pdb=" O   SER B 103 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS B 109 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 145
    Processing helix  chain 'B' and resid 155 through 160
      removed outlier: 3.716A  pdb=" N   ILE B 159 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 166
      removed outlier: 5.833A  pdb=" N   HIS B 164 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG B 165 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE B 166 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 161 through 166'
    Processing helix  chain 'B' and resid 187 through 191
    Processing helix  chain 'B' and resid 349 through 364
      removed outlier: 3.749A  pdb=" N   SER B 353 " --> pdb=" O   ILE B 349 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ALA B 364 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 390
    Processing helix  chain 'B' and resid 392 through 401
      removed outlier: 3.592A  pdb=" N   LEU B 397 " --> pdb=" O   HIS B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 428 through 435
    Processing helix  chain 'B' and resid 445 through 455
      removed outlier: 3.561A  pdb=" N   ARG B 455 " --> pdb=" O   THR B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 476
      removed outlier: 3.616A  pdb=" N   MET B 466 " --> pdb=" O   ASP B 462 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   CYS B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 515
      removed outlier: 3.504A  pdb=" N   VAL B 512 " --> pdb=" O   THR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 524
    Processing helix  chain 'B' and resid 552 through 566
      removed outlier: 3.534A  pdb=" N   ARG B 564 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN B 566 " --> pdb=" O   ARG B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 600
      removed outlier: 3.932A  pdb=" N   MET B 587 " --> pdb=" O   GLU B 583 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ARG B 589 " --> pdb=" O   ASN B 585 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE B 599 " --> pdb=" O   PHE B 595 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68
      removed outlier: 6.822A  pdb=" N   ALA A  66 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   VAL A 120 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TYR A  68 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL A 117 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ILE A 119 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174
    Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200
    Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68
      removed outlier: 6.822A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   VAL B 120 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   TYR B  68 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL B 117 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   VAL B 139 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ILE B 119 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 174
    Processing sheet with id=AA7, first strand: chain 'B' and resid 180 through 181
    Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200

    168 hydrogen bonds defined for protein.
    480 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: 1.32

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1962
        1.34 -     1.46: 1218
        1.46 -     1.58: 3066
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 6286
  Sorted by residual:
  bond pdb=" C   GLN B 458 "
       pdb=" N   PRO B 459 "
    ideal  model  delta    sigma   weight residual
    1.329  1.351 -0.022 1.18e-02 7.18e+03 3.35e+00
  bond pdb=" C   GLN A 458 "
       pdb=" N   PRO A 459 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.18e-02 7.18e+03 3.26e+00
  bond pdb=" CA  LYS A 368 "
       pdb=" C   LYS A 368 "
    ideal  model  delta    sigma   weight residual
    1.523  1.545 -0.021 1.34e-02 5.57e+03 2.55e+00
  bond pdb=" CA  LYS B 368 "
       pdb=" C   LYS B 368 "
    ideal  model  delta    sigma   weight residual
    1.523  1.544 -0.021 1.34e-02 5.57e+03 2.52e+00
  bond pdb=" N   LEU A 176 "
       pdb=" CA  LEU A 176 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.31e-02 5.83e+03 2.34e+00
  ... (remaining 6281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.00: 8384
        4.00 -     8.01: 125
        8.01 -    12.01: 19
       12.01 -    16.01: 6
       16.01 -    20.01: 2
  Bond angle restraints: 8536
  Sorted by residual:
  angle pdb=" C   PRO A 459 "
        pdb=" N   PRO A 460 "
        pdb=" CD  PRO A 460 "
      ideal   model   delta    sigma   weight residual
     125.00  104.99   20.01 4.10e+00 5.95e-02 2.38e+01
  angle pdb=" C   PRO B 459 "
        pdb=" N   PRO B 460 "
        pdb=" CD  PRO B 460 "
      ideal   model   delta    sigma   weight residual
     125.00  104.99   20.01 4.10e+00 5.95e-02 2.38e+01
  angle pdb=" CA  PRO A 460 "
        pdb=" N   PRO A 460 "
        pdb=" CD  PRO A 460 "
      ideal   model   delta    sigma   weight residual
     112.00  105.33    6.67 1.40e+00 5.10e-01 2.27e+01
  angle pdb=" CA  PRO B 460 "
        pdb=" N   PRO B 460 "
        pdb=" CD  PRO B 460 "
      ideal   model   delta    sigma   weight residual
     112.00  105.37    6.63 1.40e+00 5.10e-01 2.24e+01
  angle pdb=" N   LYS A 368 "
        pdb=" CA  LYS A 368 "
        pdb=" C   LYS A 368 "
      ideal   model   delta    sigma   weight residual
     110.80  120.35   -9.55 2.13e+00 2.20e-01 2.01e+01
  ... (remaining 8531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3329
       17.70 -    35.40: 365
       35.40 -    53.11: 64
       53.11 -    70.81: 12
       70.81 -    88.51: 4
  Dihedral angle restraints: 3774
    sinusoidal: 1554
      harmonic: 2220
  Sorted by residual:
  dihedral pdb=" CA  PHE A 367 "
           pdb=" C   PHE A 367 "
           pdb=" N   LYS A 368 "
           pdb=" CA  LYS A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -128.71  -51.29     0      5.00e+00 4.00e-02 1.05e+02
  dihedral pdb=" CA  PHE B 367 "
           pdb=" C   PHE B 367 "
           pdb=" N   LYS B 368 "
           pdb=" CA  LYS B 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -128.74  -51.26     0      5.00e+00 4.00e-02 1.05e+02
  dihedral pdb=" CB  CYS A 476 "
           pdb=" SG  CYS A 476 "
           pdb=" SG  CYS A 515 "
           pdb=" CB  CYS A 515 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.49  -88.51     1      1.00e+01 1.00e-02 9.35e+01
  ... (remaining 3771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 629
       0.053 -    0.105: 217
       0.105 -    0.158: 63
       0.158 -    0.211: 13
       0.211 -    0.263: 10
  Chirality restraints: 932
  Sorted by residual:
  chirality pdb=" CA  LYS A 368 "
            pdb=" N   LYS A 368 "
            pdb=" C   LYS A 368 "
            pdb=" CB  LYS A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  LYS B 368 "
            pdb=" N   LYS B 368 "
            pdb=" C   LYS B 368 "
            pdb=" CB  LYS B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  GLN B 458 "
            pdb=" N   GLN B 458 "
            pdb=" C   GLN B 458 "
            pdb=" CB  GLN B 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 929 not shown)

  Planarity restraints: 1106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 459 "   -0.130 5.00e-02 4.00e+02   1.98e-01 6.27e+01
        pdb=" N   PRO A 460 "    0.342 5.00e-02 4.00e+02
        pdb=" CA  PRO A 460 "   -0.119 5.00e-02 4.00e+02
        pdb=" CD  PRO A 460 "   -0.093 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 459 "    0.130 5.00e-02 4.00e+02   1.98e-01 6.25e+01
        pdb=" N   PRO B 460 "   -0.341 5.00e-02 4.00e+02
        pdb=" CA  PRO B 460 "    0.119 5.00e-02 4.00e+02
        pdb=" CD  PRO B 460 "    0.093 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 151 "   -0.076 5.00e-02 4.00e+02   1.16e-01 2.14e+01
        pdb=" N   PRO A 152 "    0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO A 152 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO A 152 "   -0.065 5.00e-02 4.00e+02
  ... (remaining 1103 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.15: 2
        2.15 -     2.84: 1965
        2.84 -     3.53: 7955
        3.53 -     4.21: 13695
        4.21 -     4.90: 23490
  Nonbonded interactions: 47107
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 439 "
            pdb=" OG1 THR B 443 "
     model   vdw
     1.468 3.040
  nonbonded pdb=" OD2 ASP A 439 "
            pdb=" OG1 THR A 443 "
     model   vdw
     1.468 3.040
  nonbonded pdb=" CB  ASP A 439 "
            pdb="CA    CA A 701 "
     model   vdw
     2.247 2.910
  nonbonded pdb=" O   THR B 443 "
            pdb="CA    CA B 701 "
     model   vdw
     2.248 2.510
  nonbonded pdb=" CB  ASP B 439 "
            pdb="CA    CA B 701 "
     model   vdw
     2.248 2.910
  ... (remaining 47102 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             1.400
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.340
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
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   0.040   6286  Z= 0.401
  Angle     :  1.298  20.014   8536  Z= 0.676
  Chirality :  0.064   0.263    932
  Planarity :  0.012   0.198   1106
  Dihedral  : 15.064  76.380   2316
  Min Nonbonded Distance : 1.468

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  : 13.91 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.74 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 10.00 %
    Twisted General : 1.44 %

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: -5.04 (0.24), residues: 726
  helix: -3.36 (0.19), residues: 304
  sheet: -2.64 (0.75), residues: 36
  loop : -3.47 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP A 463 
 HIS   0.014   0.002   HIS B 116 
 PHE   0.052   0.004   PHE B 436 
 TYR   0.064   0.004   TYR A 175 
 ARG   0.012   0.001   ARG A 467 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6946 (t0)
REVERT: A  368 LYS cc_start: 0.6373 (pttp) cc_final: 0.6167 (pttp)
REVERT: A  594 ASP cc_start: 0.8115 (t70) cc_final: 0.7628 (m-30)
REVERT: B  149 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7037 (t0)
REVERT: B  463 TRP cc_start: 0.6358 (p-90) cc_final: 0.6064 (p-90)
REVERT: B  589 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7755 (mtp180)
  outliers start: 2
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1862
  time to fit residues: 28.7331
Evaluate side-chains
  91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain B residue  149 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.2980
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
A 576 ASN
B 116 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.114237 restraints weight = 9064.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.117095 restraints weight = 5834.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118973 restraints weight = 4408.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6286  Z= 0.250
  Angle     :  0.779  12.297   8536  Z= 0.388
  Chirality :  0.045   0.158    932
  Planarity :  0.009   0.154   1106
  Dihedral  :  7.968  47.929    834
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  : 14.46 %
    Favored  : 84.99 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.18 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.29 %

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: -3.95 (0.28), residues: 726
  helix: -2.15 (0.24), residues: 324
  sheet: -2.43 (0.86), residues: 32
  loop : -3.14 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  70 
 HIS   0.004   0.001   HIS A 116 
 PHE   0.016   0.002   PHE A 595 
 TYR   0.025   0.002   TYR B 412 
 ARG   0.002   0.000   ARG A 370 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  558 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6558 (pm20)
REVERT: A  576 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8301 (t0)
REVERT: A  594 ASP cc_start: 0.8242 (t70) cc_final: 0.7942 (t0)
REVERT: B  594 ASP cc_start: 0.8296 (t70) cc_final: 0.8055 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 113
  average time/residue: 0.1629
  time to fit residues: 24.9114
Evaluate side-chains
  98 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  576 ASN
Chi-restraints excluded: chain B residue  149 ASP
Chi-restraints excluded: chain B residue  411 GLN
Chi-restraints excluded: chain B residue  528 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 71 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    0.4980
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 69 optimal weight:    0.2980
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 ASN
** B 164 HIS ** 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 = 0.3683 r_free = 0.3683 target = 0.141653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117475 restraints weight = 8922.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.120380 restraints weight = 5675.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.122359 restraints weight = 4248.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6286  Z= 0.201
  Angle     :  0.708   8.445   8536  Z= 0.361
  Chirality :  0.045   0.181    932
  Planarity :  0.006   0.099   1106
  Dihedral  :  7.543  48.038    834
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.50 %
    Favored  : 86.50 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.39 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.29 %

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: -3.50 (0.29), residues: 726
  helix: -1.50 (0.26), residues: 326
  sheet: -3.26 (0.66), residues: 46
  loop : -3.03 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.013   0.001   PHE A 595 
 TYR   0.020   0.001   TYR A 412 
 ARG   0.003   0.000   ARG B 562 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: A  514 ARG cc_start: 0.5394 (ttt-90) cc_final: 0.5166 (ptp-110)
REVERT: A  558 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6672 (pm20)
REVERT: A  594 ASP cc_start: 0.8152 (t70) cc_final: 0.7929 (t0)
REVERT: B  118 TYR cc_start: 0.8735 (m-80) cc_final: 0.8464 (m-80)
REVERT: B  576 ASN cc_start: 0.8490 (t0) cc_final: 0.8063 (t0)
REVERT: B  594 ASP cc_start: 0.8202 (t70) cc_final: 0.7893 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1601
  time to fit residues: 25.9309
Evaluate side-chains
  104 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain B residue  149 ASP
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  411 GLN
Chi-restraints excluded: chain B residue  526 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0070
   chunk 59 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** 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 = 0.3689 r_free = 0.3689 target = 0.142131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.117513 restraints weight = 9111.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.120530 restraints weight = 5822.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122532 restraints weight = 4363.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6286  Z= 0.194
  Angle     :  0.692   8.029   8536  Z= 0.355
  Chirality :  0.044   0.161    932
  Planarity :  0.006   0.100   1106
  Dihedral  :  7.373  55.231    834
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.88 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -3.15 (0.30), residues: 726
  helix: -1.16 (0.27), residues: 326
  sheet: -3.23 (0.66), residues: 46
  loop : -2.87 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A 543 
 PHE   0.010   0.001   PHE A 595 
 TYR   0.020   0.001   TYR A 412 
 ARG   0.002   0.000   ARG B 403 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7453 (pm20)
REVERT: A  471 GLU cc_start: 0.6093 (tm-30) cc_final: 0.5812 (tm-30)
REVERT: A  558 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6641 (pm20)
REVERT: A  576 ASN cc_start: 0.8546 (t0) cc_final: 0.8284 (t0)
REVERT: B  118 TYR cc_start: 0.8747 (m-80) cc_final: 0.8471 (m-80)
REVERT: B  150 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7556 (pm20)
REVERT: B  576 ASN cc_start: 0.8489 (t0) cc_final: 0.8131 (t0)
REVERT: B  594 ASP cc_start: 0.8190 (t70) cc_final: 0.7939 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 114
  average time/residue: 0.1384
  time to fit residues: 22.2554
Evaluate side-chains
  112 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain B residue  149 ASP
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.137805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.112963 restraints weight = 9192.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.115868 restraints weight = 5913.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117824 restraints weight = 4462.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6286  Z= 0.261
  Angle     :  0.721   7.394   8536  Z= 0.373
  Chirality :  0.045   0.158    932
  Planarity :  0.007   0.103   1106
  Dihedral  :  7.541  57.879    834
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.88 %
    Favored  : 85.12 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.82 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -3.02 (0.30), residues: 726
  helix: -0.95 (0.28), residues: 328
  sheet: -3.14 (0.68), residues: 42
  loop : -2.95 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 444 
 HIS   0.003   0.001   HIS A 543 
 PHE   0.014   0.001   PHE B 600 
 TYR   0.024   0.002   TYR A 412 
 ARG   0.002   0.000   ARG B 403 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  471 GLU cc_start: 0.6098 (tm-30) cc_final: 0.5852 (tm-30)
REVERT: A  547 MET cc_start: 0.6141 (mtt) cc_final: 0.5788 (mtt)
REVERT: A  554 THR cc_start: 0.7370 (m) cc_final: 0.6603 (m)
REVERT: A  558 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6653 (pm20)
REVERT: A  562 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7901 (ttp-170)
REVERT: A  576 ASN cc_start: 0.8546 (t0) cc_final: 0.8339 (t0)
REVERT: B  118 TYR cc_start: 0.8779 (m-80) cc_final: 0.8504 (m-80)
REVERT: B  511 LEU cc_start: 0.8059 (tt) cc_final: 0.7507 (tt)
REVERT: B  576 ASN cc_start: 0.8488 (t0) cc_final: 0.8268 (t0)
REVERT: B  594 ASP cc_start: 0.8156 (t70) cc_final: 0.7911 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1421
  time to fit residues: 23.2337
Evaluate side-chains
  110 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain B residue  149 ASP
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 GLN
** B 164 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.139977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.116310 restraints weight = 9018.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.119146 restraints weight = 5761.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121032 restraints weight = 4336.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6286  Z= 0.237
  Angle     :  0.723   9.105   8536  Z= 0.374
  Chirality :  0.045   0.158    932
  Planarity :  0.006   0.106   1106
  Dihedral  :  7.275  47.629    834
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.74 %
    Favored  : 85.26 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.11 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.87 (0.30), residues: 726
  helix: -0.84 (0.28), residues: 326
  sheet: -3.09 (0.69), residues: 42
  loop : -2.85 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 444 
 HIS   0.003   0.001   HIS B 543 
 PHE   0.011   0.001   PHE A 600 
 TYR   0.022   0.002   TYR A 412 
 ARG   0.003   0.000   ARG B 562 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7570 (pm20)
REVERT: A  467 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7521 (tpp80)
REVERT: A  547 MET cc_start: 0.6147 (mtt) cc_final: 0.5714 (mtt)
REVERT: A  554 THR cc_start: 0.7320 (m) cc_final: 0.6570 (m)
REVERT: A  558 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6647 (pm20)
REVERT: A  562 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.7815 (ttp-170)
REVERT: B  118 TYR cc_start: 0.8760 (m-80) cc_final: 0.8494 (m-80)
REVERT: B  150 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7599 (pm20)
REVERT: B  467 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7543 (tpp80)
REVERT: B  594 ASP cc_start: 0.8097 (t70) cc_final: 0.7886 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1590
  time to fit residues: 26.2457
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue  149 ASP
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0870
   chunk 69 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7958

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN
B 576 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.118898 restraints weight = 9133.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.121835 restraints weight = 5815.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.123763 restraints weight = 4341.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6286  Z= 0.207
  Angle     :  0.704   9.604   8536  Z= 0.365
  Chirality :  0.045   0.157    932
  Planarity :  0.006   0.108   1106
  Dihedral  :  6.785  34.215    834
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.88 %
    Favored  : 85.12 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.52 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.84 (0.30), residues: 726
  helix: -0.80 (0.28), residues: 336
  sheet: -3.03 (0.70), residues: 42
  loop : -2.90 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A 543 
 PHE   0.009   0.001   PHE B 419 
 TYR   0.020   0.001   TYR B 412 
 ARG   0.002   0.000   ARG A  84 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7542 (tpp80)
REVERT: A  558 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6701 (pm20)
REVERT: B  118 TYR cc_start: 0.8737 (m-80) cc_final: 0.8445 (m-80)
REVERT: B  150 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7609 (pm20)
REVERT: B  467 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7583 (tpp80)
  outliers start: 23
  outliers final: 9
  residues processed: 127
  average time/residue: 0.1528
  time to fit residues: 26.7316
Evaluate side-chains
  111 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0970
   chunk 34 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.136375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.111269 restraints weight = 9177.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.114144 restraints weight = 5943.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.116014 restraints weight = 4506.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6286  Z= 0.302
  Angle     :  0.806  11.671   8536  Z= 0.411
  Chirality :  0.047   0.166    932
  Planarity :  0.007   0.116   1106
  Dihedral  :  6.802  37.486    830
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.84 %
    Favored  : 84.16 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.90 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.99 (0.30), residues: 726
  helix: -0.79 (0.28), residues: 326
  sheet: -3.12 (0.69), residues: 42
  loop : -3.09 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 444 
 HIS   0.014   0.001   HIS A 590 
 PHE   0.015   0.002   PHE A 600 
 TYR   0.025   0.002   TYR B 412 
 ARG   0.002   0.000   ARG B 403 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7573 (tpp80)
REVERT: A  554 THR cc_start: 0.7358 (m) cc_final: 0.6583 (m)
REVERT: A  558 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6682 (pm20)
REVERT: B  118 TYR cc_start: 0.8787 (m-80) cc_final: 0.8483 (m-80)
REVERT: B  467 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7593 (tpp80)
  outliers start: 16
  outliers final: 13
  residues processed: 112
  average time/residue: 0.1595
  time to fit residues: 24.4186
Evaluate side-chains
  107 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 GLN
** B 164 HIS ** 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 = 0.3624 r_free = 0.3624 target = 0.136586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.112081 restraints weight = 9159.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.114947 restraints weight = 5820.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116886 restraints weight = 4370.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6286  Z= 0.292
  Angle     :  0.789  10.680   8536  Z= 0.406
  Chirality :  0.047   0.150    932
  Planarity :  0.007   0.120   1106
  Dihedral  :  6.827  38.153    830
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.39 %
    Favored  : 83.61 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.09 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.99 (0.30), residues: 726
  helix: -0.76 (0.28), residues: 322
  sheet: -3.16 (0.70), residues: 42
  loop : -3.08 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 444 
 HIS   0.004   0.001   HIS A 543 
 PHE   0.013   0.002   PHE B 600 
 TYR   0.025   0.002   TYR A 412 
 ARG   0.002   0.000   ARG B 403 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7587 (tpp80)
REVERT: A  558 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6655 (pm20)
REVERT: B  118 TYR cc_start: 0.8791 (m-80) cc_final: 0.8492 (m-80)
REVERT: B  467 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7654 (tpp80)
  outliers start: 17
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1592
  time to fit residues: 24.5020
Evaluate side-chains
  109 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0050
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.142165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117936 restraints weight = 9202.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120914 restraints weight = 5817.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122944 restraints weight = 4349.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6286  Z= 0.206
  Angle     :  0.743  11.493   8536  Z= 0.383
  Chirality :  0.045   0.158    932
  Planarity :  0.007   0.120   1106
  Dihedral  :  6.356  33.828    830
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.60 %
    Favored  : 85.40 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.54 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.73 (0.31), residues: 726
  helix: -0.58 (0.28), residues: 328
  sheet: -3.27 (0.67), residues: 46
  loop : -2.88 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.010   0.001   PHE B 419 
 TYR   0.018   0.001   TYR B 412 
 ARG   0.003   0.000   ARG A  84 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7203 (ppt170)
REVERT: A  467 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7596 (tpp80)
REVERT: A  558 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6670 (pm20)
REVERT: B  118 TYR cc_start: 0.8747 (m-80) cc_final: 0.8442 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1448
  time to fit residues: 24.4938
Evaluate side-chains
  111 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  526 PHE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0870
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0980
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 ASN
B 576 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.144497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120493 restraints weight = 9182.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.123543 restraints weight = 5745.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.125447 restraints weight = 4262.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6286  Z= 0.194
  Angle     :  0.731  11.138   8536  Z= 0.377
  Chirality :  0.044   0.155    932
  Planarity :  0.007   0.119   1106
  Dihedral  :  6.129  31.089    830
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.46 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.28 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.60 (0.31), residues: 726
  helix: -0.28 (0.29), residues: 316
  sheet: -3.18 (0.68), residues: 46
  loop : -2.95 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  70 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.011   0.001   PHE A 595 
 TYR   0.015   0.001   TYR B 412 
 ARG   0.008   0.000   ARG A 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2001.10 seconds
wall clock time: 35 minutes 20.63 seconds (2120.63 seconds total)