Starting phenix.real_space_refine
on Sun May 11 04:25:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cp5_45800/05_2025/9cp5_45800.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cp5_45800/05_2025/9cp5_45800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cp5_45800/05_2025/9cp5_45800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cp5_45800/05_2025/9cp5_45800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cp5_45800/05_2025/9cp5_45800.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cp5_45800/05_2025/9cp5_45800.cif"
  }
  resolution = 3.51
  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=  -0.003 sd=   0.085
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
     S      58      5.16       5
     Cl      1      4.86       5
     C    4842      2.51       5
     N    1182      2.21       5
     O    1367      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7450
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4253
          Classifications: {'peptide': 538}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 25, 'TRANS': 512}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1599
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "L"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1597
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.70, per 1000 atoms: 0.63
  Number of scatterers: 7450
  At special positions: 0
  Unit cell: (78.934, 85.404, 151.398, 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)
     Cl      1     17.00
     S      58     16.00
     O    1367      8.00
     N    1182      7.00
     C    4842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 171 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " 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: 1.90
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1780

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      45.2% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 68
      removed outlier: 3.835A  pdb=" N   GLU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 74 through 83
      removed outlier: 3.697A  pdb=" N   TYR A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 3.700A  pdb=" N   VAL A 103 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
    Processing helix  chain 'A' and resid 130 through 147
      removed outlier: 3.908A  pdb=" N   TYR A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 162
      removed outlier: 4.222A  pdb=" N   PHE A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 170
      removed outlier: 3.686A  pdb=" N   ALA A 169 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   THR A 170 " --> pdb=" O   PRO A 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 166 through 170'
    Processing helix  chain 'A' and resid 201 through 211
      removed outlier: 3.604A  pdb=" N   GLU A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 245
    Processing helix  chain 'A' and resid 259 through 275
      removed outlier: 3.643A  pdb=" N   THR A 274 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 287
      removed outlier: 3.732A  pdb=" N   GLY A 281 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 4.384A  pdb=" N   TRP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 324
      removed outlier: 4.152A  pdb=" N   ALA A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASN A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 363
      removed outlier: 3.836A  pdb=" N   ASP A 333 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 3.659A  pdb=" N   GLU A 369 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 370 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 370'
    Processing helix  chain 'A' and resid 376 through 379
    Processing helix  chain 'A' and resid 380 through 386
    Processing helix  chain 'A' and resid 391 through 426
      removed outlier: 3.680A  pdb=" N   TRP A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 431
      removed outlier: 3.971A  pdb=" N   PHE A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A 431 " --> pdb=" O   PRO A 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 426 through 431'
    Processing helix  chain 'A' and resid 435 through 452
    Processing helix  chain 'A' and resid 453 through 455
      No H-bonds generated for 'chain 'A' and resid 453 through 455'
    Processing helix  chain 'A' and resid 458 through 470
      removed outlier: 4.129A  pdb=" N   ILE A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 490
    Processing helix  chain 'A' and resid 492 through 505
    Processing helix  chain 'A' and resid 510 through 518
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 547 through 563
    Processing helix  chain 'A' and resid 563 through 576
    Processing helix  chain 'A' and resid 579 through 589
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.638A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.672A  pdb=" N   ASP L  83 " --> pdb=" O   GLU L  80 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA L  84 " --> pdb=" O   ALA L  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 80 through 84'
    Processing helix  chain 'L' and resid 122 through 128
      removed outlier: 3.651A  pdb=" N   LEU L 126 " --> pdb=" O   SER L 123 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER L 128 " --> pdb=" O   GLN L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 189
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.576A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU H  18 " --> pdb=" O   MET H  83 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   HIS H  80 " --> pdb=" O   SER H  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.240A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 126 through 130
      removed outlier: 3.589A  pdb=" N   SER H 126 " --> pdb=" O   LYS H 149 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLY H 145 " --> pdb=" O   LEU H 130 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   TYR H 181 " --> pdb=" O   GLY H 150 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130
      removed outlier: 3.589A  pdb=" N   SER H 126 " --> pdb=" O   LYS H 149 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLY H 145 " --> pdb=" O   LEU H 130 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   TYR H 181 " --> pdb=" O   GLY H 150 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR H 182 " --> pdb=" O   VAL H 175 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL H 175 " --> pdb=" O   THR H 182 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160
      removed outlier: 3.738A  pdb=" N   THR H 159 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN H 202 " --> pdb=" O   THR H 159 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.790A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR L  72 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.818A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 117 through 119
      removed outlier: 6.302A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 156
      removed outlier: 3.851A  pdb=" N   TRP L 149 " --> pdb=" O   ARG L 156 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1110 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: 2.32

  Time building geometry restraints manager: 2.20 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: 2252
        1.34 -     1.46: 2025
        1.46 -     1.58: 3300
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 7659
  Sorted by residual:
  bond pdb=" C   PRO A 508 "
       pdb=" N   PRO A 509 "
    ideal  model  delta    sigma   weight residual
    1.334  1.344 -0.011 8.40e-03 1.42e+04 1.66e+00
  bond pdb=" N   ASN L 213 "
       pdb=" CA  ASN L 213 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.61e+00
  bond pdb=" C   ILE A 565 "
       pdb=" N   PRO A 566 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.015 1.23e-02 6.61e+03 1.43e+00
  bond pdb=" CA  ILE A 543 "
       pdb=" CB  ILE A 543 "
    ideal  model  delta    sigma   weight residual
    1.540  1.556 -0.016 1.36e-02 5.41e+03 1.40e+00
  bond pdb=" C   SER A 392 "
       pdb=" N   PRO A 393 "
    ideal  model  delta    sigma   weight residual
    1.335  1.349 -0.014 1.28e-02 6.10e+03 1.28e+00
  ... (remaining 7654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 10073
        1.68 -     3.36: 306
        3.36 -     5.04: 37
        5.04 -     6.73: 14
        6.73 -     8.41: 14
  Bond angle restraints: 10444
  Sorted by residual:
  angle pdb=" C   SER L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.56   -8.02 1.91e+00 2.74e-01 1.77e+01
  angle pdb=" C   TYR A 191 "
        pdb=" N   SER A 192 "
        pdb=" CA  SER A 192 "
      ideal   model   delta    sigma   weight residual
     121.54  129.29   -7.75 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" C   ARG L 212 "
        pdb=" N   ASN L 213 "
        pdb=" CA  ASN L 213 "
      ideal   model   delta    sigma   weight residual
     121.70  128.44   -6.74 1.80e+00 3.09e-01 1.40e+01
  angle pdb=" C   PRO A 509 "
        pdb=" N   SER A 510 "
        pdb=" CA  SER A 510 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   GLY A 578 "
        pdb=" N   THR A 579 "
        pdb=" CA  THR A 579 "
      ideal   model   delta    sigma   weight residual
     121.54  128.22   -6.68 1.91e+00 2.74e-01 1.22e+01
  ... (remaining 10439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4016
       17.95 -    35.90: 331
       35.90 -    53.85: 68
       53.85 -    71.80: 8
       71.80 -    89.75: 11
  Dihedral angle restraints: 4434
    sinusoidal: 1641
      harmonic: 2793
  Sorted by residual:
  dihedral pdb=" CB  CYS A 171 "
           pdb=" SG  CYS A 171 "
           pdb=" SG  CYS A 180 "
           pdb=" CB  CYS A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.42   76.42     1      1.00e+01 1.00e-02 7.35e+01
  dihedral pdb=" CA  MET A 517 "
           pdb=" C   MET A 517 "
           pdb=" N   ILE A 518 "
           pdb=" CA  ILE A 518 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  THR A 579 "
           pdb=" C   THR A 579 "
           pdb=" N   LEU A 580 "
           pdb=" CA  LEU A 580 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.65  -16.35     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4431 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 825
       0.044 -    0.088: 258
       0.088 -    0.132: 79
       0.132 -    0.176: 12
       0.176 -    0.220: 4
  Chirality restraints: 1178
  Sorted by residual:
  chirality pdb=" CB  ILE A 543 "
            pdb=" CA  ILE A 543 "
            pdb=" CG1 ILE A 543 "
            pdb=" CG2 ILE A 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CG  LEU A 455 "
            pdb=" CB  LEU A 455 "
            pdb=" CD1 LEU A 455 "
            pdb=" CD2 LEU A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.79e-01
  chirality pdb=" CA  TYR A 382 "
            pdb=" N   TYR A 382 "
            pdb=" C   TYR A 382 "
            pdb=" CB  TYR A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  ... (remaining 1175 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 350 "   -0.014 2.00e-02 2.50e+03   1.55e-02 4.19e+00
        pdb=" CG  PHE A 350 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 350 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 350 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 350 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 350 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 350 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 207 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.53e+00
        pdb=" C   TRP A 207 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TRP A 207 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 208 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 365 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.83e+00
        pdb=" N   PRO A 366 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 366 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 366 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1371
        2.77 -     3.30: 6884
        3.30 -     3.84: 12734
        3.84 -     4.37: 14081
        4.37 -     4.90: 25096
  Nonbonded interactions: 60166
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L 106 "
            pdb=" OH  TYR L 174 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   CYS A  98 "
            pdb=" OG1 THR A 520 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   SER H 140 "
            pdb=" OG  SER H 191 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" ND2 ASN A  83 "
            pdb=" OD2 ASP A 301 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.318 3.040
  ... (remaining 60161 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.470
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     20.710
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
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      :  0.003   0.050   7664  Z= 0.166
  Angle     :  0.734   8.408  10454  Z= 0.381
  Chirality :  0.048   0.220   1178
  Planarity :  0.005   0.042   1292
  Dihedral  : 14.363  89.746   2639
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -1.74 (0.25), residues: 958
  helix: -0.55 (0.24), residues: 380
  sheet: -1.17 (0.39), residues: 182
  loop : -1.62 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 549 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.036   0.002   PHE A 350 
 TYR   0.020   0.001   TYR A 382 
 ARG   0.003   0.000   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19299 (  375)
  hydrogen bonds       : angle       8.06078 ( 1110)
  SS BOND              : bond        0.00205 (    5)
  SS BOND              : angle       1.16908 (   10)
  covalent geometry    : bond        0.00349 ( 7659)
  covalent geometry    : angle       0.73350 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7308 (mm-30)
REVERT: A   97 ILE cc_start: 0.8067 (mm) cc_final: 0.7659 (pt)
REVERT: A  184 GLN cc_start: 0.7409 (mm110) cc_final: 0.7094 (mm-40)
REVERT: A  220 HIS cc_start: 0.7678 (m-70) cc_final: 0.7340 (m-70)
REVERT: A  226 TRP cc_start: 0.6837 (m100) cc_final: 0.6196 (p-90)
REVERT: A  230 LEU cc_start: 0.8077 (mm) cc_final: 0.7839 (tp)
REVERT: A  299 TRP cc_start: 0.8308 (m100) cc_final: 0.7745 (m100)
REVERT: A  335 ILE cc_start: 0.7893 (mm) cc_final: 0.7473 (tp)
REVERT: A  336 MET cc_start: 0.7985 (ptt) cc_final: 0.7733 (ptp)
REVERT: A  339 CYS cc_start: 0.7004 (t) cc_final: 0.6361 (m)
REVERT: A  389 MET cc_start: 0.7499 (mmm) cc_final: 0.6993 (mtt)
REVERT: A  416 GLU cc_start: 0.8490 (tt0) cc_final: 0.8064 (tp30)
REVERT: A  444 SER cc_start: 0.8679 (m) cc_final: 0.8461 (p)
REVERT: A  457 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6943 (tt0)
REVERT: A  518 ILE cc_start: 0.8436 (pt) cc_final: 0.8200 (tp)
REVERT: A  551 TYR cc_start: 0.7117 (m-10) cc_final: 0.6889 (m-10)
REVERT: A  557 MET cc_start: 0.7669 (ppp) cc_final: 0.6739 (ppp)
REVERT: H    7 SER cc_start: 0.7673 (t) cc_final: 0.7446 (p)
REVERT: H   13 LYS cc_start: 0.8789 (mptt) cc_final: 0.8504 (mptt)
REVERT: H  116 THR cc_start: 0.8533 (m) cc_final: 0.8322 (p)
REVERT: L   13 THR cc_start: 0.8634 (p) cc_final: 0.8252 (p)
REVERT: L   50 TYR cc_start: 0.9116 (p90) cc_final: 0.8725 (p90)
REVERT: L  107 MET cc_start: 0.7964 (mmm) cc_final: 0.7459 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.2139
  time to fit residues: 62.9882
Evaluate side-chains
  145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 74 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
A 160 ASN
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  39 GLN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.177226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144704 restraints weight = 10681.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.148044 restraints weight = 6592.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.150286 restraints weight = 4810.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7664  Z= 0.150
  Angle     :  0.626   5.833  10454  Z= 0.326
  Chirality :  0.043   0.195   1178
  Planarity :  0.004   0.039   1292
  Dihedral  :  4.236  18.147   1039
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.75 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.99 (0.27), residues: 958
  helix:  0.33 (0.26), residues: 388
  sheet: -0.83 (0.40), residues: 172
  loop : -1.51 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 244 
 HIS   0.007   0.001   HIS H  80 
 PHE   0.018   0.002   PHE A 350 
 TYR   0.017   0.002   TYR H 151 
 ARG   0.005   0.001   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04863 (  375)
  hydrogen bonds       : angle       5.80859 ( 1110)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       0.81867 (   10)
  covalent geometry    : bond        0.00335 ( 7659)
  covalent geometry    : angle       0.62547 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ILE cc_start: 0.8428 (mm) cc_final: 0.8199 (mt)
REVERT: A  226 TRP cc_start: 0.6803 (m100) cc_final: 0.6580 (p-90)
REVERT: A  299 TRP cc_start: 0.7891 (m100) cc_final: 0.7676 (m100)
REVERT: A  335 ILE cc_start: 0.7837 (mm) cc_final: 0.7583 (tp)
REVERT: A  557 MET cc_start: 0.7350 (ppp) cc_final: 0.6860 (ppp)
REVERT: H   13 LYS cc_start: 0.8718 (mptt) cc_final: 0.8480 (tppt)
REVERT: H   32 TYR cc_start: 0.7354 (m-10) cc_final: 0.7096 (m-10)
REVERT: H  151 TYR cc_start: 0.7901 (p90) cc_final: 0.7694 (p90)
REVERT: L    1 GLU cc_start: 0.7582 (tp30) cc_final: 0.6954 (tp30)
REVERT: L  150 LYS cc_start: 0.5432 (mtpt) cc_final: 0.5056 (mttt)
REVERT: L  176 MET cc_start: 0.5863 (tpt) cc_final: 0.5525 (tpt)
  outliers start: 11
  outliers final: 8
  residues processed: 161
  average time/residue: 0.1977
  time to fit residues: 42.5353
Evaluate side-chains
  137 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 68 optimal weight:    0.0570
   chunk 61 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0970
   chunk 72 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 ASN
H 103 GLN
L   2 ASN
L 162 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.179165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146311 restraints weight = 10744.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.149799 restraints weight = 6646.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.151987 restraints weight = 4839.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7664  Z= 0.122
  Angle     :  0.586   6.586  10454  Z= 0.300
  Chirality :  0.042   0.204   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  4.137  18.018   1039
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.59 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.66 (0.27), residues: 958
  helix:  0.62 (0.26), residues: 390
  sheet: -0.63 (0.39), residues: 184
  loop : -1.39 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 
 PHE   0.016   0.001   PHE H  29 
 TYR   0.014   0.001   TYR H 151 
 ARG   0.003   0.001   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04219 (  375)
  hydrogen bonds       : angle       5.37780 ( 1110)
  SS BOND              : bond        0.00216 (    5)
  SS BOND              : angle       0.75020 (   10)
  covalent geometry    : bond        0.00265 ( 7659)
  covalent geometry    : angle       0.58626 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6128 (t80)
REVERT: A   97 ILE cc_start: 0.8610 (mm) cc_final: 0.8355 (mt)
REVERT: A  220 HIS cc_start: 0.6789 (m-70) cc_final: 0.6531 (m170)
REVERT: A  226 TRP cc_start: 0.6821 (m100) cc_final: 0.6542 (p-90)
REVERT: A  244 TRP cc_start: 0.7037 (t60) cc_final: 0.6740 (t60)
REVERT: A  299 TRP cc_start: 0.7808 (m100) cc_final: 0.7563 (m100)
REVERT: A  557 MET cc_start: 0.7297 (ppp) cc_final: 0.6985 (ppp)
REVERT: A  574 TRP cc_start: 0.6349 (t-100) cc_final: 0.6148 (t-100)
REVERT: H  151 TYR cc_start: 0.7969 (p90) cc_final: 0.7728 (p90)
REVERT: L    2 ASN cc_start: 0.7834 (m110) cc_final: 0.7265 (m-40)
REVERT: L   50 TYR cc_start: 0.8966 (p90) cc_final: 0.8760 (p90)
REVERT: L  150 LYS cc_start: 0.5390 (mtpt) cc_final: 0.5053 (mttt)
  outliers start: 13
  outliers final: 4
  residues processed: 144
  average time/residue: 0.2029
  time to fit residues: 39.1635
Evaluate side-chains
  124 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 119
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 68 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0470
   chunk 45 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0010
   overall best weight:    0.4884

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.188612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.150791 restraints weight = 11791.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.155123 restraints weight = 6290.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.157973 restraints weight = 4336.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7664  Z= 0.122
  Angle     :  0.572   6.464  10454  Z= 0.292
  Chirality :  0.042   0.165   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  4.040  17.579   1039
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.21 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.41 (0.28), residues: 958
  helix:  0.83 (0.26), residues: 391
  sheet: -0.41 (0.39), residues: 184
  loop : -1.29 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP L 164 
 HIS   0.005   0.001   HIS H  80 
 PHE   0.010   0.001   PHE A 350 
 TYR   0.014   0.001   TYR L 141 
 ARG   0.004   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  375)
  hydrogen bonds       : angle       5.14078 ( 1110)
  SS BOND              : bond        0.00222 (    5)
  SS BOND              : angle       0.73785 (   10)
  covalent geometry    : bond        0.00270 ( 7659)
  covalent geometry    : angle       0.57133 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6266 (t80)
REVERT: A   97 ILE cc_start: 0.8493 (mm) cc_final: 0.8180 (mt)
REVERT: A  226 TRP cc_start: 0.7014 (m100) cc_final: 0.6425 (p-90)
REVERT: A  244 TRP cc_start: 0.7600 (t60) cc_final: 0.7197 (t60)
REVERT: A  299 TRP cc_start: 0.8172 (m100) cc_final: 0.7628 (m100)
REVERT: A  339 CYS cc_start: 0.7633 (t) cc_final: 0.6845 (m)
REVERT: A  557 MET cc_start: 0.7440 (ppp) cc_final: 0.7221 (ppp)
REVERT: A  574 TRP cc_start: 0.6431 (t-100) cc_final: 0.6188 (t-100)
REVERT: H   94 TYR cc_start: 0.8660 (m-80) cc_final: 0.8273 (m-80)
REVERT: L    2 ASN cc_start: 0.8130 (m110) cc_final: 0.7620 (m-40)
REVERT: L  107 MET cc_start: 0.7759 (mmm) cc_final: 0.7369 (mmt)
REVERT: L  150 LYS cc_start: 0.5384 (mtpt) cc_final: 0.5116 (mttt)
  outliers start: 18
  outliers final: 11
  residues processed: 140
  average time/residue: 0.1892
  time to fit residues: 35.8212
Evaluate side-chains
  128 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  206 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0970
   chunk 28 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.187388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.149741 restraints weight = 11650.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.154093 restraints weight = 6243.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.156829 restraints weight = 4305.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7664  Z= 0.134
  Angle     :  0.570   6.638  10454  Z= 0.290
  Chirality :  0.042   0.146   1178
  Planarity :  0.004   0.057   1292
  Dihedral  :  4.026  16.668   1039
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.82 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.25 (0.28), residues: 958
  helix:  0.91 (0.26), residues: 392
  sheet: -0.23 (0.39), residues: 181
  loop : -1.22 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 
 PHE   0.016   0.001   PHE A  96 
 TYR   0.013   0.001   TYR A 146 
 ARG   0.004   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  375)
  hydrogen bonds       : angle       5.02760 ( 1110)
  SS BOND              : bond        0.00211 (    5)
  SS BOND              : angle       0.69573 (   10)
  covalent geometry    : bond        0.00304 ( 7659)
  covalent geometry    : angle       0.57030 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6386 (t80)
REVERT: A   97 ILE cc_start: 0.8503 (mm) cc_final: 0.8175 (mt)
REVERT: A  121 CYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8414 (p)
REVERT: A  226 TRP cc_start: 0.7092 (m100) cc_final: 0.6490 (p-90)
REVERT: A  244 TRP cc_start: 0.7707 (t60) cc_final: 0.7434 (t60)
REVERT: A  299 TRP cc_start: 0.8265 (m100) cc_final: 0.7742 (m100)
REVERT: A  336 MET cc_start: 0.7923 (ptp) cc_final: 0.7703 (ptp)
REVERT: A  339 CYS cc_start: 0.7619 (t) cc_final: 0.6869 (m)
REVERT: A  425 MET cc_start: 0.6961 (mtp) cc_final: 0.6745 (mtp)
REVERT: A  443 LEU cc_start: 0.8673 (tp) cc_final: 0.8464 (tp)
REVERT: A  574 TRP cc_start: 0.6433 (t-100) cc_final: 0.6214 (t-100)
REVERT: H   32 TYR cc_start: 0.7252 (m-10) cc_final: 0.7043 (m-10)
REVERT: L    2 ASN cc_start: 0.8178 (m110) cc_final: 0.7631 (m-40)
REVERT: L  164 TRP cc_start: 0.7770 (m-90) cc_final: 0.7399 (m-90)
  outliers start: 22
  outliers final: 13
  residues processed: 140
  average time/residue: 0.2012
  time to fit residues: 37.8387
Evaluate side-chains
  136 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  206 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0000
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.186947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.149225 restraints weight = 11661.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.153637 restraints weight = 6220.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.156433 restraints weight = 4277.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7664  Z= 0.123
  Angle     :  0.571   6.709  10454  Z= 0.290
  Chirality :  0.041   0.129   1178
  Planarity :  0.004   0.046   1292
  Dihedral  :  3.949  15.744   1039
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.81 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.12 (0.28), residues: 958
  helix:  1.06 (0.27), residues: 386
  sheet: -0.20 (0.40), residues: 181
  loop : -1.13 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 
 PHE   0.016   0.001   PHE A 466 
 TYR   0.014   0.001   TYR A 310 
 ARG   0.005   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  375)
  hydrogen bonds       : angle       4.94779 ( 1110)
  SS BOND              : bond        0.00237 (    5)
  SS BOND              : angle       0.78192 (   10)
  covalent geometry    : bond        0.00276 ( 7659)
  covalent geometry    : angle       0.57096 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6476 (t80)
REVERT: A   97 ILE cc_start: 0.8508 (mm) cc_final: 0.8172 (mt)
REVERT: A  121 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8399 (p)
REVERT: A  226 TRP cc_start: 0.6918 (m100) cc_final: 0.6436 (p-90)
REVERT: A  244 TRP cc_start: 0.7751 (t60) cc_final: 0.7530 (t60)
REVERT: A  299 TRP cc_start: 0.8209 (m100) cc_final: 0.7701 (m100)
REVERT: A  336 MET cc_start: 0.7925 (ptp) cc_final: 0.7659 (ptp)
REVERT: A  339 CYS cc_start: 0.7673 (t) cc_final: 0.6868 (m)
REVERT: A  425 MET cc_start: 0.7046 (mtp) cc_final: 0.6839 (mtp)
REVERT: A  443 LEU cc_start: 0.8653 (tp) cc_final: 0.8433 (tp)
REVERT: A  464 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8481 (tp-100)
REVERT: A  517 MET cc_start: 0.7485 (mmm) cc_final: 0.7133 (mmm)
REVERT: H   32 TYR cc_start: 0.7314 (m-10) cc_final: 0.7092 (m-10)
REVERT: H   94 TYR cc_start: 0.8616 (m-80) cc_final: 0.8181 (m-80)
REVERT: L    2 ASN cc_start: 0.8329 (m110) cc_final: 0.7812 (m-40)
REVERT: L  150 LYS cc_start: 0.5236 (mtpt) cc_final: 0.4503 (mttt)
REVERT: L  164 TRP cc_start: 0.7649 (m-90) cc_final: 0.7250 (m-90)
  outliers start: 22
  outliers final: 15
  residues processed: 143
  average time/residue: 0.1980
  time to fit residues: 38.3879
Evaluate side-chains
  138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 57 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 62 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.185118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.147963 restraints weight = 11651.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.152235 restraints weight = 6240.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.154962 restraints weight = 4297.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7664  Z= 0.143
  Angle     :  0.590   7.138  10454  Z= 0.298
  Chirality :  0.042   0.124   1178
  Planarity :  0.004   0.042   1292
  Dihedral  :  3.970  15.722   1039
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.31 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.10 (0.28), residues: 958
  helix:  1.08 (0.27), residues: 386
  sheet: -0.33 (0.39), residues: 187
  loop : -1.07 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.021   0.001   PHE A 399 
 TYR   0.012   0.001   TYR A 551 
 ARG   0.003   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  375)
  hydrogen bonds       : angle       4.93791 ( 1110)
  SS BOND              : bond        0.00264 (    5)
  SS BOND              : angle       0.80010 (   10)
  covalent geometry    : bond        0.00333 ( 7659)
  covalent geometry    : angle       0.59021 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6558 (t80)
REVERT: A   97 ILE cc_start: 0.8494 (mm) cc_final: 0.8205 (mt)
REVERT: A  121 CYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8423 (p)
REVERT: A  226 TRP cc_start: 0.6988 (m100) cc_final: 0.6500 (p-90)
REVERT: A  244 TRP cc_start: 0.7802 (t60) cc_final: 0.7482 (t60)
REVERT: A  299 TRP cc_start: 0.8208 (m100) cc_final: 0.7737 (m100)
REVERT: A  339 CYS cc_start: 0.7793 (t) cc_final: 0.6979 (m)
REVERT: A  425 MET cc_start: 0.7126 (mtp) cc_final: 0.6897 (mtp)
REVERT: A  443 LEU cc_start: 0.8647 (tp) cc_final: 0.8427 (tp)
REVERT: A  464 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8384 (tp40)
REVERT: A  503 MET cc_start: 0.7756 (mtp) cc_final: 0.7346 (ttt)
REVERT: H   32 TYR cc_start: 0.7335 (m-10) cc_final: 0.6933 (m-10)
REVERT: H   94 TYR cc_start: 0.8663 (m-80) cc_final: 0.8206 (m-80)
REVERT: L   53 SER cc_start: 0.8246 (m) cc_final: 0.8006 (p)
REVERT: L  164 TRP cc_start: 0.7668 (m-90) cc_final: 0.7229 (m-90)
  outliers start: 19
  outliers final: 14
  residues processed: 133
  average time/residue: 0.1884
  time to fit residues: 33.8530
Evaluate side-chains
  134 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  147 LEU
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 34 optimal weight:    0.2980
   chunk 75 optimal weight:    7.9990
   chunk 71 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.184801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.147522 restraints weight = 11833.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.151811 restraints weight = 6299.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.154595 restraints weight = 4331.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7664  Z= 0.135
  Angle     :  0.587   7.231  10454  Z= 0.297
  Chirality :  0.042   0.122   1178
  Planarity :  0.004   0.039   1292
  Dihedral  :  3.961  15.738   1039
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.43 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.09 (0.28), residues: 958
  helix:  1.10 (0.27), residues: 387
  sheet: -0.37 (0.39), residues: 187
  loop : -1.05 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.023   0.001   PHE A 466 
 TYR   0.011   0.001   TYR A 146 
 ARG   0.002   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  375)
  hydrogen bonds       : angle       4.90171 ( 1110)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.78513 (   10)
  covalent geometry    : bond        0.00310 ( 7659)
  covalent geometry    : angle       0.58640 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6642 (t80)
REVERT: A   97 ILE cc_start: 0.8492 (mm) cc_final: 0.8197 (mt)
REVERT: A  121 CYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7731 (p)
REVERT: A  226 TRP cc_start: 0.7005 (m100) cc_final: 0.6588 (p-90)
REVERT: A  244 TRP cc_start: 0.7802 (t60) cc_final: 0.7482 (t60)
REVERT: A  299 TRP cc_start: 0.8136 (m100) cc_final: 0.7720 (m100)
REVERT: A  339 CYS cc_start: 0.7745 (t) cc_final: 0.6792 (m)
REVERT: A  425 MET cc_start: 0.7162 (mtp) cc_final: 0.6944 (mtp)
REVERT: A  443 LEU cc_start: 0.8663 (tp) cc_final: 0.8445 (tp)
REVERT: A  503 MET cc_start: 0.7704 (mtp) cc_final: 0.7403 (ttt)
REVERT: A  517 MET cc_start: 0.7639 (mmm) cc_final: 0.7344 (mmm)
REVERT: H   32 TYR cc_start: 0.7317 (m-10) cc_final: 0.6986 (m-10)
REVERT: H   94 TYR cc_start: 0.8670 (m-80) cc_final: 0.8228 (m-80)
REVERT: L   53 SER cc_start: 0.8204 (m) cc_final: 0.7986 (p)
  outliers start: 22
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1941
  time to fit residues: 36.3622
Evaluate side-chains
  134 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.184075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.146737 restraints weight = 11823.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151021 restraints weight = 6309.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.153755 restraints weight = 4346.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7664  Z= 0.156
  Angle     :  0.614   7.497  10454  Z= 0.313
  Chirality :  0.043   0.128   1178
  Planarity :  0.004   0.039   1292
  Dihedral  :  4.045  15.741   1039
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.68 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.15 (0.28), residues: 958
  helix:  1.07 (0.27), residues: 387
  sheet: -0.49 (0.38), residues: 187
  loop : -1.04 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.017   0.001   PHE A 466 
 TYR   0.022   0.001   TYR L  50 
 ARG   0.003   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  375)
  hydrogen bonds       : angle       4.92648 ( 1110)
  SS BOND              : bond        0.00289 (    5)
  SS BOND              : angle       0.90024 (   10)
  covalent geometry    : bond        0.00363 ( 7659)
  covalent geometry    : angle       0.61372 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.6586 (t80)
REVERT: A   97 ILE cc_start: 0.8513 (mm) cc_final: 0.8228 (mt)
REVERT: A  121 CYS cc_start: 0.8753 (OUTLIER) cc_final: 0.7748 (p)
REVERT: A  226 TRP cc_start: 0.7038 (m100) cc_final: 0.6582 (p-90)
REVERT: A  244 TRP cc_start: 0.7863 (t60) cc_final: 0.7523 (t60)
REVERT: A  299 TRP cc_start: 0.8222 (m100) cc_final: 0.7750 (m100)
REVERT: A  339 CYS cc_start: 0.7816 (t) cc_final: 0.6824 (m)
REVERT: A  425 MET cc_start: 0.7220 (mtp) cc_final: 0.6990 (mtp)
REVERT: A  443 LEU cc_start: 0.8661 (tp) cc_final: 0.8456 (tp)
REVERT: A  517 MET cc_start: 0.7644 (mmm) cc_final: 0.7325 (mmm)
REVERT: H   32 TYR cc_start: 0.7447 (m-10) cc_final: 0.6978 (m-10)
REVERT: L   53 SER cc_start: 0.8265 (m) cc_final: 0.8056 (p)
REVERT: L  164 TRP cc_start: 0.7691 (m-90) cc_final: 0.7415 (m-90)
  outliers start: 24
  outliers final: 18
  residues processed: 140
  average time/residue: 0.1922
  time to fit residues: 36.4431
Evaluate side-chains
  137 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  207 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0020
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.184174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.147271 restraints weight = 11832.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.151499 restraints weight = 6266.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.154260 restraints weight = 4310.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7664  Z= 0.139
  Angle     :  0.622   9.075  10454  Z= 0.317
  Chirality :  0.043   0.282   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  4.051  15.730   1039
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.93 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.11 (0.28), residues: 958
  helix:  1.11 (0.27), residues: 386
  sheet: -0.44 (0.38), residues: 187
  loop : -1.04 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.016   0.001   PHE A 466 
 TYR   0.019   0.001   TYR L  50 
 ARG   0.003   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  375)
  hydrogen bonds       : angle       4.92633 ( 1110)
  SS BOND              : bond        0.00349 (    5)
  SS BOND              : angle       1.16302 (   10)
  covalent geometry    : bond        0.00322 ( 7659)
  covalent geometry    : angle       0.62083 (10444)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6650 (t80)
REVERT: A   97 ILE cc_start: 0.8469 (mm) cc_final: 0.8162 (mt)
REVERT: A  121 CYS cc_start: 0.8731 (OUTLIER) cc_final: 0.7749 (p)
REVERT: A  226 TRP cc_start: 0.7064 (m100) cc_final: 0.6594 (p-90)
REVERT: A  244 TRP cc_start: 0.7885 (t60) cc_final: 0.7548 (t60)
REVERT: A  299 TRP cc_start: 0.8158 (m100) cc_final: 0.7725 (m100)
REVERT: A  332 ARG cc_start: 0.5940 (tpp-160) cc_final: 0.4975 (mmt-90)
REVERT: A  335 ILE cc_start: 0.7938 (mm) cc_final: 0.7482 (tp)
REVERT: A  339 CYS cc_start: 0.7755 (t) cc_final: 0.6810 (m)
REVERT: A  411 GLN cc_start: 0.8360 (tp40) cc_final: 0.8138 (tp-100)
REVERT: A  425 MET cc_start: 0.7208 (mtp) cc_final: 0.7001 (mtp)
REVERT: A  443 LEU cc_start: 0.8655 (tp) cc_final: 0.8438 (tp)
REVERT: A  517 MET cc_start: 0.7592 (mmm) cc_final: 0.7269 (mmm)
REVERT: H   32 TYR cc_start: 0.7324 (m-10) cc_final: 0.6874 (m-10)
REVERT: H   76 ARG cc_start: 0.8695 (mtm180) cc_final: 0.8495 (ptt90)
REVERT: H   94 TYR cc_start: 0.8678 (m-80) cc_final: 0.8209 (m-80)
  outliers start: 21
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1903
  time to fit residues: 36.2144
Evaluate side-chains
  136 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 THR
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue  137 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0470
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.185051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.147908 restraints weight = 11684.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.152206 restraints weight = 6305.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.154967 restraints weight = 4346.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7664  Z= 0.147
  Angle     :  0.637   8.319  10454  Z= 0.322
  Chirality :  0.043   0.317   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  4.110  16.011   1039
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.16 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -0.11 (0.28), residues: 958
  helix:  1.09 (0.27), residues: 386
  sheet: -0.45 (0.38), residues: 190
  loop : -1.02 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.016   0.001   PHE A 466 
 TYR   0.018   0.001   TYR L  50 
 ARG   0.002   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  375)
  hydrogen bonds       : angle       4.92885 ( 1110)
  SS BOND              : bond        0.00233 (    5)
  SS BOND              : angle       1.10888 (   10)
  covalent geometry    : bond        0.00342 ( 7659)
  covalent geometry    : angle       0.63606 (10444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2673.35 seconds
wall clock time: 47 minutes 32.68 seconds (2852.68 seconds total)