Starting phenix.real_space_refine
on Fri Jun  6 08:45:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cp5_45800/06_2025/9cp5_45800.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cp5_45800/06_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_45800/06_2025/9cp5_45800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cp5_45800/06_2025/9cp5_45800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cp5_45800/06_2025/9cp5_45800.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cp5_45800/06_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-5710/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: 4.54, per 1000 atoms: 0.61
  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.83
  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: 2.55

  Time building geometry restraints manager: 2.12 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:             1.160
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.040
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.720
-------------------------------------------------------------------------------
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  : 0.830 
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: 0.2156
  time to fit residues: 63.4693
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  : 0.825 
-------------------------------------------------------------------------------
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 = 0.177287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144746 restraints weight = 10682.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.148093 restraints weight = 6593.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.150356 restraints weight = 4810.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7664  Z= 0.150
  Angle     :  0.625   5.827  10454  Z= 0.326
  Chirality :  0.043   0.196   1178
  Planarity :  0.004   0.039   1292
  Dihedral  :  4.235  18.054   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  : 12.87 %
    Favored  : 85.77 %
  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        0.04862 (  375)
  hydrogen bonds       : angle       5.81087 ( 1110)
  SS BOND              : bond        0.00262 (    5)
  SS BOND              : angle       0.81300 (   10)
  covalent geometry    : bond        0.00333 ( 7659)
  covalent geometry    : angle       0.62479 (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  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ILE cc_start: 0.8426 (mm) cc_final: 0.8198 (mt)
REVERT: A  226 TRP cc_start: 0.6803 (m100) cc_final: 0.6580 (p-90)
REVERT: A  299 TRP cc_start: 0.7889 (m100) cc_final: 0.7657 (m100)
REVERT: A  335 ILE cc_start: 0.7834 (mm) cc_final: 0.7576 (tp)
REVERT: A  557 MET cc_start: 0.7351 (ppp) cc_final: 0.6866 (ppp)
REVERT: H   13 LYS cc_start: 0.8718 (mptt) cc_final: 0.8479 (tppt)
REVERT: H   32 TYR cc_start: 0.7353 (m-10) cc_final: 0.7096 (m-10)
REVERT: H  151 TYR cc_start: 0.7902 (p90) cc_final: 0.7695 (p90)
REVERT: L    1 GLU cc_start: 0.7579 (tp30) cc_final: 0.6948 (tp30)
REVERT: L  150 LYS cc_start: 0.5437 (mtpt) cc_final: 0.5071 (mttt)
REVERT: L  176 MET cc_start: 0.5858 (tpt) cc_final: 0.5523 (tpt)
  outliers start: 11
  outliers final: 8
  residues processed: 161
  average time/residue: 0.1910
  time to fit residues: 41.1029
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  : 0.759 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    0.1980
   chunk 72 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 84 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   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 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 ASN
H 103 GLN
L   2 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.176992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.143618 restraints weight = 10756.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.147159 restraints weight = 6550.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.149463 restraints weight = 4743.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2794

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= 0.137
  Angle     :  0.595   6.694  10454  Z= 0.305
  Chirality :  0.043   0.200   1178
  Planarity :  0.004   0.037   1292
  Dihedral  :  4.176  18.243   1039
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.72 %
    Favored  : 82.55 %
  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:  0.58 (0.26), residues: 392
  sheet: -0.64 (0.39), residues: 184
  loop : -1.33 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP L 164 
 HIS   0.004   0.001   HIS H  80 
 PHE   0.016   0.002   PHE H  29 
 TYR   0.015   0.001   TYR H 151 
 ARG   0.010   0.001   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04279 (  375)
  hydrogen bonds       : angle       5.38584 ( 1110)
  SS BOND              : bond        0.00233 (    5)
  SS BOND              : angle       0.78595 (   10)
  covalent geometry    : bond        0.00309 ( 7659)
  covalent geometry    : angle       0.59466 (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
  148 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6097 (t80)
REVERT: A   97 ILE cc_start: 0.8621 (mm) cc_final: 0.8352 (mt)
REVERT: A  226 TRP cc_start: 0.6929 (m100) cc_final: 0.6537 (p-90)
REVERT: A  244 TRP cc_start: 0.7186 (t60) cc_final: 0.6836 (t60)
REVERT: A  299 TRP cc_start: 0.7975 (m100) cc_final: 0.7645 (m100)
REVERT: A  336 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7404 (ptp)
REVERT: A  557 MET cc_start: 0.7403 (ppp) cc_final: 0.7064 (ppp)
REVERT: A  574 TRP cc_start: 0.6411 (t-100) cc_final: 0.6202 (t-100)
REVERT: H   13 LYS cc_start: 0.8753 (mptt) cc_final: 0.8539 (tppt)
REVERT: H   32 TYR cc_start: 0.7582 (m-10) cc_final: 0.7377 (m-10)
REVERT: H  151 TYR cc_start: 0.7994 (p90) cc_final: 0.7462 (p90)
REVERT: L    2 ASN cc_start: 0.7940 (m110) cc_final: 0.7357 (m-40)
REVERT: L   50 TYR cc_start: 0.9011 (p90) cc_final: 0.8808 (p90)
REVERT: L  150 LYS cc_start: 0.5492 (mtpt) cc_final: 0.5213 (mttt)
  outliers start: 14
  outliers final: 8
  residues processed: 139
  average time/residue: 0.2101
  time to fit residues: 39.3898
Evaluate side-chains
  128 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  233 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  336 MET
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:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 7 optimal weight:    0.4980
   chunk 86 optimal weight:    0.1980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.4184 r_free = 0.4184 target = 0.177405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.144190 restraints weight = 10764.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.147742 restraints weight = 6518.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.150081 restraints weight = 4700.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.3026

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     :  0.570   6.342  10454  Z= 0.290
  Chirality :  0.042   0.161   1178
  Planarity :  0.004   0.038   1292
  Dihedral  :  4.045  17.503   1039
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.96 %
    Favored  : 81.19 %
  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:  0.78 (0.26), residues: 392
  sheet: -0.41 (0.39), residues: 184
  loop : -1.26 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP L 164 
 HIS   0.005   0.001   HIS H  80 
 PHE   0.012   0.001   PHE A 358 
 TYR   0.014   0.001   TYR L 141 
 ARG   0.003   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  375)
  hydrogen bonds       : angle       5.11854 ( 1110)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       0.71993 (   10)
  covalent geometry    : bond        0.00274 ( 7659)
  covalent geometry    : angle       0.56972 (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
  142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6347 (t80)
REVERT: A   97 ILE cc_start: 0.8584 (mm) cc_final: 0.8262 (mt)
REVERT: A  226 TRP cc_start: 0.6964 (m100) cc_final: 0.6569 (p-90)
REVERT: A  244 TRP cc_start: 0.7364 (t60) cc_final: 0.7118 (t60)
REVERT: A  299 TRP cc_start: 0.8008 (m100) cc_final: 0.7605 (m100)
REVERT: A  339 CYS cc_start: 0.7355 (t) cc_final: 0.6897 (m)
REVERT: H   94 TYR cc_start: 0.8651 (m-80) cc_final: 0.8379 (m-80)
REVERT: H  151 TYR cc_start: 0.7971 (p90) cc_final: 0.7541 (p90)
REVERT: L    2 ASN cc_start: 0.7919 (m110) cc_final: 0.7352 (m-40)
REVERT: L  107 MET cc_start: 0.7659 (mmm) cc_final: 0.7388 (mmt)
REVERT: L  150 LYS cc_start: 0.5451 (mtpt) cc_final: 0.5223 (mttt)
REVERT: L  193 TYR cc_start: 0.4786 (m-80) cc_final: 0.4547 (m-10)
  outliers start: 15
  outliers final: 10
  residues processed: 137
  average time/residue: 0.1962
  time to fit residues: 36.7052
Evaluate side-chains
  130 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
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 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  212 VAL
Chi-restraints excluded: chain L residue   21 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0370
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.174935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.142074 restraints weight = 10691.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145412 restraints weight = 6650.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.147585 restraints weight = 4895.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7664  Z= 0.139
  Angle     :  0.582   6.645  10454  Z= 0.297
  Chirality :  0.042   0.159   1178
  Planarity :  0.004   0.055   1292
  Dihedral  :  4.054  16.736   1039
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.32 %
    Favored  : 79.33 %
  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: -0.26 (0.28), residues: 958
  helix:  0.95 (0.27), residues: 386
  sheet: -0.40 (0.39), residues: 184
  loop : -1.14 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.011   0.001   PHE A 358 
 TYR   0.013   0.001   TYR A 146 
 ARG   0.004   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  375)
  hydrogen bonds       : angle       5.04732 ( 1110)
  SS BOND              : bond        0.00230 (    5)
  SS BOND              : angle       0.70519 (   10)
  covalent geometry    : bond        0.00318 ( 7659)
  covalent geometry    : angle       0.58177 (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
  145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6509 (t80)
REVERT: A   97 ILE cc_start: 0.8599 (mm) cc_final: 0.8258 (mt)
REVERT: A  299 TRP cc_start: 0.7914 (m100) cc_final: 0.7682 (m100)
REVERT: A  339 CYS cc_start: 0.7300 (t) cc_final: 0.6917 (m)
REVERT: A  443 LEU cc_start: 0.8716 (tp) cc_final: 0.8452 (tp)
REVERT: H  151 TYR cc_start: 0.8044 (p90) cc_final: 0.7648 (p90)
REVERT: L    2 ASN cc_start: 0.7957 (m110) cc_final: 0.7406 (m-40)
  outliers start: 19
  outliers final: 13
  residues processed: 139
  average time/residue: 0.2056
  time to fit residues: 38.2970
Evaluate side-chains
  131 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
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  392 SER
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  212 VAL
Chi-restraints excluded: chain L residue   21 MET
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:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0570
   chunk 8 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0050
   chunk 5 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4312

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.176550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.143921 restraints weight = 10733.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.147264 restraints weight = 6625.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.149403 restraints weight = 4854.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3478

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= 0.117
  Angle     :  0.576   7.364  10454  Z= 0.290
  Chirality :  0.041   0.128   1178
  Planarity :  0.004   0.045   1292
  Dihedral  :  3.981  17.201   1039
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.69 %
    Favored  : 78.59 %
  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: -0.16 (0.28), residues: 958
  helix:  1.06 (0.27), residues: 387
  sheet: -0.36 (0.39), residues: 184
  loop : -1.12 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.013   0.001   PHE A 466 
 TYR   0.022   0.001   TYR A 310 
 ARG   0.004   0.000   ARG A 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  375)
  hydrogen bonds       : angle       4.92283 ( 1110)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       0.76686 (   10)
  covalent geometry    : bond        0.00263 ( 7659)
  covalent geometry    : angle       0.57622 (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
  148 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A   78 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6503 (t80)
REVERT: A   97 ILE cc_start: 0.8591 (mm) cc_final: 0.8245 (mt)
REVERT: A  121 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (p)
REVERT: A  299 TRP cc_start: 0.7932 (m100) cc_final: 0.7560 (m100)
REVERT: A  443 LEU cc_start: 0.8690 (tp) cc_final: 0.8460 (tp)
REVERT: A  464 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8389 (tp-100)
REVERT: A  517 MET cc_start: 0.7524 (mmm) cc_final: 0.7231 (mmm)
REVERT: H   94 TYR cc_start: 0.8609 (m-80) cc_final: 0.8291 (m-80)
REVERT: H  151 TYR cc_start: 0.8100 (p90) cc_final: 0.7734 (p90)
REVERT: L    2 ASN cc_start: 0.8018 (m110) cc_final: 0.7485 (m-40)
REVERT: L  150 LYS cc_start: 0.5125 (mtpt) cc_final: 0.4350 (mttt)
  outliers start: 22
  outliers final: 13
  residues processed: 142
  average time/residue: 0.1929
  time to fit residues: 37.1937
Evaluate side-chains
  134 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
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  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  564 CYS
Chi-restraints excluded: chain H residue    5 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 45 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.176017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.138287 restraints weight = 11767.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.142321 restraints weight = 6432.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.144876 restraints weight = 4494.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.073   7664  Z= 0.334
  Angle     :  0.767   8.677  10454  Z= 0.391
  Chirality :  0.048   0.168   1178
  Planarity :  0.005   0.045   1292
  Dihedral  :  4.628  17.431   1039
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.95 %
    Favored  : 78.09 %
  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: -0.58 (0.27), residues: 958
  helix:  0.64 (0.26), residues: 385
  sheet: -0.80 (0.37), residues: 192
  loop : -1.12 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP L 164 
 HIS   0.005   0.002   HIS L 199 
 PHE   0.022   0.002   PHE A  88 
 TYR   0.019   0.002   TYR A 551 
 ARG   0.006   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04814 (  375)
  hydrogen bonds       : angle       5.42852 ( 1110)
  SS BOND              : bond        0.00442 (    5)
  SS BOND              : angle       1.24201 (   10)
  covalent geometry    : bond        0.00779 ( 7659)
  covalent geometry    : angle       0.76682 (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
  161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   78 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6394 (t80)
REVERT: A   97 ILE cc_start: 0.8656 (mm) cc_final: 0.8318 (mt)
REVERT: A  121 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (p)
REVERT: A  339 CYS cc_start: 0.8245 (t) cc_final: 0.7040 (m)
REVERT: L  150 LYS cc_start: 0.5490 (mtpt) cc_final: 0.5078 (mttt)
REVERT: L  167 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7271 (tp40)
  outliers start: 32
  outliers final: 22
  residues processed: 152
  average time/residue: 0.1978
  time to fit residues: 40.8155
Evaluate side-chains
  151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  263 ILE
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  335 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  392 SER
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   17 SER
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  206 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 464 GLN
H  39 GLN
L 162 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.182116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.144814 restraints weight = 11772.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.149086 restraints weight = 6260.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.151828 restraints weight = 4298.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7664  Z= 0.143
  Angle     :  0.643   9.973  10454  Z= 0.325
  Chirality :  0.043   0.132   1178
  Planarity :  0.004   0.052   1292
  Dihedral  :  4.345  19.795   1039
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.16 %
    Favored  : 76.49 %
  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: -0.30 (0.28), residues: 958
  helix:  0.93 (0.27), residues: 386
  sheet: -0.65 (0.38), residues: 186
  loop : -1.05 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.020   0.001   PHE A 399 
 TYR   0.013   0.001   TYR A 544 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 (  375)
  hydrogen bonds       : angle       5.09498 ( 1110)
  SS BOND              : bond        0.00255 (    5)
  SS BOND              : angle       1.23362 (   10)
  covalent geometry    : bond        0.00327 ( 7659)
  covalent geometry    : angle       0.64266 (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
  152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A   78 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6616 (t80)
REVERT: A   97 ILE cc_start: 0.8662 (mm) cc_final: 0.8316 (mt)
REVERT: A  121 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8010 (p)
REVERT: A  299 TRP cc_start: 0.8280 (m100) cc_final: 0.7882 (m100)
REVERT: A  339 CYS cc_start: 0.7971 (t) cc_final: 0.6922 (m)
REVERT: A  426 TYR cc_start: 0.7341 (m-10) cc_final: 0.7031 (m-80)
REVERT: A  464 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8168 (tp40)
REVERT: A  517 MET cc_start: 0.7650 (mmm) cc_final: 0.7367 (mmm)
REVERT: H   94 TYR cc_start: 0.8787 (m-80) cc_final: 0.8337 (m-80)
REVERT: L  119 PHE cc_start: 0.6867 (m-80) cc_final: 0.6553 (m-10)
  outliers start: 19
  outliers final: 12
  residues processed: 147
  average time/residue: 0.2104
  time to fit residues: 41.4254
Evaluate side-chains
  139 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
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  279 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  464 GLN
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  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:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0170
   chunk 63 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
A 142 HIS
A 464 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.183381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.145700 restraints weight = 11778.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.150026 restraints weight = 6276.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.152793 restraints weight = 4314.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7664  Z= 0.132
  Angle     :  0.653  10.842  10454  Z= 0.330
  Chirality :  0.042   0.130   1178
  Planarity :  0.004   0.050   1292
  Dihedral  :  4.259  22.968   1039
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.03 %
    Favored  : 75.87 %
  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: -0.22 (0.28), residues: 958
  helix:  1.03 (0.27), residues: 385
  sheet: -0.71 (0.38), residues: 193
  loop : -0.98 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.002   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.021   0.002   PHE A 466 
 TYR   0.016   0.001   TYR A 551 
 ARG   0.002   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  375)
  hydrogen bonds       : angle       5.01819 ( 1110)
  SS BOND              : bond        0.00228 (    5)
  SS BOND              : angle       1.13397 (   10)
  covalent geometry    : bond        0.00302 ( 7659)
  covalent geometry    : angle       0.65240 (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
  146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   78 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: A   97 ILE cc_start: 0.8608 (mm) cc_final: 0.8306 (mt)
REVERT: A  121 CYS cc_start: 0.8812 (OUTLIER) cc_final: 0.7980 (p)
REVERT: A  299 TRP cc_start: 0.8221 (m100) cc_final: 0.7807 (m100)
REVERT: A  339 CYS cc_start: 0.7731 (t) cc_final: 0.6955 (m)
REVERT: A  426 TYR cc_start: 0.7280 (m-10) cc_final: 0.7063 (m-80)
REVERT: A  503 MET cc_start: 0.7845 (mtp) cc_final: 0.7559 (ttt)
REVERT: A  517 MET cc_start: 0.7656 (mmm) cc_final: 0.7356 (mmm)
REVERT: A  557 MET cc_start: 0.7359 (ttp) cc_final: 0.7151 (tmm)
REVERT: H   94 TYR cc_start: 0.8757 (m-80) cc_final: 0.8340 (m-80)
REVERT: L  119 PHE cc_start: 0.7061 (m-80) cc_final: 0.6731 (m-10)
REVERT: L  167 GLN cc_start: 0.7509 (mm-40) cc_final: 0.6971 (tp40)
  outliers start: 17
  outliers final: 13
  residues processed: 142
  average time/residue: 0.1956
  time to fit residues: 37.5942
Evaluate side-chains
  140 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
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  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  560 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain L residue   21 MET
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:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0870
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0770
   chunk 34 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.4916

-------------------------------------------------------------------------------
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 = 0.4321 r_free = 0.4321 target = 0.183479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.146821 restraints weight = 11772.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.151076 restraints weight = 6227.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.153801 restraints weight = 4271.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7664  Z= 0.139
  Angle     :  0.653   8.350  10454  Z= 0.331
  Chirality :  0.043   0.196   1178
  Planarity :  0.004   0.051   1292
  Dihedral  :  4.224  20.386   1039
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.52 %
    Favored  : 75.37 %
  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: -0.20 (0.28), residues: 958
  helix:  1.03 (0.27), residues: 386
  sheet: -0.65 (0.38), residues: 193
  loop : -0.98 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.001   TRP L 164 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.019   0.002   PHE A 466 
 TYR   0.020   0.001   TYR A 551 
 ARG   0.004   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  375)
  hydrogen bonds       : angle       5.03780 ( 1110)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       1.10395 (   10)
  covalent geometry    : bond        0.00320 ( 7659)
  covalent geometry    : angle       0.65229 (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
  147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A   78 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.6863 (t80)
REVERT: A   97 ILE cc_start: 0.8566 (mm) cc_final: 0.8275 (mt)
REVERT: A  299 TRP cc_start: 0.8222 (m100) cc_final: 0.7800 (m100)
REVERT: A  332 ARG cc_start: 0.6029 (tpp-160) cc_final: 0.4662 (mpt180)
REVERT: A  335 ILE cc_start: 0.7862 (mm) cc_final: 0.7616 (tp)
REVERT: A  339 CYS cc_start: 0.7600 (t) cc_final: 0.6882 (m)
REVERT: A  411 GLN cc_start: 0.8459 (tp40) cc_final: 0.8118 (tp-100)
REVERT: A  426 TYR cc_start: 0.7229 (m-10) cc_final: 0.7017 (m-80)
REVERT: A  443 LEU cc_start: 0.8805 (tp) cc_final: 0.8590 (tp)
REVERT: A  503 MET cc_start: 0.7566 (mtp) cc_final: 0.7286 (ttt)
REVERT: A  517 MET cc_start: 0.7618 (mmm) cc_final: 0.7302 (mmm)
REVERT: H   94 TYR cc_start: 0.8738 (m-80) cc_final: 0.8328 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1935
  time to fit residues: 37.0507
Evaluate side-chains
  138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  279 SER
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  557 MET
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  212 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   21 MET
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 14 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 90 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 411 GLN
A 464 GLN
L 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.183571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.147077 restraints weight = 11616.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.151336 restraints weight = 6153.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.154052 restraints weight = 4216.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7664  Z= 0.147
  Angle     :  0.666   8.252  10454  Z= 0.337
  Chirality :  0.044   0.299   1178
  Planarity :  0.004   0.050   1292
  Dihedral  :  4.242  19.322   1039
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.65 %
    Favored  : 74.88 %
  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: -0.19 (0.28), residues: 958
  helix:  0.98 (0.27), residues: 386
  sheet: -0.50 (0.38), residues: 194
  loop : -1.00 (0.34), residues: 378

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   0.023   0.002   PHE A 113 
 TYR   0.025   0.002   TYR A 551 
 ARG   0.003   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  375)
  hydrogen bonds       : angle       5.04876 ( 1110)
  SS BOND              : bond        0.00226 (    5)
  SS BOND              : angle       1.09672 (   10)
  covalent geometry    : bond        0.00344 ( 7659)
  covalent geometry    : angle       0.66563 (10444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2737.38 seconds
wall clock time: 48 minutes 14.54 seconds (2894.54 seconds total)