Starting phenix.real_space_refine
on Sun May 11 08:41:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u63_41942/05_2025/8u63_41942.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u63_41942/05_2025/8u63_41942.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u63_41942/05_2025/8u63_41942.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u63_41942/05_2025/8u63_41942.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u63_41942/05_2025/8u63_41942.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u63_41942/05_2025/8u63_41942.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4894      2.51       5
     N    1350      2.21       5
     O    1468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7758
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3836
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 465}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.86, per 1000 atoms: 1.14
  Number of scatterers: 7758
  At special positions: 0
  Unit cell: (105.777, 99.207, 106.434, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1468      8.00
     N    1350      7.00
     C    4894      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      44.6% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 15
      removed outlier: 3.613A  pdb=" N   VAL A  11 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A  12 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 131 through 145
      removed outlier: 3.861A  pdb=" N   GLY A 137 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 205 through 215
    Processing helix  chain 'A' and resid 253 through 263
    Processing helix  chain 'A' and resid 294 through 338
      removed outlier: 3.881A  pdb=" N   ALA A 300 " --> pdb=" O   GLU A 296 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR A 326 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS A 327 " --> pdb=" O   GLN A 323 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   MET A 337 " --> pdb=" O   GLN A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 351
      removed outlier: 3.965A  pdb=" N   LEU A 349 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA A 350 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 361
      removed outlier: 4.063A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 393
      removed outlier: 3.863A  pdb=" N   THR A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TRP A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 4.017A  pdb=" N   VAL A 408 " --> pdb=" O   HIS A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 416
      removed outlier: 3.752A  pdb=" N   GLU A 413 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ALA A 414 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR A 415 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A 416 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 416'
    Processing helix  chain 'A' and resid 441 through 446
      removed outlier: 3.518A  pdb=" N   GLN A 444 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 480
      removed outlier: 3.833A  pdb=" N   GLU A 474 " --> pdb=" O   ARG A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 509
      removed outlier: 3.744A  pdb=" N   ASN A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 15
      removed outlier: 3.612A  pdb=" N   VAL B  11 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU B  12 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 131 through 145
      removed outlier: 3.861A  pdb=" N   GLY B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 205 through 215
    Processing helix  chain 'B' and resid 253 through 263
    Processing helix  chain 'B' and resid 294 through 338
      removed outlier: 3.882A  pdb=" N   ALA B 300 " --> pdb=" O   GLU B 296 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR B 326 " --> pdb=" O   ARG B 322 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS B 327 " --> pdb=" O   GLN B 323 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   MET B 337 " --> pdb=" O   GLN B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 351
      removed outlier: 3.965A  pdb=" N   LEU B 349 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA B 350 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 361
      removed outlier: 4.062A  pdb=" N   VAL B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
      removed outlier: 3.864A  pdb=" N   THR B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TRP B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 409
      removed outlier: 4.018A  pdb=" N   VAL B 408 " --> pdb=" O   HIS B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 416
      removed outlier: 3.753A  pdb=" N   GLU B 413 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ALA B 414 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR B 415 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN B 416 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 410 through 416'
    Processing helix  chain 'B' and resid 441 through 446
      removed outlier: 3.517A  pdb=" N   GLN B 444 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 480
      removed outlier: 3.834A  pdb=" N   GLU B 474 " --> pdb=" O   ARG B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 509
      removed outlier: 3.744A  pdb=" N   ASN B 505 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27
      removed outlier: 4.133A  pdb=" N   GLN A  45 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU A  33 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   GLU A 101 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU A  93 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199
      removed outlier: 5.571A  pdb=" N   VAL A 182 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG A 173 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 184 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TRP A 280 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A 273 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   LEU A 282 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   SER A 284 " --> pdb=" O   MET A 269 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   MET A 269 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   SER A 267 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235
      removed outlier: 3.627A  pdb=" N   GLN A 240 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 377
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27
      removed outlier: 4.133A  pdb=" N   GLN B  45 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU B  33 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   GLU B 101 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   LEU B  93 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199
      removed outlier: 5.572A  pdb=" N   VAL B 182 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG B 173 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA B 184 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TRP B 280 " --> pdb=" O   PHE B 174 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LEU B 273 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   LEU B 282 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL B 271 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   SER B 284 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   MET B 269 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLY B 286 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   SER B 267 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 235
      removed outlier: 3.627A  pdb=" N   GLN B 240 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 372 through 377

    393 hydrogen bonds defined for protein.
    1095 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: 2.43

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1437
        1.32 -     1.45: 1913
        1.45 -     1.57: 4488
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 7916
  Sorted by residual:
  bond pdb=" CA  VAL A 231 "
       pdb=" CB  VAL A 231 "
    ideal  model  delta    sigma   weight residual
    1.538  1.529  0.010 8.80e-03 1.29e+04 1.21e+00
  bond pdb=" CB  GLN B  64 "
       pdb=" CG  GLN B  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.53e-01
  bond pdb=" CA  VAL B 231 "
       pdb=" CB  VAL B 231 "
    ideal  model  delta    sigma   weight residual
    1.538  1.530  0.008 8.80e-03 1.29e+04 9.18e-01
  bond pdb=" CB  GLN A  64 "
       pdb=" CG  GLN A  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.75e-01
  bond pdb=" CB  GLN B 372 "
       pdb=" CG  GLN B 372 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.65e-01
  ... (remaining 7911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 10570
        1.68 -     3.36: 151
        3.36 -     5.04: 29
        5.04 -     6.72: 4
        6.72 -     8.40: 6
  Bond angle restraints: 10760
  Sorted by residual:
  angle pdb=" CB  MET A 392 "
        pdb=" CG  MET A 392 "
        pdb=" SD  MET A 392 "
      ideal   model   delta    sigma   weight residual
     112.70  104.76    7.94 3.00e+00 1.11e-01 7.01e+00
  angle pdb=" CB  MET B 392 "
        pdb=" CG  MET B 392 "
        pdb=" SD  MET B 392 "
      ideal   model   delta    sigma   weight residual
     112.70  104.76    7.94 3.00e+00 1.11e-01 7.01e+00
  angle pdb=" CB  MET A 338 "
        pdb=" CG  MET A 338 "
        pdb=" SD  MET A 338 "
      ideal   model   delta    sigma   weight residual
     112.70  120.16   -7.46 3.00e+00 1.11e-01 6.19e+00
  angle pdb=" CB  MET B 338 "
        pdb=" CG  MET B 338 "
        pdb=" SD  MET B 338 "
      ideal   model   delta    sigma   weight residual
     112.70  120.16   -7.46 3.00e+00 1.11e-01 6.18e+00
  angle pdb=" CA  MET A 392 "
        pdb=" CB  MET A 392 "
        pdb=" CG  MET A 392 "
      ideal   model   delta    sigma   weight residual
     114.10  119.07   -4.97 2.00e+00 2.50e-01 6.17e+00
  ... (remaining 10755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4100
       17.73 -    35.46: 510
       35.46 -    53.19: 130
       53.19 -    70.92: 44
       70.92 -    88.65: 18
  Dihedral angle restraints: 4802
    sinusoidal: 1954
      harmonic: 2848
  Sorted by residual:
  dihedral pdb=" CA  ARG A 324 "
           pdb=" C   ARG A 324 "
           pdb=" N   GLU A 325 "
           pdb=" CA  GLU A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.02   15.98     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  ARG B 324 "
           pdb=" C   ARG B 324 "
           pdb=" N   GLU B 325 "
           pdb=" CA  GLU B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.06   15.94     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CG  ARG B 386 "
           pdb=" CD  ARG B 386 "
           pdb=" NE  ARG B 386 "
           pdb=" CZ  ARG B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.59  -43.59     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 4799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 715
       0.027 -    0.054: 298
       0.054 -    0.081: 106
       0.081 -    0.108: 67
       0.108 -    0.135: 22
  Chirality restraints: 1208
  Sorted by residual:
  chirality pdb=" CA  ILE B 220 "
            pdb=" N   ILE B 220 "
            pdb=" C   ILE B 220 "
            pdb=" CB  ILE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ILE A 220 "
            pdb=" N   ILE A 220 "
            pdb=" C   ILE A 220 "
            pdb=" CB  ILE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  VAL B  53 "
            pdb=" N   VAL B  53 "
            pdb=" C   VAL B  53 "
            pdb=" CB  VAL B  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 1205 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 231 "    0.030 5.00e-02 4.00e+02   4.57e-02 3.34e+00
        pdb=" N   PRO B 232 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 232 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 232 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 231 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO A 232 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 289 "   -0.022 5.00e-02 4.00e+02   3.34e-02 1.79e+00
        pdb=" N   PRO A 290 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 178
        2.70 -     3.25: 7408
        3.25 -     3.80: 12140
        3.80 -     4.35: 15907
        4.35 -     4.90: 26649
  Nonbonded interactions: 62282
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  65 "
            pdb=" OD1 ASP A  67 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" OD1 ASP B  67 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" O   SER A 309 "
            pdb=" OG  SER A 313 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   SER B 309 "
            pdb=" OG  SER B 313 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   GLY A 305 "
            pdb=" OG  SER A 309 "
     model   vdw
     2.276 3.040
  ... (remaining 62277 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             15.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     24.190
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
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   0.064   7918  Z= 0.162
  Angle     :  0.559   8.401  10760  Z= 0.278
  Chirality :  0.041   0.135   1208
  Planarity :  0.004   0.046   1402
  Dihedral  : 17.941  88.648   2954
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 27.62 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.74 (0.25), residues: 972
  helix: -0.09 (0.24), residues: 400
  sheet: -0.28 (0.36), residues: 164
  loop : -0.84 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 280 
 HIS   0.011   0.001   HIS A 295 
 PHE   0.009   0.001   PHE A 199 
 TYR   0.023   0.002   TYR B 225 
 ARG   0.007   0.001   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20424 (  393)
  hydrogen bonds       : angle       7.51952 ( 1095)
  covalent geometry    : bond        0.00284 ( 7916)
  covalent geometry    : angle       0.55858 (10760)
  Misc. bond           : bond        0.06334 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 197
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 THR cc_start: 0.8300 (p) cc_final: 0.8075 (p)
REVERT: A  333 GLN cc_start: 0.7942 (tt0) cc_final: 0.7671 (tt0)
REVERT: A  480 MET cc_start: 0.8073 (mmm) cc_final: 0.7658 (tpp)
REVERT: B   79 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7483 (mmt-90)
REVERT: B  372 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7139 (tm-30)
REVERT: B  435 VAL cc_start: 0.8460 (m) cc_final: 0.8117 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 197
  average time/residue: 0.2546
  time to fit residues: 63.4301
Evaluate side-chains
  189 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  489 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0980
   chunk 50 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
A 433 ASN
B 262 ASN
B 302 GLN
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.150151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130406 restraints weight = 10652.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.18
r_work: 0.3507 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7918  Z= 0.152
  Angle     :  0.576   8.476  10760  Z= 0.285
  Chirality :  0.042   0.141   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.819  55.617   1104
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.64 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.23 (0.26), residues: 972
  helix:  1.03 (0.25), residues: 408
  sheet:  0.28 (0.37), residues: 160
  loop : -0.74 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 280 
 HIS   0.010   0.002   HIS A 295 
 PHE   0.012   0.002   PHE A 199 
 TYR   0.009   0.001   TYR A 400 
 ARG   0.007   0.001   ARG A 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  393)
  hydrogen bonds       : angle       5.12305 ( 1095)
  covalent geometry    : bond        0.00350 ( 7916)
  covalent geometry    : angle       0.57625 (10760)
  Misc. bond           : bond        0.00012 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8586 (m) cc_final: 0.8322 (t)
REVERT: A  139 MET cc_start: 0.6913 (mtm) cc_final: 0.6711 (mtm)
REVERT: A  154 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7181 (mt-10)
REVERT: A  164 THR cc_start: 0.8382 (p) cc_final: 0.8129 (p)
REVERT: A  167 ASP cc_start: 0.8159 (m-30) cc_final: 0.7831 (m-30)
REVERT: A  206 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7254 (tp30)
REVERT: A  308 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7658 (mp)
REVERT: A  319 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6717 (tm-30)
REVERT: B   64 GLN cc_start: 0.6952 (mp10) cc_final: 0.6623 (mp10)
REVERT: B   94 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: B  139 MET cc_start: 0.7282 (mtm) cc_final: 0.6893 (mtm)
REVERT: B  337 MET cc_start: 0.7521 (mpm) cc_final: 0.7310 (mpm)
  outliers start: 20
  outliers final: 7
  residues processed: 214
  average time/residue: 0.2508
  time to fit residues: 68.3308
Evaluate side-chains
  203 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  369 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0670
   chunk 21 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
A 351 GLN
A 433 ASN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 262 ASN
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.150146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130239 restraints weight = 10786.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.20
r_work: 0.3506 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7918  Z= 0.147
  Angle     :  0.548   8.011  10760  Z= 0.271
  Chirality :  0.042   0.140   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.633  56.462   1102
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.12 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.56 (0.26), residues: 972
  helix:  1.42 (0.25), residues: 406
  sheet:  0.41 (0.38), residues: 160
  loop : -0.69 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 437 
 HIS   0.010   0.001   HIS B 295 
 PHE   0.012   0.001   PHE A 199 
 TYR   0.007   0.001   TYR A 400 
 ARG   0.008   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03514 (  393)
  hydrogen bonds       : angle       4.78579 ( 1095)
  covalent geometry    : bond        0.00342 ( 7916)
  covalent geometry    : angle       0.54846 (10760)
  Misc. bond           : bond        0.00030 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 196
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   96 SER cc_start: 0.8601 (m) cc_final: 0.8325 (t)
REVERT: A  139 MET cc_start: 0.7101 (mtm) cc_final: 0.6434 (mtm)
REVERT: A  154 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: A  163 MET cc_start: 0.7988 (mtp) cc_final: 0.7772 (ttm)
REVERT: A  164 THR cc_start: 0.8387 (p) cc_final: 0.8173 (p)
REVERT: A  304 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8239 (mt)
REVERT: A  337 MET cc_start: 0.6914 (mpm) cc_final: 0.6611 (mpm)
REVERT: B  139 MET cc_start: 0.7224 (mtm) cc_final: 0.6905 (mtm)
REVERT: B  316 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6902 (mt-10)
  outliers start: 26
  outliers final: 13
  residues processed: 211
  average time/residue: 0.2384
  time to fit residues: 64.8307
Evaluate side-chains
  203 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 189
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  489 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  408 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0770
   chunk 41 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9990
   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 306 GLN
A 351 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 GLN
B 262 ASN
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129243 restraints weight = 10724.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.23
r_work: 0.3493 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7918  Z= 0.181
  Angle     :  0.584   8.981  10760  Z= 0.282
  Chirality :  0.043   0.141   1208
  Planarity :  0.005   0.051   1402
  Dihedral  :  5.707  54.643   1102
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 25.83 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.68 (0.27), residues: 972
  helix:  1.57 (0.26), residues: 404
  sheet:  0.50 (0.39), residues: 160
  loop : -0.69 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 295 
 PHE   0.012   0.002   PHE A 199 
 TYR   0.007   0.001   TYR A 415 
 ARG   0.009   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  393)
  hydrogen bonds       : angle       4.69543 ( 1095)
  covalent geometry    : bond        0.00425 ( 7916)
  covalent geometry    : angle       0.58367 (10760)
  Misc. bond           : bond        0.00030 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8661 (m) cc_final: 0.8370 (t)
REVERT: A  139 MET cc_start: 0.7255 (mtm) cc_final: 0.6499 (mtm)
REVERT: A  154 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6971 (mt-10)
REVERT: A  163 MET cc_start: 0.8024 (mtp) cc_final: 0.7767 (ttm)
REVERT: A  304 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8212 (mt)
REVERT: A  337 MET cc_start: 0.6999 (mpm) cc_final: 0.6681 (mpm)
REVERT: B   94 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8119 (mp)
REVERT: B  139 MET cc_start: 0.7173 (mtm) cc_final: 0.6841 (mtm)
REVERT: B  158 ARG cc_start: 0.7686 (tpm170) cc_final: 0.7463 (tpm170)
REVERT: B  316 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7037 (mt-10)
REVERT: B  435 VAL cc_start: 0.8580 (m) cc_final: 0.8361 (p)
  outliers start: 28
  outliers final: 15
  residues processed: 211
  average time/residue: 0.2091
  time to fit residues: 57.8433
Evaluate side-chains
  215 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  408 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 ASN
A 306 GLN
A 351 GLN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.149115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128682 restraints weight = 10655.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.22
r_work: 0.3487 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7918  Z= 0.214
  Angle     :  0.605  10.192  10760  Z= 0.294
  Chirality :  0.044   0.144   1208
  Planarity :  0.005   0.041   1402
  Dihedral  :  5.786  52.705   1102
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.55 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.72 (0.27), residues: 972
  helix:  1.59 (0.26), residues: 404
  sheet:  0.49 (0.39), residues: 160
  loop : -0.63 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 280 
 HIS   0.008   0.001   HIS B 295 
 PHE   0.013   0.002   PHE A  34 
 TYR   0.008   0.002   TYR A 415 
 ARG   0.010   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  393)
  hydrogen bonds       : angle       4.72109 ( 1095)
  covalent geometry    : bond        0.00503 ( 7916)
  covalent geometry    : angle       0.60539 (10760)
  Misc. bond           : bond        0.00026 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 202
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8739 (m) cc_final: 0.8440 (t)
REVERT: A  139 MET cc_start: 0.7339 (mtm) cc_final: 0.6605 (mtm)
REVERT: A  154 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6920 (mt-10)
REVERT: A  163 MET cc_start: 0.8062 (mtp) cc_final: 0.7811 (ttm)
REVERT: A  246 PHE cc_start: 0.8896 (m-80) cc_final: 0.8692 (m-80)
REVERT: A  319 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6880 (tm-30)
REVERT: A  337 MET cc_start: 0.7078 (mpm) cc_final: 0.6774 (mpm)
REVERT: B   94 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8096 (mp)
REVERT: B  139 MET cc_start: 0.7195 (mtm) cc_final: 0.6833 (mtm)
REVERT: B  158 ARG cc_start: 0.7657 (tpm170) cc_final: 0.7427 (tpm170)
REVERT: B  316 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7072 (mt-10)
REVERT: B  324 ARG cc_start: 0.8260 (ptm160) cc_final: 0.7919 (ptm160)
REVERT: B  435 VAL cc_start: 0.8577 (m) cc_final: 0.8360 (p)
  outliers start: 26
  outliers final: 20
  residues processed: 217
  average time/residue: 0.2246
  time to fit residues: 62.7049
Evaluate side-chains
  215 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0770
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 351 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 306 GLN
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.149181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128894 restraints weight = 10566.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.18
r_work: 0.3491 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7918  Z= 0.207
  Angle     :  0.609  10.459  10760  Z= 0.296
  Chirality :  0.044   0.138   1208
  Planarity :  0.005   0.059   1402
  Dihedral  :  5.801  52.956   1102
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 26.07 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.77 (0.27), residues: 972
  helix:  1.65 (0.25), residues: 406
  sheet:  0.44 (0.39), residues: 160
  loop : -0.60 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 391 
 HIS   0.007   0.001   HIS B 295 
 PHE   0.013   0.002   PHE A  34 
 TYR   0.008   0.001   TYR A 415 
 ARG   0.009   0.001   ARG A 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  393)
  hydrogen bonds       : angle       4.68117 ( 1095)
  covalent geometry    : bond        0.00488 ( 7916)
  covalent geometry    : angle       0.60933 (10760)
  Misc. bond           : bond        0.00028 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 197
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8740 (m) cc_final: 0.8458 (t)
REVERT: A  154 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6951 (mt-10)
REVERT: A  319 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6890 (tm-30)
REVERT: A  337 MET cc_start: 0.7063 (mpm) cc_final: 0.6763 (mpm)
REVERT: B   64 GLN cc_start: 0.7087 (mp10) cc_final: 0.6861 (mp10)
REVERT: B   94 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: B  139 MET cc_start: 0.7209 (mtm) cc_final: 0.6876 (mtm)
REVERT: B  273 LEU cc_start: 0.8524 (mt) cc_final: 0.8268 (mp)
REVERT: B  316 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7048 (mt-10)
REVERT: B  324 ARG cc_start: 0.8265 (ptm160) cc_final: 0.7906 (ptm160)
REVERT: B  435 VAL cc_start: 0.8587 (m) cc_final: 0.8352 (p)
  outliers start: 31
  outliers final: 23
  residues processed: 216
  average time/residue: 0.2299
  time to fit residues: 63.6677
Evaluate side-chains
  218 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 194
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0980
   chunk 89 optimal weight:    0.0010
   chunk 54 optimal weight:    0.0970
   chunk 6 optimal weight:    0.4980
   chunk 71 optimal weight:    0.0970
   chunk 20 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
B 389 HIS
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.151687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131327 restraints weight = 10590.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.24
r_work: 0.3523 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7918  Z= 0.104
  Angle     :  0.542   7.656  10760  Z= 0.267
  Chirality :  0.042   0.137   1208
  Planarity :  0.005   0.039   1402
  Dihedral  :  5.678  58.307   1102
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.86 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: 972
  helix:  1.85 (0.26), residues: 408
  sheet:  0.33 (0.38), residues: 170
  loop : -0.41 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 391 
 HIS   0.008   0.001   HIS B 295 
 PHE   0.011   0.001   PHE B  34 
 TYR   0.008   0.001   TYR A 409 
 ARG   0.005   0.001   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02970 (  393)
  hydrogen bonds       : angle       4.43868 ( 1095)
  covalent geometry    : bond        0.00241 ( 7916)
  covalent geometry    : angle       0.54164 (10760)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8568 (m) cc_final: 0.8318 (t)
REVERT: A  103 GLU cc_start: 0.8130 (tt0) cc_final: 0.7564 (tt0)
REVERT: A  154 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6936 (mt-10)
REVERT: A  163 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7791 (ttm)
REVERT: A  288 ARG cc_start: 0.8754 (mpp80) cc_final: 0.8417 (mpp80)
REVERT: A  304 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8195 (mt)
REVERT: A  319 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6857 (tm-30)
REVERT: A  337 MET cc_start: 0.7082 (mpm) cc_final: 0.6798 (mpm)
REVERT: B   79 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7850 (mtt-85)
REVERT: B   94 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8077 (mp)
REVERT: B  158 ARG cc_start: 0.7592 (tpm170) cc_final: 0.7358 (tpm170)
REVERT: B  273 LEU cc_start: 0.8492 (mt) cc_final: 0.8209 (mp)
REVERT: B  316 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7081 (mt-10)
REVERT: B  319 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6962 (tm-30)
REVERT: B  324 ARG cc_start: 0.8187 (ptm160) cc_final: 0.7832 (ptm160)
REVERT: B  435 VAL cc_start: 0.8549 (m) cc_final: 0.8289 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 212
  average time/residue: 0.2570
  time to fit residues: 68.9808
Evaluate side-chains
  210 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 193
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0870
   chunk 1 optimal weight:    0.0870
   chunk 23 optimal weight:    0.0870
   overall best weight:    0.2114

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 GLN
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.151225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.130665 restraints weight = 10746.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.23
r_work: 0.3521 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7918  Z= 0.111
  Angle     :  0.546   8.127  10760  Z= 0.268
  Chirality :  0.041   0.145   1208
  Planarity :  0.005   0.059   1402
  Dihedral  :  5.617  58.120   1102
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.74 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.14 (0.27), residues: 972
  helix:  1.96 (0.26), residues: 404
  sheet:  0.40 (0.39), residues: 170
  loop : -0.30 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 391 
 HIS   0.014   0.001   HIS A 295 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.009   0.001   TYR B 172 
 ARG   0.009   0.001   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02823 (  393)
  hydrogen bonds       : angle       4.40785 ( 1095)
  covalent geometry    : bond        0.00259 ( 7916)
  covalent geometry    : angle       0.54595 (10760)
  Misc. bond           : bond        0.00030 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8562 (m) cc_final: 0.8305 (t)
REVERT: A  154 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6982 (mt-10)
REVERT: A  163 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7727 (ttm)
REVERT: A  288 ARG cc_start: 0.8729 (mpp80) cc_final: 0.8328 (mpp80)
REVERT: A  304 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8214 (mt)
REVERT: A  319 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6892 (tm-30)
REVERT: B   94 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8077 (mp)
REVERT: B  158 ARG cc_start: 0.7554 (tpm170) cc_final: 0.7301 (tpm170)
REVERT: B  316 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7105 (mt-10)
REVERT: B  324 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7908 (ptm160)
REVERT: B  357 MET cc_start: 0.8166 (mtm) cc_final: 0.7888 (mtt)
  outliers start: 20
  outliers final: 16
  residues processed: 210
  average time/residue: 0.2588
  time to fit residues: 69.3648
Evaluate side-chains
  215 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0870
   chunk 97 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0870
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.150532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.130220 restraints weight = 10820.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.22
r_work: 0.3511 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7918  Z= 0.136
  Angle     :  0.567   9.232  10760  Z= 0.278
  Chirality :  0.042   0.153   1208
  Planarity :  0.005   0.078   1402
  Dihedral  :  5.660  56.938   1102
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.79 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.12 (0.27), residues: 972
  helix:  1.98 (0.26), residues: 404
  sheet:  0.39 (0.39), residues: 170
  loop : -0.34 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 391 
 HIS   0.013   0.001   HIS A 295 
 PHE   0.010   0.001   PHE A  34 
 TYR   0.014   0.001   TYR B 166 
 ARG   0.007   0.001   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02920 (  393)
  hydrogen bonds       : angle       4.43851 ( 1095)
  covalent geometry    : bond        0.00320 ( 7916)
  covalent geometry    : angle       0.56696 (10760)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 206
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8583 (m) cc_final: 0.8319 (t)
REVERT: A  154 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7009 (mt-10)
REVERT: A  163 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7787 (ttm)
REVERT: A  288 ARG cc_start: 0.8691 (mpp80) cc_final: 0.8287 (mpp80)
REVERT: A  304 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8207 (mt)
REVERT: A  319 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6897 (tm-30)
REVERT: B   94 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8066 (mp)
REVERT: B  158 ARG cc_start: 0.7571 (tpm170) cc_final: 0.7331 (tpm170)
REVERT: B  273 LEU cc_start: 0.8507 (mt) cc_final: 0.8245 (mp)
REVERT: B  275 GLN cc_start: 0.8096 (pp30) cc_final: 0.7686 (pt0)
REVERT: B  316 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7051 (mt-10)
REVERT: B  324 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7901 (ptm160)
REVERT: B  357 MET cc_start: 0.8200 (mtm) cc_final: 0.7926 (mtt)
  outliers start: 26
  outliers final: 20
  residues processed: 219
  average time/residue: 0.2384
  time to fit residues: 67.1945
Evaluate side-chains
  225 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 2 optimal weight:    0.2980
   chunk 59 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0070
   chunk 72 optimal weight:    0.0470
   chunk 11 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.151089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130512 restraints weight = 10655.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.21
r_work: 0.3511 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7918  Z= 0.131
  Angle     :  0.572   9.260  10760  Z= 0.279
  Chirality :  0.042   0.158   1208
  Planarity :  0.005   0.067   1402
  Dihedral  :  5.649  56.955   1102
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 26.90 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.13 (0.27), residues: 972
  helix:  2.00 (0.26), residues: 404
  sheet:  0.35 (0.39), residues: 170
  loop : -0.33 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 391 
 HIS   0.013   0.001   HIS A 295 
 PHE   0.010   0.001   PHE B  34 
 TYR   0.011   0.001   TYR B 166 
 ARG   0.008   0.001   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02877 (  393)
  hydrogen bonds       : angle       4.42452 ( 1095)
  covalent geometry    : bond        0.00310 ( 7916)
  covalent geometry    : angle       0.57218 (10760)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 SER cc_start: 0.8590 (m) cc_final: 0.8327 (t)
REVERT: A  154 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6964 (mt-10)
REVERT: A  163 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7779 (ttm)
REVERT: A  288 ARG cc_start: 0.8691 (mpp80) cc_final: 0.8288 (mpp80)
REVERT: A  304 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8226 (mt)
REVERT: A  319 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6902 (tm-30)
REVERT: B   94 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8064 (mp)
REVERT: B  158 ARG cc_start: 0.7571 (tpm170) cc_final: 0.7347 (tpm170)
REVERT: B  273 LEU cc_start: 0.8498 (mt) cc_final: 0.8235 (mp)
REVERT: B  324 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7914 (ptm160)
REVERT: B  435 VAL cc_start: 0.8561 (m) cc_final: 0.8339 (p)
  outliers start: 25
  outliers final: 22
  residues processed: 216
  average time/residue: 0.2358
  time to fit residues: 65.6762
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  240 GLN
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 44 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0670
   chunk 31 optimal weight:    0.8980
   chunk 88 optimal weight:    0.4980
   chunk 58 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0970
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 306 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.150551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.130112 restraints weight = 10667.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.23
r_work: 0.3511 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7918  Z= 0.131
  Angle     :  0.568   9.221  10760  Z= 0.279
  Chirality :  0.042   0.153   1208
  Planarity :  0.005   0.061   1402
  Dihedral  :  5.644  56.923   1102
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 27.50 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.13 (0.27), residues: 972
  helix:  2.01 (0.26), residues: 404
  sheet:  0.37 (0.39), residues: 170
  loop : -0.36 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 280 
 HIS   0.015   0.001   HIS A 295 
 PHE   0.010   0.001   PHE A  34 
 TYR   0.010   0.001   TYR B 166 
 ARG   0.006   0.001   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02902 (  393)
  hydrogen bonds       : angle       4.41740 ( 1095)
  covalent geometry    : bond        0.00309 ( 7916)
  covalent geometry    : angle       0.56776 (10760)
  Misc. bond           : bond        0.00029 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5071.40 seconds
wall clock time: 88 minutes 23.75 seconds (5303.75 seconds total)