Starting phenix.real_space_refine
on Wed Sep 17 05:45:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gh4_51346/09_2025/9gh4_51346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gh4_51346/09_2025/9gh4_51346.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gh4_51346/09_2025/9gh4_51346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gh4_51346/09_2025/9gh4_51346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gh4_51346/09_2025/9gh4_51346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gh4_51346/09_2025/9gh4_51346.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.017
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       6      5.16       5
     C    3333      2.51       5
     N     978      2.21       5
     O    1137      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5454
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1818
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 1, 'TRANS': 248}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.39, per 1000 atoms: 0.25
  Number of scatterers: 5454
  At special positions: 0
  Unit cell: (60.59, 58.93, 137.78, 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       6     16.00
     O    1137      8.00
     N     978      7.00
     C    3333      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 252.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1302

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      11.2% alpha, 32.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 254 through 261
      removed outlier: 3.644A  pdb=" N   TYR A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.616A  pdb=" N   LYS A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 238
    Processing helix  chain 'B' and resid 245 through 250
    Processing helix  chain 'B' and resid 254 through 261
      removed outlier: 3.644A  pdb=" N   TYR B 258 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 273
      removed outlier: 3.617A  pdb=" N   LYS B 272 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 238
    Processing helix  chain 'C' and resid 245 through 250
    Processing helix  chain 'C' and resid 254 through 261
      removed outlier: 3.644A  pdb=" N   TYR C 258 " --> pdb=" O   ARG C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 273
      removed outlier: 3.616A  pdb=" N   LYS C 272 " --> pdb=" O   LYS C 268 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 6.827A  pdb=" N   SER A  66 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLY A  83 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE A  68 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   SER A  94 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY A 111 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   PHE A  96 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LYS A 113 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   SER A  98 " --> pdb=" O   LYS A 113 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   THR A 115 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN A 114 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN A 129 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   ASN A 151 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN A 129 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.802A  pdb=" N   VAL A  45 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LYS A  59 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A  73 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE A  87 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA A 101 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN A 114 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN A 129 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR A 157 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A 189 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165
      removed outlier: 6.773A  pdb=" N   LYS A 164 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 215
      removed outlier: 6.114A  pdb=" N   LYS A 213 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL C 189 " --> pdb=" O   SER C 204 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR C 157 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASN C 114 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN C 129 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL C 116 " --> pdb=" O   GLN C 129 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE C  87 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG C  73 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS C  59 " --> pdb=" O   ALA C  74 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL C  45 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 6.827A  pdb=" N   SER C  66 " --> pdb=" O   ALA C  81 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLY C  83 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE C  68 " --> pdb=" O   GLY C  83 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   SER C  94 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY C 111 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   PHE C  96 " --> pdb=" O   GLY C 111 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LYS C 113 " --> pdb=" O   PHE C  96 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   SER C  98 " --> pdb=" O   LYS C 113 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   THR C 115 " --> pdb=" O   SER C  98 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASN C 114 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN C 129 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL C 116 " --> pdb=" O   GLN C 129 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   ASN C 151 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN C 129 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 31
      removed outlier: 6.828A  pdb=" N   SER B  66 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLY B  83 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   PHE B  68 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   SER B  94 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY B 111 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   PHE B  96 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LYS B 113 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   SER B  98 " --> pdb=" O   LYS B 113 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   THR B 115 " --> pdb=" O   SER B  98 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN B 114 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN B 129 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 8.741A  pdb=" N   ASN B 151 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   GLN B 129 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 46
      removed outlier: 6.801A  pdb=" N   VAL B  45 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS B  59 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG B  73 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE B  87 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA B 101 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN B 114 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLN B 129 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR B 157 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL B 189 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165
      removed outlier: 6.773A  pdb=" N   LYS B 164 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 165
      removed outlier: 6.774A  pdb=" N   LYS C 164 " --> pdb=" O   ILE C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    145 hydrogen bonds defined for protein.
    417 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1899
        1.34 -     1.46: 1035
        1.46 -     1.57: 2592
        1.57 -     1.69: 0
        1.69 -     1.80: 12
  Bond restraints: 5538
  Sorted by residual:
  bond pdb=" C   VAL C 205 "
       pdb=" O   VAL C 205 "
    ideal  model  delta    sigma   weight residual
    1.242  1.229  0.014 1.23e-02 6.61e+03 1.21e+00
  bond pdb=" C   VAL B 205 "
       pdb=" O   VAL B 205 "
    ideal  model  delta    sigma   weight residual
    1.242  1.229  0.013 1.23e-02 6.61e+03 1.17e+00
  bond pdb=" C   VAL A 205 "
       pdb=" O   VAL A 205 "
    ideal  model  delta    sigma   weight residual
    1.242  1.229  0.013 1.23e-02 6.61e+03 1.11e+00
  bond pdb=" CB  GLU A 142 "
       pdb=" CG  GLU A 142 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  GLU B 142 "
       pdb=" CG  GLU B 142 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.04e+00
  ... (remaining 5533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 7392
        2.09 -     4.17: 57
        4.17 -     6.26: 9
        6.26 -     8.35: 6
        8.35 -    10.44: 3
  Bond angle restraints: 7467
  Sorted by residual:
  angle pdb=" CA  LEU C 235 "
        pdb=" CB  LEU C 235 "
        pdb=" CG  LEU C 235 "
      ideal   model   delta    sigma   weight residual
     116.30  126.74  -10.44 3.50e+00 8.16e-02 8.89e+00
  angle pdb=" CA  LEU A 235 "
        pdb=" CB  LEU A 235 "
        pdb=" CG  LEU A 235 "
      ideal   model   delta    sigma   weight residual
     116.30  126.72  -10.42 3.50e+00 8.16e-02 8.86e+00
  angle pdb=" CA  LEU B 235 "
        pdb=" CB  LEU B 235 "
        pdb=" CG  LEU B 235 "
      ideal   model   delta    sigma   weight residual
     116.30  126.69  -10.39 3.50e+00 8.16e-02 8.82e+00
  angle pdb=" N   GLY C  55 "
        pdb=" CA  GLY C  55 "
        pdb=" C   GLY C  55 "
      ideal   model   delta    sigma   weight residual
     111.21  113.84   -2.63 1.04e+00 9.25e-01 6.38e+00
  angle pdb=" N   GLY A  55 "
        pdb=" CA  GLY A  55 "
        pdb=" C   GLY A  55 "
      ideal   model   delta    sigma   weight residual
     111.21  113.82   -2.61 1.04e+00 9.25e-01 6.29e+00
  ... (remaining 7462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 2791
       17.83 -    35.66: 308
       35.66 -    53.49: 90
       53.49 -    71.32: 6
       71.32 -    89.15: 6
  Dihedral angle restraints: 3201
    sinusoidal: 1131
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" CG  LYS A  50 "
           pdb=" CD  LYS A  50 "
           pdb=" CE  LYS A  50 "
           pdb=" NZ  LYS A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.24  -59.76     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS C  50 "
           pdb=" CD  LYS C  50 "
           pdb=" CE  LYS C  50 "
           pdb=" NZ  LYS C  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.25  -59.75     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS B  50 "
           pdb=" CD  LYS B  50 "
           pdb=" CE  LYS B  50 "
           pdb=" NZ  LYS B  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.28  -59.72     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3198 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 356
       0.023 -    0.046: 211
       0.046 -    0.068: 140
       0.068 -    0.091: 31
       0.091 -    0.114: 60
  Chirality restraints: 798
  Sorted by residual:
  chirality pdb=" CA  ILE B 181 "
            pdb=" N   ILE B 181 "
            pdb=" C   ILE B 181 "
            pdb=" CB  ILE B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.26e-01
  chirality pdb=" CA  ILE C 159 "
            pdb=" N   ILE C 159 "
            pdb=" C   ILE C 159 "
            pdb=" CB  ILE C 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.24e-01
  chirality pdb=" CA  ILE A 159 "
            pdb=" N   ILE A 159 "
            pdb=" C   ILE A 159 "
            pdb=" CB  ILE A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 795 not shown)

  Planarity restraints: 1014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  26 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO C  27 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C  27 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  27 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  26 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A  27 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  26 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B  27 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B  27 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  27 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1011 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 763
        2.76 -     3.29: 5555
        3.29 -     3.83: 9824
        3.83 -     4.36: 12312
        4.36 -     4.90: 20983
  Nonbonded interactions: 49437
  Sorted by model distance:
  nonbonded pdb=" N   GLY B 220 "
            pdb=" OE1 GLN B 234 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" N   GLY A 220 "
            pdb=" OE1 GLN A 234 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" N   GLY C 220 "
            pdb=" OE1 GLN C 234 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" O   ALA A 261 "
            pdb=" NZ  LYS B 272 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   LEU A 191 "
            pdb=" OG  SER A 195 "
     model   vdw
     2.278 3.040
  ... (remaining 49432 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.600
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6643
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      :  0.002   0.031   5538  Z= 0.128
  Angle     :  0.600  10.436   7467  Z= 0.331
  Chirality :  0.044   0.114    798
  Planarity :  0.003   0.038   1014
  Dihedral  : 16.589  89.148   1899
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 31.22 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.02 (0.29), residues: 744
  helix: -2.34 (0.48), residues: 84
  sheet:  0.11 (0.45), residues: 135
  loop : -1.67 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 233 
 TYR   0.013   0.002   TYR A 258 
 PHE   0.004   0.001   PHE A 138 
 TRP   0.005   0.001   TRP A 269 
 HIS   0.002   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5538)
  covalent geometry    : angle       0.60008 ( 7467)
  hydrogen bonds       : bond        0.28008 (  130)
  hydrogen bonds       : angle       9.17295 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.5726 (m-40) cc_final: 0.5411 (m-40)
REVERT: A   90 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6570 (mmtm)
REVERT: A  100 ASN cc_start: 0.6878 (m-40) cc_final: 0.6625 (m-40)
REVERT: A  130 VAL cc_start: 0.7695 (t) cc_final: 0.7221 (m)
REVERT: A  164 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7223 (mtmm)
REVERT: A  174 ILE cc_start: 0.8376 (mm) cc_final: 0.8072 (mm)
REVERT: A  194 ASN cc_start: 0.7790 (m-40) cc_final: 0.7579 (m-40)
REVERT: A  228 ASP cc_start: 0.7759 (m-30) cc_final: 0.7504 (m-30)
REVERT: B   70 THR cc_start: 0.8129 (m) cc_final: 0.7630 (p)
REVERT: B  100 ASN cc_start: 0.6736 (m-40) cc_final: 0.6511 (m-40)
REVERT: B  130 VAL cc_start: 0.7612 (t) cc_final: 0.7164 (m)
REVERT: B  150 LYS cc_start: 0.8102 (pttt) cc_final: 0.7145 (ptpp)
REVERT: B  171 ASP cc_start: 0.7386 (m-30) cc_final: 0.6720 (m-30)
REVERT: C  130 VAL cc_start: 0.7762 (t) cc_final: 0.7314 (m)
REVERT: C  150 LYS cc_start: 0.8130 (pttt) cc_final: 0.7235 (ptpp)
  outliers start: 6
  outliers final: 5
  residues processed: 145
  average time/residue: 0.0671
  time to fit residues: 13.2798
Evaluate side-chains
  109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain C residue  128 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 129 GLN
A 133 ASN
A 154 ASN
A 161 ASN
A 177 ASN
B  85 HIS
B 133 ASN
B 172 ASN
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 216 ASN
C  44 ASN
C  85 HIS
C 161 ASN
C 216 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.117167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.105308 restraints weight = 8169.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.107733 restraints weight = 4647.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.109475 restraints weight = 2966.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.110604 restraints weight = 2044.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.111354 restraints weight = 1511.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5538  Z= 0.246
  Angle     :  0.663   8.171   7467  Z= 0.377
  Chirality :  0.052   0.159    798
  Planarity :  0.004   0.038   1014
  Dihedral  :  6.347  53.253    788
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 25.75 %
    Favored  : 67.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.27), residues: 744
  helix: -2.78 (0.39), residues: 90
  sheet: -0.09 (0.38), residues: 183
  loop : -2.03 (0.24), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 212 
 TYR   0.014   0.003   TYR A 147 
 PHE   0.014   0.002   PHE C 119 
 TRP   0.006   0.002   TRP C 246 
 HIS   0.004   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 5538)
  covalent geometry    : angle       0.66256 ( 7467)
  hydrogen bonds       : bond        0.04053 (  130)
  hydrogen bonds       : angle       6.35374 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 ASN cc_start: 0.7464 (m-40) cc_final: 0.7213 (m-40)
REVERT: A  120 ASN cc_start: 0.7745 (m-40) cc_final: 0.7540 (m-40)
REVERT: A  130 VAL cc_start: 0.7761 (t) cc_final: 0.7443 (m)
REVERT: A  140 MET cc_start: 0.7232 (tmm) cc_final: 0.6633 (ttt)
REVERT: A  151 ASN cc_start: 0.7656 (t0) cc_final: 0.7385 (t0)
REVERT: A  159 ILE cc_start: 0.8093 (mp) cc_final: 0.7545 (tt)
REVERT: B   94 SER cc_start: 0.8300 (m) cc_final: 0.7683 (p)
REVERT: B  130 VAL cc_start: 0.7841 (t) cc_final: 0.7366 (m)
REVERT: B  140 MET cc_start: 0.7166 (tmm) cc_final: 0.6559 (ttt)
REVERT: B  150 LYS cc_start: 0.8085 (pttt) cc_final: 0.7680 (ptpp)
REVERT: B  171 ASP cc_start: 0.6959 (m-30) cc_final: 0.6616 (m-30)
REVERT: B  242 ASP cc_start: 0.7407 (t0) cc_final: 0.7102 (t0)
REVERT: C  117 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7745 (m)
REVERT: C  120 ASN cc_start: 0.7948 (m-40) cc_final: 0.7560 (m-40)
  outliers start: 40
  outliers final: 17
  residues processed: 175
  average time/residue: 0.0670
  time to fit residues: 15.8382
Evaluate side-chains
  133 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  156 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 35 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  92 HIS
A 172 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN
B 154 ASN
B 161 ASN
B 172 ASN
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
C 133 ASN
** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 HIS
C 194 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.111728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.100124 restraints weight = 8536.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.102530 restraints weight = 4610.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.104180 restraints weight = 2826.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.105326 restraints weight = 1915.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.106188 restraints weight = 1398.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5538  Z= 0.198
  Angle     :  0.580   6.699   7467  Z= 0.331
  Chirality :  0.049   0.140    798
  Planarity :  0.003   0.034   1014
  Dihedral  :  6.145  53.392    787
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 31.39 %
    Favored  : 64.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.26), residues: 744
  helix: -2.80 (0.41), residues: 90
  sheet: -0.51 (0.41), residues: 147
  loop : -2.10 (0.23), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.014   0.002   TYR B 147 
 PHE   0.023   0.002   PHE C 134 
 TRP   0.005   0.001   TRP A 246 
 HIS   0.004   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 5538)
  covalent geometry    : angle       0.58004 ( 7467)
  hydrogen bonds       : bond        0.03503 (  130)
  hydrogen bonds       : angle       6.00060 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.5629 (m-40) cc_final: 0.5409 (m-40)
REVERT: A   90 LYS cc_start: 0.7184 (mmtm) cc_final: 0.6937 (mmtm)
REVERT: A  120 ASN cc_start: 0.7838 (m-40) cc_final: 0.7547 (m-40)
REVERT: A  130 VAL cc_start: 0.7769 (t) cc_final: 0.7422 (m)
REVERT: A  151 ASN cc_start: 0.7741 (t0) cc_final: 0.7405 (t0)
REVERT: A  159 ILE cc_start: 0.7962 (mp) cc_final: 0.7487 (tt)
REVERT: A  164 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7803 (mtmm)
REVERT: B   94 SER cc_start: 0.8245 (m) cc_final: 0.7509 (p)
REVERT: B  117 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7673 (m)
REVERT: B  119 PHE cc_start: 0.8110 (t80) cc_final: 0.7808 (t80)
REVERT: B  130 VAL cc_start: 0.7805 (t) cc_final: 0.7274 (m)
REVERT: B  140 MET cc_start: 0.7125 (tmm) cc_final: 0.6393 (ttt)
REVERT: B  150 LYS cc_start: 0.8171 (pttt) cc_final: 0.7695 (ptpp)
REVERT: B  159 ILE cc_start: 0.8307 (mp) cc_final: 0.7720 (tt)
REVERT: B  171 ASP cc_start: 0.7022 (m-30) cc_final: 0.6701 (m-30)
REVERT: B  194 ASN cc_start: 0.7831 (m-40) cc_final: 0.7614 (m-40)
REVERT: C   59 LYS cc_start: 0.6916 (mttm) cc_final: 0.6653 (mttm)
REVERT: C  128 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6978 (m-80)
  outliers start: 25
  outliers final: 18
  residues processed: 157
  average time/residue: 0.0637
  time to fit residues: 13.7869
Evaluate side-chains
  152 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  150 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0170
   chunk 55 optimal weight:    0.0170
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 187 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.106568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.096292 restraints weight = 8611.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.098519 restraints weight = 4686.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.099944 restraints weight = 2871.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.101010 restraints weight = 1939.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.101771 restraints weight = 1408.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5538  Z= 0.232
  Angle     :  0.589   6.839   7467  Z= 0.345
  Chirality :  0.051   0.148    798
  Planarity :  0.003   0.035   1014
  Dihedral  :  6.482  54.819    787
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 31.92 %
    Favored  : 63.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.90 (0.26), residues: 744
  helix: -2.95 (0.39), residues: 90
  sheet: -0.78 (0.41), residues: 147
  loop : -2.22 (0.22), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 212 
 TYR   0.011   0.002   TYR A  56 
 PHE   0.025   0.002   PHE C 134 
 TRP   0.006   0.002   TRP C 246 
 HIS   0.005   0.002   HIS C 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 5538)
  covalent geometry    : angle       0.58941 ( 7467)
  hydrogen bonds       : bond        0.03286 (  130)
  hydrogen bonds       : angle       5.98385 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.5909 (m-40) cc_final: 0.5555 (m-40)
REVERT: A  120 ASN cc_start: 0.7896 (m-40) cc_final: 0.7528 (m-40)
REVERT: A  128 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6796 (m-80)
REVERT: A  140 MET cc_start: 0.7314 (tmm) cc_final: 0.5196 (ttt)
REVERT: A  150 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7869 (ptpt)
REVERT: A  151 ASN cc_start: 0.7893 (t0) cc_final: 0.7644 (t0)
REVERT: B   63 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7159 (ttpp)
REVERT: B   90 LYS cc_start: 0.7645 (mttm) cc_final: 0.7244 (mttm)
REVERT: B  128 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7269 (m-80)
REVERT: B  130 VAL cc_start: 0.7743 (t) cc_final: 0.7218 (m)
REVERT: B  140 MET cc_start: 0.7225 (tmm) cc_final: 0.5616 (ttt)
REVERT: B  149 TYR cc_start: 0.7378 (m-80) cc_final: 0.7165 (m-80)
REVERT: B  150 LYS cc_start: 0.8186 (pttt) cc_final: 0.7791 (ptpp)
REVERT: B  159 ILE cc_start: 0.8284 (mp) cc_final: 0.7813 (tt)
REVERT: B  171 ASP cc_start: 0.7025 (m-30) cc_final: 0.6674 (m-30)
REVERT: B  188 SER cc_start: 0.8337 (m) cc_final: 0.8102 (t)
REVERT: B  223 SER cc_start: 0.7847 (p) cc_final: 0.7412 (m)
REVERT: C  128 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7157 (m-80)
REVERT: C  193 ASN cc_start: 0.7361 (t0) cc_final: 0.7158 (t0)
  outliers start: 27
  outliers final: 19
  residues processed: 157
  average time/residue: 0.0656
  time to fit residues: 13.9739
Evaluate side-chains
  143 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 239 ASN
B 151 ASN
B 177 ASN
** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 194 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.107232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.096843 restraints weight = 8738.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.099128 restraints weight = 4730.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.100658 restraints weight = 2876.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.101711 restraints weight = 1931.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.102387 restraints weight = 1397.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5538  Z= 0.208
  Angle     :  0.566   6.581   7467  Z= 0.330
  Chirality :  0.050   0.146    798
  Planarity :  0.003   0.034   1014
  Dihedral  :  6.440  55.266    787
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 32.63 %
    Favored  : 61.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.04 (0.25), residues: 744
  helix: -3.07 (0.38), residues: 90
  sheet: -0.92 (0.40), residues: 147
  loop : -2.30 (0.22), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 212 
 TYR   0.011   0.002   TYR A 236 
 PHE   0.023   0.002   PHE C 134 
 TRP   0.005   0.002   TRP C 246 
 HIS   0.012   0.003   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 5538)
  covalent geometry    : angle       0.56602 ( 7467)
  hydrogen bonds       : bond        0.03001 (  130)
  hydrogen bonds       : angle       5.84917 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.6066 (m-40) cc_final: 0.5858 (m-40)
REVERT: A   90 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6836 (mmtm)
REVERT: A  140 MET cc_start: 0.7276 (tmm) cc_final: 0.6088 (ttp)
REVERT: A  151 ASN cc_start: 0.7930 (t0) cc_final: 0.7665 (t0)
REVERT: B   63 LYS cc_start: 0.7325 (ttpp) cc_final: 0.7083 (ttpp)
REVERT: B   90 LYS cc_start: 0.7634 (mttm) cc_final: 0.7258 (mttm)
REVERT: B  130 VAL cc_start: 0.7744 (t) cc_final: 0.7189 (m)
REVERT: B  150 LYS cc_start: 0.8197 (pttt) cc_final: 0.7812 (ptpp)
REVERT: B  159 ILE cc_start: 0.8254 (mp) cc_final: 0.7827 (tt)
REVERT: B  188 SER cc_start: 0.8305 (m) cc_final: 0.8087 (t)
REVERT: B  223 SER cc_start: 0.7877 (p) cc_final: 0.7412 (m)
REVERT: C   86 ASN cc_start: 0.7659 (m-40) cc_final: 0.7169 (m110)
REVERT: C  128 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7138 (m-80)
  outliers start: 31
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0681
  time to fit residues: 14.1551
Evaluate side-chains
  150 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 194 ASN
B 151 ASN
C 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.105387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.094987 restraints weight = 8773.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.097484 restraints weight = 4520.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.099127 restraints weight = 2629.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.100198 restraints weight = 1695.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.100866 restraints weight = 1194.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5538  Z= 0.214
  Angle     :  0.573   6.572   7467  Z= 0.333
  Chirality :  0.050   0.145    798
  Planarity :  0.003   0.035   1014
  Dihedral  :  6.477  55.480    787
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 32.63 %
    Favored  : 61.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.25), residues: 744
  helix: -3.10 (0.38), residues: 90
  sheet: -1.02 (0.40), residues: 147
  loop : -2.39 (0.22), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 233 
 TYR   0.018   0.002   TYR B 149 
 PHE   0.028   0.002   PHE A 134 
 TRP   0.005   0.002   TRP C 246 
 HIS   0.006   0.002   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 5538)
  covalent geometry    : angle       0.57263 ( 7467)
  hydrogen bonds       : bond        0.03055 (  130)
  hydrogen bonds       : angle       5.77763 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.6124 (m-40) cc_final: 0.5919 (m-40)
REVERT: A   90 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6847 (mmtm)
REVERT: A  100 ASN cc_start: 0.7568 (m-40) cc_final: 0.7233 (m-40)
REVERT: A  130 VAL cc_start: 0.7861 (t) cc_final: 0.7388 (m)
REVERT: A  140 MET cc_start: 0.7192 (tmm) cc_final: 0.6016 (ttp)
REVERT: A  151 ASN cc_start: 0.8021 (t0) cc_final: 0.7677 (t0)
REVERT: B   63 LYS cc_start: 0.7398 (ttpp) cc_final: 0.7171 (ttpp)
REVERT: B   90 LYS cc_start: 0.7609 (mttm) cc_final: 0.7118 (mttm)
REVERT: B  117 SER cc_start: 0.7839 (m) cc_final: 0.7625 (m)
REVERT: B  150 LYS cc_start: 0.8380 (pttt) cc_final: 0.7865 (ptpp)
REVERT: B  159 ILE cc_start: 0.8156 (mp) cc_final: 0.7738 (tt)
REVERT: B  223 SER cc_start: 0.7845 (p) cc_final: 0.7401 (m)
REVERT: C  128 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6974 (m-80)
REVERT: C  233 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7574 (ttp-170)
  outliers start: 36
  outliers final: 30
  residues processed: 157
  average time/residue: 0.0714
  time to fit residues: 15.0716
Evaluate side-chains
  160 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 34 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0980
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 172 ASN
C 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.105942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.095455 restraints weight = 8868.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.097981 restraints weight = 4533.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.099655 restraints weight = 2638.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.100704 restraints weight = 1692.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.101450 restraints weight = 1194.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5538  Z= 0.182
  Angle     :  0.558   6.424   7467  Z= 0.322
  Chirality :  0.049   0.148    798
  Planarity :  0.003   0.034   1014
  Dihedral  :  6.358  55.766    787
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 32.98 %
    Favored  : 60.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.25), residues: 744
  helix: -3.06 (0.38), residues: 90
  sheet: -0.99 (0.40), residues: 147
  loop : -2.46 (0.21), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 233 
 TYR   0.014   0.002   TYR B 149 
 PHE   0.027   0.002   PHE A 134 
 TRP   0.004   0.001   TRP C 269 
 HIS   0.011   0.003   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 5538)
  covalent geometry    : angle       0.55805 ( 7467)
  hydrogen bonds       : bond        0.02794 (  130)
  hydrogen bonds       : angle       5.69320 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7170 (mmtm) cc_final: 0.6818 (mmtm)
REVERT: A  100 ASN cc_start: 0.7577 (m-40) cc_final: 0.7230 (m-40)
REVERT: A  120 ASN cc_start: 0.7985 (m-40) cc_final: 0.7607 (m-40)
REVERT: A  130 VAL cc_start: 0.7888 (t) cc_final: 0.7364 (m)
REVERT: A  140 MET cc_start: 0.7134 (tmm) cc_final: 0.6201 (ttt)
REVERT: A  151 ASN cc_start: 0.7995 (t0) cc_final: 0.7586 (t0)
REVERT: B   90 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7076 (mttm)
REVERT: B  117 SER cc_start: 0.7811 (m) cc_final: 0.7596 (m)
REVERT: B  150 LYS cc_start: 0.8426 (pttt) cc_final: 0.8023 (ptpp)
REVERT: B  151 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7349 (m-40)
REVERT: B  159 ILE cc_start: 0.8139 (mp) cc_final: 0.7742 (tt)
REVERT: B  223 SER cc_start: 0.7894 (p) cc_final: 0.7405 (m)
REVERT: C  128 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6957 (m-80)
REVERT: C  233 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7540 (ttp-170)
  outliers start: 36
  outliers final: 28
  residues processed: 154
  average time/residue: 0.0711
  time to fit residues: 14.6254
Evaluate side-chains
  160 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  235 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 58 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
A  85 HIS
A 194 ASN
B 151 ASN
C 172 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.106147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.095863 restraints weight = 8683.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.098374 restraints weight = 4465.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.100028 restraints weight = 2591.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.101098 restraints weight = 1656.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101757 restraints weight = 1161.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5538  Z= 0.196
  Angle     :  0.572   6.842   7467  Z= 0.330
  Chirality :  0.050   0.154    798
  Planarity :  0.003   0.035   1014
  Dihedral  :  6.392  55.960    787
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 34.57 %
    Favored  : 59.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.25 (0.25), residues: 744
  helix: -3.00 (0.39), residues: 90
  sheet: -1.02 (0.40), residues: 147
  loop : -2.51 (0.21), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 212 
 TYR   0.014   0.002   TYR B 149 
 PHE   0.025   0.002   PHE C 134 
 TRP   0.005   0.001   TRP C 246 
 HIS   0.005   0.002   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 5538)
  covalent geometry    : angle       0.57187 ( 7467)
  hydrogen bonds       : bond        0.02815 (  130)
  hydrogen bonds       : angle       5.67330 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7229 (mmtm) cc_final: 0.6894 (mmtm)
REVERT: A  100 ASN cc_start: 0.7501 (m-40) cc_final: 0.7129 (m-40)
REVERT: A  130 VAL cc_start: 0.7892 (t) cc_final: 0.7414 (m)
REVERT: A  140 MET cc_start: 0.7140 (tmm) cc_final: 0.6179 (ttt)
REVERT: A  151 ASN cc_start: 0.8067 (t0) cc_final: 0.7653 (t0)
REVERT: A  161 ASN cc_start: 0.6640 (OUTLIER) cc_final: 0.6430 (t0)
REVERT: B   63 LYS cc_start: 0.7400 (ttpp) cc_final: 0.7199 (ttpp)
REVERT: B   90 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7080 (mttm)
REVERT: B  117 SER cc_start: 0.7803 (m) cc_final: 0.7573 (m)
REVERT: B  140 MET cc_start: 0.7101 (tmm) cc_final: 0.6334 (ttt)
REVERT: B  150 LYS cc_start: 0.8403 (pttt) cc_final: 0.8021 (ptpp)
REVERT: B  151 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7357 (m-40)
REVERT: B  159 ILE cc_start: 0.8131 (mp) cc_final: 0.7749 (tt)
REVERT: B  223 SER cc_start: 0.7898 (p) cc_final: 0.7414 (m)
REVERT: C  128 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6909 (m-80)
REVERT: C  233 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7551 (ttp-170)
  outliers start: 36
  outliers final: 29
  residues processed: 146
  average time/residue: 0.0742
  time to fit residues: 14.3897
Evaluate side-chains
  151 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  235 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0270
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.106546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.096426 restraints weight = 8742.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.098923 restraints weight = 4486.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.100607 restraints weight = 2611.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.101696 restraints weight = 1664.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.102329 restraints weight = 1155.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5538  Z= 0.168
  Angle     :  0.559   7.316   7467  Z= 0.322
  Chirality :  0.049   0.152    798
  Planarity :  0.003   0.035   1014
  Dihedral  :  6.310  56.239    787
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 35.63 %
    Favored  : 58.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.25), residues: 744
  helix: -3.01 (0.39), residues: 90
  sheet: -1.00 (0.40), residues: 147
  loop : -2.51 (0.21), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  73 
 TYR   0.032   0.002   TYR A 149 
 PHE   0.029   0.002   PHE B 134 
 TRP   0.005   0.001   TRP A 269 
 HIS   0.006   0.002   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5538)
  covalent geometry    : angle       0.55899 ( 7467)
  hydrogen bonds       : bond        0.02653 (  130)
  hydrogen bonds       : angle       5.64927 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7171 (mmtm) cc_final: 0.6854 (mmtm)
REVERT: A  100 ASN cc_start: 0.7502 (m-40) cc_final: 0.7194 (m-40)
REVERT: A  120 ASN cc_start: 0.7952 (m-40) cc_final: 0.7736 (m-40)
REVERT: A  130 VAL cc_start: 0.7889 (t) cc_final: 0.7372 (m)
REVERT: A  140 MET cc_start: 0.7102 (tmm) cc_final: 0.6192 (ttt)
REVERT: A  151 ASN cc_start: 0.8018 (t0) cc_final: 0.7581 (t0)
REVERT: B   63 LYS cc_start: 0.7404 (ttpp) cc_final: 0.7178 (ttpp)
REVERT: B   90 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7088 (mttm)
REVERT: B  117 SER cc_start: 0.7743 (m) cc_final: 0.7515 (m)
REVERT: B  140 MET cc_start: 0.7143 (tmm) cc_final: 0.6416 (ttt)
REVERT: B  149 TYR cc_start: 0.7076 (m-80) cc_final: 0.6102 (m-10)
REVERT: B  150 LYS cc_start: 0.8388 (pttt) cc_final: 0.8032 (ptpp)
REVERT: B  151 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7298 (m-40)
REVERT: B  159 ILE cc_start: 0.8108 (mp) cc_final: 0.7750 (tt)
REVERT: B  223 SER cc_start: 0.7903 (p) cc_final: 0.7390 (m)
REVERT: C  128 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6778 (m-80)
REVERT: C  233 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7565 (ttp-170)
  outliers start: 32
  outliers final: 27
  residues processed: 151
  average time/residue: 0.0680
  time to fit residues: 13.8174
Evaluate side-chains
  153 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 172 ASN
B 151 ASN
C 172 ASN
C 187 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.110194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099602 restraints weight = 8658.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.102194 restraints weight = 4532.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.103902 restraints weight = 2678.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.105018 restraints weight = 1724.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.105814 restraints weight = 1205.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5538  Z= 0.217
  Angle     :  0.590   7.552   7467  Z= 0.340
  Chirality :  0.051   0.267    798
  Planarity :  0.003   0.035   1014
  Dihedral  :  6.457  55.726    787
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 35.10 %
    Favored  : 59.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.24), residues: 744
  helix: -3.14 (0.38), residues: 93
  sheet: -1.15 (0.39), residues: 147
  loop : -2.57 (0.21), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  73 
 TYR   0.023   0.002   TYR A 149 
 PHE   0.027   0.002   PHE B 134 
 TRP   0.005   0.002   TRP C 246 
 HIS   0.007   0.002   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 5538)
  covalent geometry    : angle       0.59047 ( 7467)
  hydrogen bonds       : bond        0.02886 (  130)
  hydrogen bonds       : angle       5.70663 (  417)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.7235 (mmtm) cc_final: 0.6909 (mmtm)
REVERT: A  100 ASN cc_start: 0.7474 (m-40) cc_final: 0.7094 (m-40)
REVERT: A  130 VAL cc_start: 0.7904 (t) cc_final: 0.7389 (m)
REVERT: A  140 MET cc_start: 0.7143 (tmm) cc_final: 0.6225 (ttt)
REVERT: A  151 ASN cc_start: 0.8045 (t0) cc_final: 0.7610 (t0)
REVERT: A  161 ASN cc_start: 0.6835 (OUTLIER) cc_final: 0.6504 (t0)
REVERT: B   63 LYS cc_start: 0.7352 (ttpp) cc_final: 0.7138 (ttpp)
REVERT: B   90 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7113 (mttm)
REVERT: B  117 SER cc_start: 0.7788 (m) cc_final: 0.7556 (m)
REVERT: B  140 MET cc_start: 0.7233 (tmm) cc_final: 0.6351 (ttt)
REVERT: B  150 LYS cc_start: 0.8319 (pttt) cc_final: 0.7853 (ptpp)
REVERT: B  151 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7271 (t0)
REVERT: B  159 ILE cc_start: 0.8132 (mp) cc_final: 0.7842 (tt)
REVERT: B  223 SER cc_start: 0.7909 (p) cc_final: 0.7403 (m)
REVERT: C  128 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6909 (m-80)
REVERT: C  159 ILE cc_start: 0.8050 (mp) cc_final: 0.7335 (tt)
REVERT: C  233 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7563 (ttp-170)
  outliers start: 33
  outliers final: 28
  residues processed: 153
  average time/residue: 0.0698
  time to fit residues: 14.3398
Evaluate side-chains
  157 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   85 HIS
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  128 TYR
Chi-restraints excluded: chain C residue  131 THR
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  226 SER
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 70 optimal weight:    0.0970
   chunk 59 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 172 ASN
A 194 ASN
B 151 ASN
** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 HIS
C 172 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.111465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100683 restraints weight = 8645.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.103325 restraints weight = 4537.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.105063 restraints weight = 2660.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.106051 restraints weight = 1715.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.106834 restraints weight = 1222.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   5538  Z= 0.149
  Angle     :  0.557   7.680   7467  Z= 0.320
  Chirality :  0.050   0.168    798
  Planarity :  0.003   0.036   1014
  Dihedral  :  6.300  56.356    787
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 35.98 %
    Favored  : 58.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.32 (0.24), residues: 744
  helix: -2.99 (0.39), residues: 90
  sheet: -1.13 (0.39), residues: 147
  loop : -2.55 (0.21), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  73 
 TYR   0.018   0.002   TYR A 149 
 PHE   0.026   0.002   PHE B 134 
 TRP   0.006   0.001   TRP A 269 
 HIS   0.005   0.002   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5538)
  covalent geometry    : angle       0.55742 ( 7467)
  hydrogen bonds       : bond        0.02493 (  130)
  hydrogen bonds       : angle       5.63190 (  417)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1195.94 seconds
wall clock time: 21 minutes 32.23 seconds (1292.23 seconds total)