Starting phenix.real_space_refine
on Tue Jul 29 05:21:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgb_22320/07_2025/7jgb_22320.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgb_22320/07_2025/7jgb_22320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jgb_22320/07_2025/7jgb_22320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgb_22320/07_2025/7jgb_22320.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgb_22320/07_2025/7jgb_22320.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgb_22320/07_2025/7jgb_22320.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.006 sd=   0.141
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4941 atoms to isotropic.
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      26      5.16       5
     C    4847      2.51       5
     N    1174      2.21       5
     O    1214      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7261
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "a"
      Number of atoms: 1602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1602
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 10, 'TRANS': 196}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "b"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 341
          Classifications: {'peptide': 45}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 41}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "d"
      Number of atoms: 311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 311
          Classifications: {'peptide': 40}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 37}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "1"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 560
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "2"
      Number of atoms: 552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 552
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "3"
      Number of atoms: 548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 548
          Classifications: {'peptide': 80}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 76}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "4"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 560
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "5"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 550
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "6"
      Number of atoms: 556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 556
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "7"
      Number of atoms: 556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 556
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "8"
      Number of atoms: 569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 569
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "9"
      Number of atoms: 556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 556
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 5.10, per 1000 atoms: 0.70
  Number of scatterers: 7261
  At special positions: 0
  Unit cell: (79.31, 94.76, 88.58, 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      26     16.00
     O    1214      8.00
     N    1174      7.00
     C    4847      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: 2.06
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 0 sheets defined
      90.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'a' and resid 32 through 53
      removed outlier: 3.812A  pdb=" N   THR a  38 " --> pdb=" O   ALA a  34 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 62 through 81
      removed outlier: 3.657A  pdb=" N   TRP a  66 " --> pdb=" O   VAL a  62 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN a  72 " --> pdb=" O   ALA a  68 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 88 through 106
      removed outlier: 4.102A  pdb=" N   LEU a  92 " --> pdb=" O   PHE a  88 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ILE a 100 " --> pdb=" O   ILE a  96 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER a 103 " --> pdb=" O   PHE a  99 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 107 through 109
      No H-bonds generated for 'chain 'a' and resid 107 through 109'
    Processing helix  chain 'a' and resid 126 through 129
    Processing helix  chain 'a' and resid 130 through 154
      removed outlier: 3.680A  pdb=" N   VAL a 134 " --> pdb=" O   ASP a 130 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE a 140 " --> pdb=" O   ALA a 136 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 156 through 165
      removed outlier: 3.907A  pdb=" N   ILE a 160 " --> pdb=" O   VAL a 156 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 170 through 203
      removed outlier: 3.965A  pdb=" N   VAL a 176 " --> pdb=" O   PRO a 172 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU a 179 " --> pdb=" O   ILE a 175 " (cutoff:3.500A)
      Proline residue:  a 182  - end of helix
      removed outlier: 4.002A  pdb=" N   ARG a 188 " --> pdb=" O   SER a 184 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU a 189 " --> pdb=" O   LEU a 185 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLY a 196 " --> pdb=" O   ASN a 192 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA a 201 " --> pdb=" O   GLY a 197 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 204 through 206
      No H-bonds generated for 'chain 'a' and resid 204 through 206'
    Processing helix  chain 'a' and resid 207 through 246
      removed outlier: 4.866A  pdb=" N   PHE a 213 " --> pdb=" O   TYR a 209 " (cutoff:3.500A)
      Proline residue:  a 214  - end of helix
      removed outlier: 3.840A  pdb=" N   PHE a 224 " --> pdb=" O   THR a 220 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU a 246 " --> pdb=" O   SER a 242 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 29 through 49
      removed outlier: 4.295A  pdb=" N   ALA b  33 " --> pdb=" O   GLY b  29 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL b  41 " --> pdb=" O   ILE b  37 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 49 through 64
    Processing helix  chain 'd' and resid 2 through 22
    Processing helix  chain 'd' and resid 22 through 39
    Processing helix  chain '1' and resid 6 through 46
    Processing helix  chain '1' and resid 49 through 81
      removed outlier: 4.272A  pdb=" N   THR 1  55 " --> pdb=" O   GLY 1  51 " (cutoff:3.500A)
      Proline residue:  1  56  - end of helix
    Processing helix  chain '2' and resid 6 through 46
    Processing helix  chain '2' and resid 49 through 80
      removed outlier: 4.569A  pdb=" N   THR 2  55 " --> pdb=" O   GLY 2  51 " (cutoff:3.500A)
      Proline residue:  2  56  - end of helix
    Processing helix  chain '3' and resid 6 through 46
    Processing helix  chain '3' and resid 49 through 81
      removed outlier: 4.759A  pdb=" N   THR 3  55 " --> pdb=" O   GLY 3  51 " (cutoff:3.500A)
      Proline residue:  3  56  - end of helix
      removed outlier: 3.770A  pdb=" N   ALA 3  67 " --> pdb=" O   LEU 3  63 " (cutoff:3.500A)
    Processing helix  chain '4' and resid 6 through 46
      removed outlier: 3.710A  pdb=" N   ARG 4  45 " --> pdb=" O   SER 4  41 " (cutoff:3.500A)
    Processing helix  chain '4' and resid 49 through 80
      removed outlier: 5.220A  pdb=" N   THR 4  55 " --> pdb=" O   GLY 4  51 " (cutoff:3.500A)
      Proline residue:  4  56  - end of helix
      removed outlier: 3.685A  pdb=" N   ALA 4  67 " --> pdb=" O   LEU 4  63 " (cutoff:3.500A)
    Processing helix  chain '5' and resid 6 through 46
    Processing helix  chain '5' and resid 49 through 81
      Proline residue:  5  56  - end of helix
    Processing helix  chain '6' and resid 6 through 46
      removed outlier: 3.550A  pdb=" N   ALA 6  38 " --> pdb=" O   ILE 6  34 " (cutoff:3.500A)
    Processing helix  chain '6' and resid 47 through 53
      removed outlier: 4.157A  pdb=" N   GLY 6  51 " --> pdb=" O   PRO 6  47 " (cutoff:3.500A)
    Processing helix  chain '6' and resid 53 through 81
      removed outlier: 3.962A  pdb=" N   ALA 6  67 " --> pdb=" O   LEU 6  63 " (cutoff:3.500A)
    Processing helix  chain '7' and resid 6 through 46
      removed outlier: 3.572A  pdb=" N   ALA 7  38 " --> pdb=" O   ILE 7  34 " (cutoff:3.500A)
    Processing helix  chain '7' and resid 49 through 82
      removed outlier: 4.376A  pdb=" N   THR 7  55 " --> pdb=" O   GLY 7  51 " (cutoff:3.500A)
      Proline residue:  7  56  - end of helix
    Processing helix  chain '8' and resid 4 through 46
      removed outlier: 3.568A  pdb=" N   ILE 8   8 " --> pdb=" O   ASP 8   4 " (cutoff:3.500A)
    Processing helix  chain '8' and resid 49 through 82
      removed outlier: 4.432A  pdb=" N   THR 8  55 " --> pdb=" O   GLY 8  51 " (cutoff:3.500A)
      Proline residue:  8  56  - end of helix
    Processing helix  chain '9' and resid 6 through 46
    Processing helix  chain '9' and resid 49 through 81
      removed outlier: 4.066A  pdb=" N   THR 9  55 " --> pdb=" O   GLY 9  51 " (cutoff:3.500A)
      Proline residue:  9  56  - end of helix
      removed outlier: 3.617A  pdb=" N   ALA 9  66 " --> pdb=" O   GLY 9  62 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASN 9  71 " --> pdb=" O   ALA 9  67 " (cutoff:3.500A)

    731 hydrogen bonds defined for protein.
    2190 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 2.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2272
        1.34 -     1.46: 1682
        1.46 -     1.58: 3416
        1.58 -     1.69: 0
        1.69 -     1.81: 51
  Bond restraints: 7421
  Sorted by residual:
  bond pdb=" N   GLY b  20 "
       pdb=" CA  GLY b  20 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.32e+00
  bond pdb=" CG  ARG d  38 "
       pdb=" CD  ARG d  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.466  0.054 3.00e-02 1.11e+03 3.24e+00
  bond pdb=" CB  VAL b  56 "
       pdb=" CG1 VAL b  56 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.94e+00
  bond pdb=" CB  LYS b  55 "
       pdb=" CG  LYS b  55 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 3.00e-02 1.11e+03 2.63e+00
  bond pdb=" CB  ILE 2  43 "
       pdb=" CG2 ILE 2  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.48e+00
  ... (remaining 7416 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 9585
        1.27 -     2.54: 413
        2.54 -     3.80: 77
        3.80 -     5.07: 11
        5.07 -     6.34: 1
  Bond angle restraints: 10087
  Sorted by residual:
  angle pdb=" N   THR 4  82 "
        pdb=" CA  THR 4  82 "
        pdb=" C   THR 4  82 "
      ideal   model   delta    sigma   weight residual
     109.57  113.62   -4.05 1.23e+00 6.61e-01 1.08e+01
  angle pdb=" C   ALA 4  81 "
        pdb=" N   THR 4  82 "
        pdb=" CA  THR 4  82 "
      ideal   model   delta    sigma   weight residual
     120.83  124.76   -3.93 1.43e+00 4.89e-01 7.54e+00
  angle pdb=" CA  TYR a 145 "
        pdb=" CB  TYR a 145 "
        pdb=" CG  TYR a 145 "
      ideal   model   delta    sigma   weight residual
     113.90  118.07   -4.17 1.80e+00 3.09e-01 5.36e+00
  angle pdb=" CA  TRP a 208 "
        pdb=" CB  TRP a 208 "
        pdb=" CG  TRP a 208 "
      ideal   model   delta    sigma   weight residual
     113.60  117.56   -3.96 1.90e+00 2.77e-01 4.34e+00
  angle pdb=" N   PHE a 133 "
        pdb=" CA  PHE a 133 "
        pdb=" CB  PHE a 133 "
      ideal   model   delta    sigma   weight residual
     110.16  107.14    3.02 1.48e+00 4.57e-01 4.17e+00
  ... (remaining 10082 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3814
       17.92 -    35.83: 299
       35.83 -    53.75: 37
       53.75 -    71.66: 10
       71.66 -    89.58: 7
  Dihedral angle restraints: 4167
    sinusoidal: 1423
      harmonic: 2744
  Sorted by residual:
  dihedral pdb=" CA  GLN 4  46 "
           pdb=" C   GLN 4  46 "
           pdb=" N   PRO 4  47 "
           pdb=" CA  PRO 4  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.86  -23.14     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  ARG d  38 "
           pdb=" C   ARG d  38 "
           pdb=" N   ALA d  39 "
           pdb=" CA  ALA d  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.99  -20.01     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  VAL b  49 "
           pdb=" C   VAL b  49 "
           pdb=" N   VAL b  50 "
           pdb=" CA  VAL b  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 4164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 711
       0.032 -    0.064: 321
       0.064 -    0.096: 139
       0.096 -    0.128: 26
       0.128 -    0.160: 7
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CA  PRO 5  47 "
            pdb=" N   PRO 5  47 "
            pdb=" C   PRO 5  47 "
            pdb=" CB  PRO 5  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  PRO 4  47 "
            pdb=" N   PRO 4  47 "
            pdb=" C   PRO 4  47 "
            pdb=" CB  PRO 4  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  PRO 3  47 "
            pdb=" N   PRO 3  47 "
            pdb=" C   PRO 3  47 "
            pdb=" CB  PRO 3  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1201 not shown)

  Planarity restraints: 1271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL b  50 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.39e+00
        pdb=" N   PRO b  51 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO b  51 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO b  51 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE d  18 "    0.010 2.00e-02 2.50e+03   1.92e-02 3.71e+00
        pdb=" C   ILE d  18 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ILE d  18 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL d  19 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP a 208 "   -0.017 2.00e-02 2.50e+03   1.07e-02 2.88e+00
        pdb=" CG  TRP a 208 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP a 208 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP a 208 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP a 208 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP a 208 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP a 208 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP a 208 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP a 208 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP a 208 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1268 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 2875
        2.88 -     3.38: 8228
        3.38 -     3.89: 12291
        3.89 -     4.39: 13946
        4.39 -     4.90: 23299
  Nonbonded interactions: 60639
  Sorted by model distance:
  nonbonded pdb=" OG  SER a  80 "
            pdb=" OG  SER a 242 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   ARG d  38 "
            pdb=" N   ALA d  40 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" O   PHE 9  78 "
            pdb=" OG1 THR 9  82 "
     model   vdw
     2.435 3.040
  nonbonded pdb=" OH  TYR 4  68 "
            pdb=" OD1 ASN 5  71 "
     model   vdw
     2.438 3.040
  nonbonded pdb=" OG  SER 8  41 "
            pdb=" NH1 ARG 8  45 "
     model   vdw
     2.441 3.120
  ... (remaining 60634 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
  selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 through 84))
  selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
  selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
  selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 47 through 84))
  selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
  selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
  selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
  selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ 
A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 51 through 84))
}

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:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.220
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
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      :  0.007   0.057   7421  Z= 0.310
  Angle     :  0.644   6.339  10087  Z= 0.390
  Chirality :  0.043   0.160   1204
  Planarity :  0.005   0.052   1271
  Dihedral  : 13.529  89.580   2447
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.80 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.25), residues: 996
  helix:  0.30 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.59 (0.52), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP a 208 
 HIS   0.003   0.001   HIS a 158 
 PHE   0.025   0.002   PHE a  99 
 TYR   0.021   0.003   TYR a  48 
 ARG   0.004   0.001   ARG 3  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08408 (  731)
  hydrogen bonds       : angle       5.18588 ( 2190)
  covalent geometry    : bond        0.00679 ( 7421)
  covalent geometry    : angle       0.64383 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: a  188 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8012 (ttm-80)
REVERT: 3   78 PHE cc_start: 0.6786 (m-10) cc_final: 0.6573 (m-10)
REVERT: 4   54 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.5703 (m-10)
REVERT: 5   75 MET cc_start: 0.7528 (ttp) cc_final: 0.7023 (ttp)
REVERT: 6   41 SER cc_start: 0.8183 (m) cc_final: 0.7902 (t)
REVERT: 7   75 MET cc_start: 0.7162 (tmm) cc_final: 0.6631 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 112
  average time/residue: 0.1806
  time to fit residues: 29.2648
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   37 VAL
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 7 residue   55 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
d  32 ASN
5   6 ASN
9  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.160237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.148896 restraints weight = 10668.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.151707 restraints weight = 5219.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.153984 restraints weight = 3236.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7421  Z= 0.170
  Angle     :  0.570   7.946  10087  Z= 0.302
  Chirality :  0.041   0.141   1204
  Planarity :  0.005   0.046   1271
  Dihedral  :  4.704  45.353   1054
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.35 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.27), residues: 996
  helix:  2.08 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.26 (0.57), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP a 212 
 HIS   0.002   0.001   HIS a 146 
 PHE   0.020   0.001   PHE a 221 
 TYR   0.015   0.001   TYR a 145 
 ARG   0.004   0.000   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04921 (  731)
  hydrogen bonds       : angle       4.25243 ( 2190)
  covalent geometry    : bond        0.00366 ( 7421)
  covalent geometry    : angle       0.56972 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
REVERT: a   64 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7101 (mt)
REVERT: 3   78 PHE cc_start: 0.6645 (m-10) cc_final: 0.6412 (m-10)
REVERT: 4   54 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6291 (m-10)
REVERT: 5   75 MET cc_start: 0.7536 (ttp) cc_final: 0.6901 (ttp)
REVERT: 6   41 SER cc_start: 0.8423 (m) cc_final: 0.8013 (t)
REVERT: 7   75 MET cc_start: 0.7233 (tmm) cc_final: 0.7030 (tmm)
  outliers start: 12
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1432
  time to fit residues: 25.6458
Evaluate side-chains
  124 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain d residue   37 VAL
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 4 residue   75 MET
Chi-restraints excluded: chain 6 residue    6 ASN
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 8 residue    3 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0970
   chunk 24 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
a 243 GLN
** 4  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.154916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.142485 restraints weight = 10627.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.145508 restraints weight = 5129.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.147399 restraints weight = 2944.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7421  Z= 0.161
  Angle     :  0.553   7.142  10087  Z= 0.288
  Chirality :  0.041   0.140   1204
  Planarity :  0.005   0.042   1271
  Dihedral  :  4.474  48.344   1053
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.62 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.35 (0.27), residues: 996
  helix:  2.65 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.16 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP a 208 
 HIS   0.002   0.001   HIS a 146 
 PHE   0.017   0.001   PHE a 221 
 TYR   0.014   0.001   TYR a 145 
 ARG   0.003   0.000   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04560 (  731)
  hydrogen bonds       : angle       4.06104 ( 2190)
  covalent geometry    : bond        0.00349 ( 7421)
  covalent geometry    : angle       0.55290 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: a   64 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7169 (mt)
REVERT: a  112 GLN cc_start: 0.7184 (tt0) cc_final: 0.6971 (tt0)
REVERT: 1   21 MET cc_start: 0.7915 (mmm) cc_final: 0.7557 (mmm)
REVERT: 3   78 PHE cc_start: 0.6423 (m-10) cc_final: 0.6202 (m-10)
REVERT: 4   46 GLN cc_start: 0.6625 (mm-40) cc_final: 0.6406 (mm110)
REVERT: 4   54 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6368 (m-10)
REVERT: 4   75 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6944 (ttp)
REVERT: 5   75 MET cc_start: 0.7651 (ttp) cc_final: 0.7016 (ttp)
REVERT: 6   41 SER cc_start: 0.8315 (m) cc_final: 0.7961 (t)
REVERT: 8    6 ASN cc_start: 0.7084 (m-40) cc_final: 0.6800 (m-40)
  outliers start: 16
  outliers final: 9
  residues processed: 121
  average time/residue: 0.1535
  time to fit residues: 27.4675
Evaluate side-chains
  127 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain a residue  243 GLN
Chi-restraints excluded: chain d residue   37 VAL
Chi-restraints excluded: chain 4 residue    6 ASN
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 4 residue   75 MET
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 7 residue    6 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   chunk 0 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
4  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.152837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.140392 restraints weight = 10643.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143457 restraints weight = 5108.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145362 restraints weight = 2920.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7421  Z= 0.194
  Angle     :  0.575   7.146  10087  Z= 0.300
  Chirality :  0.041   0.155   1204
  Planarity :  0.005   0.041   1271
  Dihedral  :  4.564  48.478   1053
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.82 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.38 (0.27), residues: 996
  helix:  2.67 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.20 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.014   0.001   PHE a 221 
 TYR   0.019   0.002   TYR a 145 
 ARG   0.005   0.000   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04771 (  731)
  hydrogen bonds       : angle       4.13011 ( 2190)
  covalent geometry    : bond        0.00424 ( 7421)
  covalent geometry    : angle       0.57522 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7498 (mt)
REVERT: a   64 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7156 (mt)
REVERT: a  112 GLN cc_start: 0.7274 (tt0) cc_final: 0.7066 (tt0)
REVERT: 1   21 MET cc_start: 0.7951 (mmm) cc_final: 0.7607 (mmm)
REVERT: 4   46 GLN cc_start: 0.6793 (mm110) cc_final: 0.6563 (mm110)
REVERT: 4   54 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6447 (m-10)
REVERT: 5   21 MET cc_start: 0.6952 (tpt) cc_final: 0.6656 (tpt)
REVERT: 5   75 MET cc_start: 0.7662 (ttp) cc_final: 0.7064 (ttp)
REVERT: 6   41 SER cc_start: 0.8408 (m) cc_final: 0.8045 (t)
REVERT: 8    6 ASN cc_start: 0.7057 (m-40) cc_final: 0.6792 (m-40)
  outliers start: 22
  outliers final: 14
  residues processed: 129
  average time/residue: 0.1428
  time to fit residues: 26.7979
Evaluate side-chains
  130 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 LEU
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain a residue  243 GLN
Chi-restraints excluded: chain b residue   53 ILE
Chi-restraints excluded: chain b residue   56 VAL
Chi-restraints excluded: chain d residue   37 VAL
Chi-restraints excluded: chain 4 residue    6 ASN
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 4 residue   75 MET
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 80 optimal weight:    0.4980
   chunk 88 optimal weight:    0.0010
   chunk 46 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0070
   chunk 12 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.3004

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 243 GLN
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.144308 restraints weight = 10417.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147306 restraints weight = 5109.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.149173 restraints weight = 2970.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7421  Z= 0.128
  Angle     :  0.532   9.529  10087  Z= 0.267
  Chirality :  0.039   0.174   1204
  Planarity :  0.004   0.042   1271
  Dihedral  :  4.191  46.991   1053
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.71 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.90 (0.27), residues: 996
  helix:  3.03 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.12 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.011   0.001   PHE a 221 
 TYR   0.015   0.001   TYR a 145 
 ARG   0.005   0.000   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  731)
  hydrogen bonds       : angle       3.88240 ( 2190)
  covalent geometry    : bond        0.00264 ( 7421)
  covalent geometry    : angle       0.53234 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: a   64 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7082 (mt)
REVERT: 1   21 MET cc_start: 0.7969 (mmm) cc_final: 0.7603 (mmm)
REVERT: 3   78 PHE cc_start: 0.6086 (m-10) cc_final: 0.5858 (m-10)
REVERT: 4   54 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6382 (m-10)
REVERT: 5   71 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6351 (m-40)
REVERT: 5   75 MET cc_start: 0.7642 (ttp) cc_final: 0.6858 (ttp)
REVERT: 6   41 SER cc_start: 0.8412 (m) cc_final: 0.8007 (t)
REVERT: 7   75 MET cc_start: 0.7521 (tmm) cc_final: 0.6875 (tmm)
REVERT: 8    6 ASN cc_start: 0.6930 (m-40) cc_final: 0.6654 (m-40)
  outliers start: 22
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1773
  time to fit residues: 31.6328
Evaluate side-chains
  129 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain a residue  243 GLN
Chi-restraints excluded: chain b residue   46 SER
Chi-restraints excluded: chain d residue    3 ILE
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 1 residue   85 LEU
Chi-restraints excluded: chain 2 residue   21 MET
Chi-restraints excluded: chain 2 residue   58 PHE
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 5 residue   71 ASN
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0070
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 243 GLN
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
6  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.160233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.148350 restraints weight = 10550.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.151338 restraints weight = 5075.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.153183 restraints weight = 2934.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7421  Z= 0.154
  Angle     :  0.550   8.114  10087  Z= 0.279
  Chirality :  0.040   0.178   1204
  Planarity :  0.004   0.039   1271
  Dihedral  :  4.166  47.648   1052
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.71 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.92 (0.27), residues: 996
  helix:  3.04 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.05 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.015   0.001   PHE 7  80 
 TYR   0.017   0.001   TYR a 145 
 ARG   0.009   0.001   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04244 (  731)
  hydrogen bonds       : angle       3.93250 ( 2190)
  covalent geometry    : bond        0.00332 ( 7421)
  covalent geometry    : angle       0.54952 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7458 (mt)
REVERT: a   64 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7036 (mt)
REVERT: 1   21 MET cc_start: 0.7804 (mmm) cc_final: 0.7401 (mmm)
REVERT: 3   78 PHE cc_start: 0.6115 (m-10) cc_final: 0.5894 (m-10)
REVERT: 4   54 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6483 (m-10)
REVERT: 4   75 MET cc_start: 0.6974 (ttp) cc_final: 0.6685 (ttp)
REVERT: 5   75 MET cc_start: 0.7621 (ttp) cc_final: 0.7116 (ttp)
REVERT: 6   41 SER cc_start: 0.8529 (m) cc_final: 0.8132 (t)
REVERT: 7   21 MET cc_start: 0.7287 (mmm) cc_final: 0.6580 (mmm)
REVERT: 7   75 MET cc_start: 0.7441 (tmm) cc_final: 0.6879 (tmm)
REVERT: 8    6 ASN cc_start: 0.6685 (m-40) cc_final: 0.6483 (m-40)
  outliers start: 26
  outliers final: 17
  residues processed: 126
  average time/residue: 0.2126
  time to fit residues: 38.5050
Evaluate side-chains
  130 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 LEU
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain a residue  243 GLN
Chi-restraints excluded: chain b residue   46 SER
Chi-restraints excluded: chain d residue    3 ILE
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 1 residue   85 LEU
Chi-restraints excluded: chain 2 residue   58 PHE
Chi-restraints excluded: chain 4 residue    6 ASN
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Chi-restraints excluded: chain 8 residue    8 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0010
   chunk 31 optimal weight:    0.0970
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.3584

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.160795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.148877 restraints weight = 10480.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.151927 restraints weight = 5047.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.153757 restraints weight = 2894.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7421  Z= 0.136
  Angle     :  0.549   7.910  10087  Z= 0.277
  Chirality :  0.039   0.195   1204
  Planarity :  0.005   0.043   1271
  Dihedral  :  4.108  47.045   1052
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.30 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.02 (0.27), residues: 996
  helix:  3.11 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.10 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.012   0.001   PHE 2  78 
 TYR   0.015   0.001   TYR a 145 
 ARG   0.011   0.001   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  731)
  hydrogen bonds       : angle       3.87339 ( 2190)
  covalent geometry    : bond        0.00291 ( 7421)
  covalent geometry    : angle       0.54932 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: a   64 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7011 (mt)
REVERT: 1   21 MET cc_start: 0.7817 (mmm) cc_final: 0.7426 (mmm)
REVERT: 3   78 PHE cc_start: 0.5967 (m-10) cc_final: 0.5745 (m-10)
REVERT: 4   54 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6488 (m-10)
REVERT: 5   75 MET cc_start: 0.7621 (ttp) cc_final: 0.7182 (ttp)
REVERT: 6   41 SER cc_start: 0.8518 (m) cc_final: 0.8087 (t)
REVERT: 7   75 MET cc_start: 0.7481 (tmm) cc_final: 0.6948 (tmm)
REVERT: 8    6 ASN cc_start: 0.6689 (m-40) cc_final: 0.6470 (m-40)
  outliers start: 21
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1488
  time to fit residues: 26.5759
Evaluate side-chains
  128 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain b residue   53 ILE
Chi-restraints excluded: chain b residue   56 VAL
Chi-restraints excluded: chain d residue    3 ILE
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 1 residue   85 LEU
Chi-restraints excluded: chain 2 residue   58 PHE
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 6 residue   54 PHE
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Chi-restraints excluded: chain 7 residue   59 ILE
Chi-restraints excluded: chain 8 residue    3 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 99 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
8  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.159922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148357 restraints weight = 10655.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.151278 restraints weight = 5107.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.153069 restraints weight = 2947.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7421  Z= 0.176
  Angle     :  0.589   9.025  10087  Z= 0.297
  Chirality :  0.041   0.172   1204
  Planarity :  0.005   0.045   1271
  Dihedral  :  4.246  47.635   1052
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 17.71 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.81 (0.27), residues: 996
  helix:  2.97 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.12 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.015   0.001   PHE 7  80 
 TYR   0.018   0.001   TYR a 145 
 ARG   0.012   0.001   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04480 (  731)
  hydrogen bonds       : angle       3.98902 ( 2190)
  covalent geometry    : bond        0.00384 ( 7421)
  covalent geometry    : angle       0.58908 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7470 (mt)
REVERT: a   64 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7071 (mt)
REVERT: 1   21 MET cc_start: 0.7801 (mmm) cc_final: 0.7388 (mmm)
REVERT: 3   78 PHE cc_start: 0.6021 (m-10) cc_final: 0.5808 (m-10)
REVERT: 4   54 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6560 (m-10)
REVERT: 5   75 MET cc_start: 0.7655 (ttp) cc_final: 0.7058 (ttp)
REVERT: 6   41 SER cc_start: 0.8577 (m) cc_final: 0.8165 (t)
REVERT: 7   21 MET cc_start: 0.7336 (mmm) cc_final: 0.6579 (mmm)
REVERT: 7   75 MET cc_start: 0.7494 (tmm) cc_final: 0.6864 (tmm)
REVERT: 8    6 ASN cc_start: 0.6728 (m-40) cc_final: 0.6516 (m-40)
  outliers start: 27
  outliers final: 19
  residues processed: 137
  average time/residue: 0.1441
  time to fit residues: 28.9750
Evaluate side-chains
  144 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 LEU
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain b residue   46 SER
Chi-restraints excluded: chain b residue   53 ILE
Chi-restraints excluded: chain b residue   56 VAL
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 2 residue   58 PHE
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 6 residue   43 ILE
Chi-restraints excluded: chain 6 residue   54 PHE
Chi-restraints excluded: chain 6 residue   55 THR
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Chi-restraints excluded: chain 7 residue   59 ILE
Chi-restraints excluded: chain 8 residue    3 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0970
   chunk 78 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0470
   chunk 13 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.164071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.152657 restraints weight = 10577.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.155529 restraints weight = 5170.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.157279 restraints weight = 3015.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7421  Z= 0.141
  Angle     :  0.601  15.143  10087  Z= 0.292
  Chirality :  0.040   0.236   1204
  Planarity :  0.005   0.042   1271
  Dihedral  :  4.145  46.416   1052
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 18.60 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.00 (0.27), residues: 996
  helix:  3.08 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop : -0.99 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.012   0.001   PHE 2  78 
 TYR   0.016   0.001   TYR a 145 
 ARG   0.011   0.001   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  731)
  hydrogen bonds       : angle       3.87521 ( 2190)
  covalent geometry    : bond        0.00304 ( 7421)
  covalent geometry    : angle       0.60056 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7319 (mp)
REVERT: a   64 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6974 (mt)
REVERT: 1   21 MET cc_start: 0.7759 (mmm) cc_final: 0.7360 (mmm)
REVERT: 4   54 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6462 (m-10)
REVERT: 4   75 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5643 (ttp)
REVERT: 5   75 MET cc_start: 0.7602 (ttp) cc_final: 0.7081 (ttp)
REVERT: 6   41 SER cc_start: 0.8541 (m) cc_final: 0.8114 (t)
REVERT: 7   21 MET cc_start: 0.7232 (mmm) cc_final: 0.6466 (mmm)
REVERT: 7   75 MET cc_start: 0.7508 (tmm) cc_final: 0.6921 (tmm)
  outliers start: 24
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1529
  time to fit residues: 27.7411
Evaluate side-chains
  135 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 LEU
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain b residue   46 SER
Chi-restraints excluded: chain b residue   56 VAL
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 2 residue   58 PHE
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 4 residue   75 MET
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 6 residue   43 ILE
Chi-restraints excluded: chain 6 residue   54 PHE
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Chi-restraints excluded: chain 7 residue   59 ILE
Chi-restraints excluded: chain 8 residue    3 LEU
Chi-restraints excluded: chain 8 residue    8 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.159729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.148129 restraints weight = 10706.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.151066 restraints weight = 5122.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.152926 restraints weight = 2946.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7421  Z= 0.183
  Angle     :  0.651  19.888  10087  Z= 0.318
  Chirality :  0.042   0.242   1204
  Planarity :  0.005   0.054   1271
  Dihedral  :  4.284  47.567   1052
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.05 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.75 (0.27), residues: 996
  helix:  2.90 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.03 (0.60), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.017   0.001   PHE 7  80 
 TYR   0.019   0.002   TYR a 145 
 ARG   0.013   0.001   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04529 (  731)
  hydrogen bonds       : angle       4.01448 ( 2190)
  covalent geometry    : bond        0.00402 ( 7421)
  covalent geometry    : angle       0.65116 (10087)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7462 (mt)
REVERT: a   64 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7157 (mt)
REVERT: 1   21 MET cc_start: 0.7760 (mmm) cc_final: 0.7361 (mmm)
REVERT: 4   54 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6547 (m-10)
REVERT: 5   75 MET cc_start: 0.7680 (ttp) cc_final: 0.7106 (ttp)
REVERT: 6   41 SER cc_start: 0.8582 (m) cc_final: 0.8166 (t)
REVERT: 7   21 MET cc_start: 0.7245 (mmm) cc_final: 0.6549 (mmm)
REVERT: 7   75 MET cc_start: 0.7548 (tmm) cc_final: 0.6779 (tmm)
  outliers start: 22
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1480
  time to fit residues: 26.6563
Evaluate side-chains
  133 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 LEU
Chi-restraints excluded: chain a residue   54 THR
Chi-restraints excluded: chain a residue   64 LEU
Chi-restraints excluded: chain a residue   92 LEU
Chi-restraints excluded: chain a residue  131 ILE
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  208 TRP
Chi-restraints excluded: chain b residue   46 SER
Chi-restraints excluded: chain b residue   53 ILE
Chi-restraints excluded: chain b residue   56 VAL
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 2 residue   58 PHE
Chi-restraints excluded: chain 4 residue   54 PHE
Chi-restraints excluded: chain 6 residue   21 MET
Chi-restraints excluded: chain 6 residue   43 ILE
Chi-restraints excluded: chain 6 residue   54 PHE
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Chi-restraints excluded: chain 7 residue   55 THR
Chi-restraints excluded: chain 7 residue   59 ILE
Chi-restraints excluded: chain 8 residue    3 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0060
   chunk 54 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 66 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
** 3  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.163061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.151472 restraints weight = 10569.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.154509 restraints weight = 5018.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156384 restraints weight = 2846.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7421  Z= 0.145
  Angle     :  0.614  12.837  10087  Z= 0.302
  Chirality :  0.040   0.234   1204
  Planarity :  0.005   0.050   1271
  Dihedral  :  4.170  46.389   1052
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.20 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.98 (0.27), residues: 996
  helix:  3.05 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -0.90 (0.61), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 
 PHE   0.013   0.001   PHE 2  78 
 TYR   0.017   0.001   TYR a 145 
 ARG   0.013   0.001   ARG d  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04225 (  731)
  hydrogen bonds       : angle       3.91008 ( 2190)
  covalent geometry    : bond        0.00311 ( 7421)
  covalent geometry    : angle       0.61429 (10087)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2477.85 seconds
wall clock time: 45 minutes 25.95 seconds (2725.95 seconds total)