Starting phenix.real_space_refine
on Wed Mar  4 05:00:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgb_22320/03_2026/7jgb_22320.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgb_22320/03_2026/7jgb_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgb_22320/03_2026/7jgb_22320.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgb_22320/03_2026/7jgb_22320.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jgb_22320/03_2026/7jgb_22320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgb_22320/03_2026/7jgb_22320.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.006 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'GLU:plan': 2}
          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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 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: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU: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: 1.66, per 1000 atoms: 0.23
  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: 0.72
  Conformation dependent library (CDL) restraints added in 278.8 milliseconds
  

  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: 0.10
  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: 0.94

  Time building geometry restraints manager: 0.89 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:             2.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.360
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.870
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG 3  52 
 TYR   0.021   0.003   TYR a  48 
 PHE   0.025   0.002   PHE a  99 
 TRP   0.028   0.003   TRP a 208 
 HIS   0.003   0.001   HIS a 158 

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

*********************** 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  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: a  188 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8015 (ttm-80)
REVERT: 3   78 PHE cc_start: 0.6786 (m-10) cc_final: 0.6573 (m-10)
REVERT: 4   54 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5703 (m-10)
REVERT: 5   75 MET cc_start: 0.7528 (ttp) cc_final: 0.7024 (ttp)
REVERT: 6   41 SER cc_start: 0.8184 (m) cc_final: 0.7902 (t)
REVERT: 7   75 MET cc_start: 0.7161 (tmm) cc_final: 0.6489 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 112
  average time/residue: 0.0583
  time to fit residues: 9.7289
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  : 0.239 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.3980
   chunk 97 optimal weight:    0.0670
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.0070
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.2334

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

Flipped N/Q/H residues before XYZ refinement:
a 146 HIS
** a 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  32 ASN
5   6 ASN
9  50 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.163034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.151603 restraints weight = 10824.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.154725 restraints weight = 5097.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.156633 restraints weight = 2850.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.157833 restraints weight = 1846.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.158558 restraints weight = 1338.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.1595

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= 0.135
  Angle     :  0.551   8.335  10087  Z= 0.284
  Chirality :  0.040   0.136   1204
  Planarity :  0.005   0.045   1271
  Dihedral  :  4.409  42.623   1054
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.90 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.27), residues: 996
  helix:  2.32 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.27 (0.55), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG d  38 
 TYR   0.014   0.001   TYR a 145 
 PHE   0.020   0.001   PHE a 221 
 TRP   0.018   0.002   TRP a 212 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7421)
  covalent geometry    : angle       0.55051 (10087)
  hydrogen bonds       : bond        0.04468 (  731)
  hydrogen bonds       : angle       4.09556 ( 2190)

*********************** 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
  127 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: 4   54 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.6049 (m-10)
REVERT: 5   75 MET cc_start: 0.7445 (ttp) cc_final: 0.6779 (ttp)
REVERT: 6   41 SER cc_start: 0.8417 (m) cc_final: 0.8025 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 119
  average time/residue: 0.0575
  time to fit residues: 10.2862
Evaluate side-chains
  122 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
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 4 residue   54 PHE
Chi-restraints excluded: chain 4 residue   75 MET
Chi-restraints excluded: chain 6 residue    6 ASN
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 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.153199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.140796 restraints weight = 10541.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.143798 restraints weight = 5082.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145669 restraints weight = 2913.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146844 restraints weight = 1937.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.147621 restraints weight = 1452.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7421  Z= 0.199
  Angle     :  0.584   7.203  10087  Z= 0.309
  Chirality :  0.042   0.152   1204
  Planarity :  0.005   0.041   1271
  Dihedral  :  4.453  49.080   1052
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.88 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.27), residues: 996
  helix:  2.58 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.20 (0.57), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG 2  52 
 TYR   0.018   0.002   TYR a 145 
 PHE   0.016   0.001   PHE a 221 
 TRP   0.020   0.002   TRP a 208 
 HIS   0.002   0.001   HIS a 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7421)
  covalent geometry    : angle       0.58381 (10087)
  hydrogen bonds       : bond        0.04928 (  731)
  hydrogen bonds       : angle       4.16164 ( 2190)

*********************** 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  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: 1   21 MET cc_start: 0.7812 (mmm) cc_final: 0.7471 (mmm)
REVERT: 3   78 PHE cc_start: 0.6372 (m-10) cc_final: 0.6125 (m-10)
REVERT: 4   54 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6420 (m-10)
REVERT: 5   75 MET cc_start: 0.7700 (ttp) cc_final: 0.7058 (ttp)
REVERT: 6   41 SER cc_start: 0.8343 (m) cc_final: 0.7983 (t)
REVERT: 8    6 ASN cc_start: 0.7024 (m-40) cc_final: 0.6776 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0590
  time to fit residues: 10.5959
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  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
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 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   21 MET
Chi-restraints excluded: chain 6 residue   64 VAL
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 76 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
4  46 GLN
8  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.147492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.134642 restraints weight = 10920.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137771 restraints weight = 5252.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.139637 restraints weight = 3004.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.140888 restraints weight = 2005.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.141673 restraints weight = 1489.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.2209

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= 0.182
  Angle     :  0.564   7.127  10087  Z= 0.295
  Chirality :  0.041   0.150   1204
  Planarity :  0.005   0.041   1271
  Dihedral  :  4.389  48.875   1052
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.52 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.46 (0.27), residues: 996
  helix:  2.73 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.23 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG 6  52 
 TYR   0.017   0.002   TYR a 145 
 PHE   0.014   0.001   PHE a 221 
 TRP   0.021   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 7421)
  covalent geometry    : angle       0.56391 (10087)
  hydrogen bonds       : bond        0.04645 (  731)
  hydrogen bonds       : angle       4.07630 ( 2190)

*********************** 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
  139 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7575 (tp)
REVERT: 1   21 MET cc_start: 0.7914 (mmm) cc_final: 0.7521 (mmm)
REVERT: 3   78 PHE cc_start: 0.6210 (m-10) cc_final: 0.5987 (m-10)
REVERT: 4   54 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6408 (m-10)
REVERT: 5   21 MET cc_start: 0.6959 (tpt) cc_final: 0.6697 (tpt)
REVERT: 5   71 ASN cc_start: 0.6604 (OUTLIER) cc_final: 0.6356 (m-40)
REVERT: 5   75 MET cc_start: 0.7671 (ttp) cc_final: 0.7059 (ttp)
REVERT: 6   41 SER cc_start: 0.8355 (m) cc_final: 0.7986 (t)
REVERT: 7   75 MET cc_start: 0.7551 (tmm) cc_final: 0.6886 (tmm)
REVERT: 8    6 ASN cc_start: 0.6953 (m-40) cc_final: 0.6698 (m-40)
  outliers start: 21
  outliers final: 13
  residues processed: 128
  average time/residue: 0.0552
  time to fit residues: 10.6117
Evaluate side-chains
  133 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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   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 d residue   37 VAL
Chi-restraints excluded: chain 1 residue   54 PHE
Chi-restraints excluded: chain 1 residue   85 LEU
Chi-restraints excluded: chain 4 residue    6 ASN
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 7 residue    6 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0870
   chunk 30 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0870
   chunk 94 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.3736

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.155727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.143006 restraints weight = 10544.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.146155 restraints weight = 5054.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.148072 restraints weight = 2884.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.149244 restraints weight = 1916.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150041 restraints weight = 1441.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.2434

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= 0.137
  Angle     :  0.536   7.303  10087  Z= 0.272
  Chirality :  0.039   0.171   1204
  Planarity :  0.004   0.040   1271
  Dihedral  :  4.191  47.913   1052
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.86 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.86 (0.27), residues: 996
  helix:  3.00 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.16 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG d  38 
 TYR   0.015   0.001   TYR a 145 
 PHE   0.014   0.001   PHE 7  80 
 TRP   0.018   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7421)
  covalent geometry    : angle       0.53604 (10087)
  hydrogen bonds       : bond        0.04183 (  731)
  hydrogen bonds       : angle       3.90780 ( 2190)

*********************** 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
  125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: 1   21 MET cc_start: 0.7990 (mmm) cc_final: 0.7589 (mmm)
REVERT: 3   78 PHE cc_start: 0.5972 (m-10) cc_final: 0.5748 (m-10)
REVERT: 4   54 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6351 (m-10)
REVERT: 4   75 MET cc_start: 0.6875 (ttp) cc_final: 0.6620 (ttp)
REVERT: 5   75 MET cc_start: 0.7686 (ttp) cc_final: 0.6865 (ttp)
REVERT: 6   41 SER cc_start: 0.8328 (m) cc_final: 0.7965 (t)
REVERT: 7   75 MET cc_start: 0.7556 (tmm) cc_final: 0.6890 (tmm)
REVERT: 8    6 ASN cc_start: 0.6948 (m-40) cc_final: 0.6667 (m-40)
  outliers start: 20
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0601
  time to fit residues: 10.2345
Evaluate side-chains
  118 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
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 b residue   53 ILE
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 7 residue    6 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**
6  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.153530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.140863 restraints weight = 10615.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.143945 restraints weight = 5062.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.145860 restraints weight = 2903.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.147087 restraints weight = 1932.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.147872 restraints weight = 1445.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7421  Z= 0.186
  Angle     :  0.572   7.410  10087  Z= 0.296
  Chirality :  0.041   0.178   1204
  Planarity :  0.005   0.040   1271
  Dihedral  :  4.321  48.140   1052
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.56 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.68 (0.27), residues: 996
  helix:  2.87 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.11 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG d  38 
 TYR   0.018   0.002   TYR a 145 
 PHE   0.013   0.001   PHE b  31 
 TRP   0.020   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7421)
  covalent geometry    : angle       0.57209 (10087)
  hydrogen bonds       : bond        0.04617 (  731)
  hydrogen bonds       : angle       4.04451 ( 2190)

*********************** 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
  138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7428 (mt)
REVERT: 1   21 MET cc_start: 0.7979 (mmm) cc_final: 0.7527 (mmm)
REVERT: 3   78 PHE cc_start: 0.6039 (m-10) cc_final: 0.5804 (m-10)
REVERT: 4   54 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6444 (m-10)
REVERT: 4   75 MET cc_start: 0.7030 (ttp) cc_final: 0.6757 (ttp)
REVERT: 5   75 MET cc_start: 0.7695 (ttp) cc_final: 0.7173 (ttp)
REVERT: 6   41 SER cc_start: 0.8353 (m) cc_final: 0.7997 (t)
REVERT: 7   75 MET cc_start: 0.7564 (tmm) cc_final: 0.6966 (tmm)
REVERT: 8    6 ASN cc_start: 0.7053 (m-40) cc_final: 0.6769 (m-40)
  outliers start: 22
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0609
  time to fit residues: 11.5744
Evaluate side-chains
  134 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
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   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 d residue   37 VAL
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   55 THR
Chi-restraints excluded: chain 6 residue   64 VAL
Chi-restraints excluded: chain 7 residue    6 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 88 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   chunk 16 optimal weight:    0.6980
   chunk 71 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0870
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.162886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.151292 restraints weight = 10580.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.154243 restraints weight = 5079.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.156048 restraints weight = 2921.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.157184 restraints weight = 1953.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.157919 restraints weight = 1466.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.2718

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= 0.138
  Angle     :  0.559   8.729  10087  Z= 0.281
  Chirality :  0.039   0.192   1204
  Planarity :  0.004   0.041   1271
  Dihedral  :  4.166  47.252   1052
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.93 (0.27), residues: 996
  helix:  3.05 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.09 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG d  38 
 TYR   0.016   0.001   TYR a 145 
 PHE   0.015   0.001   PHE 7  80 
 TRP   0.018   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7421)
  covalent geometry    : angle       0.55895 (10087)
  hydrogen bonds       : bond        0.04132 (  731)
  hydrogen bonds       : angle       3.87637 ( 2190)

*********************** 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
  131 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: 1   21 MET cc_start: 0.7712 (mmm) cc_final: 0.7299 (mmm)
REVERT: 4   54 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6466 (m-10)
REVERT: 5   75 MET cc_start: 0.7597 (ttp) cc_final: 0.7110 (ttp)
REVERT: 6   41 SER cc_start: 0.8514 (m) cc_final: 0.8080 (t)
REVERT: 7   75 MET cc_start: 0.7427 (tmm) cc_final: 0.6790 (tmm)
  outliers start: 20
  outliers final: 18
  residues processed: 121
  average time/residue: 0.0578
  time to fit residues: 10.4045
Evaluate side-chains
  130 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
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   37 VAL
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 2 residue   78 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   59 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0570
   chunk 43 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
a 146 HIS
** 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 = 0.4039 r_free = 0.4039 target = 0.162546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.151076 restraints weight = 10618.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.153864 restraints weight = 5287.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.155949 restraints weight = 3324.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.157620 restraints weight = 1931.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.157720 restraints weight = 1357.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7421  Z= 0.158
  Angle     :  0.586  12.411  10087  Z= 0.292
  Chirality :  0.040   0.216   1204
  Planarity :  0.005   0.044   1271
  Dihedral  :  4.195  47.385   1052
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.60 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.89 (0.27), residues: 996
  helix:  3.01 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.01 (0.59), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG d  38 
 TYR   0.017   0.001   TYR a 145 
 PHE   0.012   0.001   PHE b  31 
 TRP   0.018   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7421)
  covalent geometry    : angle       0.58623 (10087)
  hydrogen bonds       : bond        0.04293 (  731)
  hydrogen bonds       : angle       3.92872 ( 2190)

*********************** 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
  134 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   21 MET cc_start: 0.7734 (mmm) cc_final: 0.7312 (mmm)
REVERT: 4   54 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6527 (m-10)
REVERT: 5   75 MET cc_start: 0.7631 (ttp) cc_final: 0.7041 (ttp)
REVERT: 6   41 SER cc_start: 0.8531 (m) cc_final: 0.8113 (t)
REVERT: 7   75 MET cc_start: 0.7437 (tmm) cc_final: 0.6789 (tmm)
  outliers start: 22
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0591
  time to fit residues: 10.8819
Evaluate side-chains
  130 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
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 d residue   37 VAL
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   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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0770
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.162876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.151502 restraints weight = 10481.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.154387 restraints weight = 5230.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156316 restraints weight = 3235.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.157728 restraints weight = 1926.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.157854 restraints weight = 1449.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.2891

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= 0.149
  Angle     :  0.575  10.011  10087  Z= 0.287
  Chirality :  0.040   0.223   1204
  Planarity :  0.005   0.044   1271
  Dihedral  :  4.130  46.609   1052
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.98 (0.27), residues: 996
  helix:  3.06 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop : -0.93 (0.59), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG d  38 
 TYR   0.016   0.001   TYR a 145 
 PHE   0.017   0.001   PHE 7  80 
 TRP   0.018   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7421)
  covalent geometry    : angle       0.57478 (10087)
  hydrogen bonds       : bond        0.04195 (  731)
  hydrogen bonds       : angle       3.89269 ( 2190)

*********************** 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
  132 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: 1   21 MET cc_start: 0.7725 (mmm) cc_final: 0.7320 (mmm)
REVERT: 4   54 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6462 (m-10)
REVERT: 5   75 MET cc_start: 0.7625 (ttp) cc_final: 0.7073 (ttp)
REVERT: 6   41 SER cc_start: 0.8534 (m) cc_final: 0.8107 (t)
REVERT: 7   75 MET cc_start: 0.7463 (tmm) cc_final: 0.6875 (tmm)
  outliers start: 22
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0570
  time to fit residues: 10.3992
Evaluate side-chains
  128 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 THR
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   37 VAL
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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 5 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 96 optimal weight:    0.1980
   chunk 49 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.162762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.151163 restraints weight = 10580.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154228 restraints weight = 5004.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156109 restraints weight = 2835.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.157261 restraints weight = 1867.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.158008 restraints weight = 1380.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7421  Z= 0.153
  Angle     :  0.610  16.858  10087  Z= 0.298
  Chirality :  0.040   0.242   1204
  Planarity :  0.005   0.051   1271
  Dihedral  :  4.161  46.666   1052
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.75 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.96 (0.27), residues: 996
  helix:  3.04 (0.17), residues: 874
  sheet:  None (None), residues: 0
  loop : -0.91 (0.61), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG d  38 
 TYR   0.016   0.001   TYR a 145 
 PHE   0.012   0.001   PHE b  31 
 TRP   0.017   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7421)
  covalent geometry    : angle       0.60988 (10087)
  hydrogen bonds       : bond        0.04243 (  731)
  hydrogen bonds       : angle       3.91316 ( 2190)

********************** 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
  126 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: a   45 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7493 (mt)
REVERT: 1   21 MET cc_start: 0.7705 (mmm) cc_final: 0.7300 (mmm)
REVERT: 4   54 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6500 (m-10)
REVERT: 5   75 MET cc_start: 0.7581 (ttp) cc_final: 0.7100 (ttp)
REVERT: 6   41 SER cc_start: 0.8528 (m) cc_final: 0.8088 (t)
REVERT: 7   75 MET cc_start: 0.7486 (tmm) cc_final: 0.6888 (tmm)
  outliers start: 21
  outliers final: 19
  residues processed: 118
  average time/residue: 0.0567
  time to fit residues: 10.0595
Evaluate side-chains
  125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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   62 VAL
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   37 VAL
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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 85 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0040
   chunk 52 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0010
   overall best weight:    0.3798

-------------------------------------------------------------------------------
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  37 ASN
** 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 = 0.4056 r_free = 0.4056 target = 0.163491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.151841 restraints weight = 10689.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.154894 restraints weight = 5080.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.156780 restraints weight = 2892.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.157943 restraints weight = 1907.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.158695 restraints weight = 1408.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7421  Z= 0.143
  Angle     :  0.632  18.840  10087  Z= 0.303
  Chirality :  0.040   0.244   1204
  Planarity :  0.005   0.050   1271
  Dihedral  :  4.111  46.218   1052
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.90 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.07 (0.27), residues: 996
  helix:  3.10 (0.17), residues: 874
  sheet:  None (None), residues: 0
  loop : -0.84 (0.61), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG d  38 
 TYR   0.016   0.001   TYR a 145 
 PHE   0.018   0.001   PHE 7  80 
 TRP   0.016   0.002   TRP a 208 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7421)
  covalent geometry    : angle       0.63174 (10087)
  hydrogen bonds       : bond        0.04116 (  731)
  hydrogen bonds       : angle       3.88507 ( 2190)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1106.44 seconds
wall clock time: 19 minutes 43.90 seconds (1183.90 seconds total)