Starting phenix.real_space_refine
on Wed Feb 12 05:34:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5k_37295/02_2025/8w5k_37295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5k_37295/02_2025/8w5k_37295.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5k_37295/02_2025/8w5k_37295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5k_37295/02_2025/8w5k_37295.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5k_37295/02_2025/8w5k_37295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5k_37295/02_2025/8w5k_37295.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      22      5.16       5
     C    4741      2.51       5
     N    1225      2.21       5
     O    1390      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7379
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "B"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "C"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 303
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 267
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "E"
      Number of atoms: 342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 342
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 4, 'TRANS': 37}
    Chain: "J"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "K"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 303
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "L"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 267
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "M"
      Number of atoms: 342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 342
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 4, 'TRANS': 37}
    Chain: "F"
      Number of atoms: 2369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2369
          Classifications: {'peptide': 307}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 9, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "I"
      Number of atoms: 2369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2369
          Classifications: {'peptide': 307}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 9, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "I"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'46E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.37, per 1000 atoms: 0.73
  Number of scatterers: 7379
  At special positions: 0
  Unit cell: (94.8024, 104.498, 142.204, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     P       1     15.00
     O    1390      8.00
     N    1225      7.00
     C    4741      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: 1.93
  Conformation dependent library (CDL) restraints added in 935.3 milliseconds
  

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 2 sheets defined
      37.2% alpha, 36.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'B' and resid 86 through 135
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'C' and resid 14 through 49
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'D' and resid 30 through 51
    Processing helix  chain 'D' and resid 51 through 58
      removed outlier: 4.142A  pdb=" N   ASP D  55 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 44
      removed outlier: 4.265A  pdb=" N   ASN E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   VAL E  27 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   ILE E  33 " --> pdb=" O   HIS E  29 " (cutoff:3.500A)
      Proline residue:  E  34  - end of helix
    Processing helix  chain 'E' and resid 49 through 55
    Processing helix  chain 'J' and resid 87 through 135
      Proline residue:  J 112  - end of helix
    Processing helix  chain 'K' and resid 14 through 49
      Proline residue:  K  39  - end of helix
    Processing helix  chain 'L' and resid 30 through 51
    Processing helix  chain 'L' and resid 51 through 58
      removed outlier: 3.818A  pdb=" N   ASP L  55 " --> pdb=" O   SER L  51 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA L  58 " --> pdb=" O   MET L  54 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 20 through 31
      removed outlier: 3.604A  pdb=" N   HIS M  29 " --> pdb=" O   HIS M  25 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 31 through 44
    Processing helix  chain 'M' and resid 49 through 55
    Processing helix  chain 'F' and resid 50 through 55
    Processing helix  chain 'F' and resid 62 through 66
    Processing helix  chain 'F' and resid 67 through 72
    Processing helix  chain 'F' and resid 364 through 373
    Processing helix  chain 'I' and resid 50 through 55
    Processing helix  chain 'I' and resid 62 through 66
    Processing helix  chain 'I' and resid 67 through 72
    Processing helix  chain 'I' and resid 364 through 373
      removed outlier: 3.588A  pdb=" N   GLN I 372 " --> pdb=" O   LEU I 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 361 through 362
      removed outlier: 7.437A  pdb=" N   THR F 361 " --> pdb=" O   ASP F  87 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ASN F  89 " --> pdb=" O   THR F 361 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN F  89 " --> pdb=" O   PHE F 359 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS F 323 " --> pdb=" O   ASP F 319 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL F 267 " --> pdb=" O   VAL F 263 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   VAL F 196 " --> pdb=" O   ASN F 184 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   ASN F 184 " --> pdb=" O   VAL F 196 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   VAL F 198 " --> pdb=" O   THR F 182 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   THR F 182 " --> pdb=" O   VAL F 198 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   SER F 200 " --> pdb=" O   VAL F 180 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   VAL F 180 " --> pdb=" O   SER F 200 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   LEU F 202 " --> pdb=" O   VAL F 178 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   VAL F 178 " --> pdb=" O   LEU F 202 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   SER F 204 " --> pdb=" O   PHE F 176 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   PHE F 176 " --> pdb=" O   SER F 204 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   CYS F 165 " --> pdb=" O   ASN F 184 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   PHE F  98 " --> pdb=" O   PHE F  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 93
      removed outlier: 6.755A  pdb=" N   PHE I  98 " --> pdb=" O   PHE I  92 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   CYS I 165 " --> pdb=" O   ASN I 184 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   THR I 194 " --> pdb=" O   PRO I 185 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LEU I 209 " --> pdb=" O   VAL I 205 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LYS I 323 " --> pdb=" O   ASP I 319 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   GLY I  83 " --> pdb=" O   CYS I 355 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   LEU I 357 " --> pdb=" O   GLY I  83 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ARG I  85 " --> pdb=" O   LEU I 357 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   PHE I 359 " --> pdb=" O   ARG I  85 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASP I  87 " --> pdb=" O   PHE I 359 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   THR I 361 " --> pdb=" O   ASP I  87 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ASN I  89 " --> pdb=" O   THR I 361 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1374
        1.33 -     1.45: 1926
        1.45 -     1.57: 4200
        1.57 -     1.69: 2
        1.69 -     1.81: 36
  Bond restraints: 7538
  Sorted by residual:
  bond pdb=" CG  GLU C  19 "
       pdb=" CD  GLU C  19 "
    ideal  model  delta    sigma   weight residual
    1.516  1.471  0.045 2.50e-02 1.60e+03 3.26e+00
  bond pdb=" N   ASP I 134 "
       pdb=" CA  ASP I 134 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.021 1.77e-02 3.19e+03 1.39e+00
  bond pdb=" CB  PRO E  34 "
       pdb=" CG  PRO E  34 "
    ideal  model  delta    sigma   weight residual
    1.492  1.551 -0.059 5.00e-02 4.00e+02 1.39e+00
  bond pdb=" CA  ASP F 134 "
       pdb=" CB  ASP F 134 "
    ideal  model  delta    sigma   weight residual
    1.532  1.549 -0.017 1.43e-02 4.89e+03 1.38e+00
  bond pdb=" CA  VAL K  37 "
       pdb=" C   VAL K  37 "
    ideal  model  delta    sigma   weight residual
    1.519  1.532 -0.013 1.14e-02 7.69e+03 1.26e+00
  ... (remaining 7533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 9954
        1.85 -     3.70: 207
        3.70 -     5.54: 35
        5.54 -     7.39: 14
        7.39 -     9.24: 9
  Bond angle restraints: 10219
  Sorted by residual:
  angle pdb=" CA  GLU C  19 "
        pdb=" CB  GLU C  19 "
        pdb=" CG  GLU C  19 "
      ideal   model   delta    sigma   weight residual
     114.10  123.34   -9.24 2.00e+00 2.50e-01 2.13e+01
  angle pdb=" C   ASN I 133 "
        pdb=" N   ASP I 134 "
        pdb=" CA  ASP I 134 "
      ideal   model   delta    sigma   weight residual
     125.66  133.77   -8.11 1.85e+00 2.92e-01 1.92e+01
  angle pdb=" N   GLU C  19 "
        pdb=" CA  GLU C  19 "
        pdb=" CB  GLU C  19 "
      ideal   model   delta    sigma   weight residual
     110.28  116.32   -6.04 1.55e+00 4.16e-01 1.52e+01
  angle pdb=" CA  PRO E  34 "
        pdb=" N   PRO E  34 "
        pdb=" CD  PRO E  34 "
      ideal   model   delta    sigma   weight residual
     112.00  106.75    5.25 1.40e+00 5.10e-01 1.40e+01
  angle pdb=" C   ASN F 133 "
        pdb=" N   ASP F 134 "
        pdb=" CA  ASP F 134 "
      ideal   model   delta    sigma   weight residual
     124.31  130.08   -5.77 1.67e+00 3.59e-01 1.19e+01
  ... (remaining 10214 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.27: 3998
       22.27 -    44.53: 382
       44.53 -    66.80: 62
       66.80 -    89.06: 12
       89.06 -   111.33: 1
  Dihedral angle restraints: 4455
    sinusoidal: 1737
      harmonic: 2718
  Sorted by residual:
  dihedral pdb=" CA  ASN F  95 "
           pdb=" C   ASN F  95 "
           pdb=" N   PRO F  96 "
           pdb=" CA  PRO F  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.89   29.11     0      5.00e+00 4.00e-02 3.39e+01
  dihedral pdb=" CA  ASN F 133 "
           pdb=" C   ASN F 133 "
           pdb=" N   ASP F 134 "
           pdb=" CA  ASP F 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.69  -27.31     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  ASN I  95 "
           pdb=" C   ASN I  95 "
           pdb=" N   PRO I  96 "
           pdb=" CA  PRO I  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.89   26.11     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 4452 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 894
       0.047 -    0.095: 207
       0.095 -    0.142: 54
       0.142 -    0.190: 1
       0.190 -    0.237: 1
  Chirality restraints: 1157
  Sorted by residual:
  chirality pdb=" CA  GLU C  19 "
            pdb=" N   GLU C  19 "
            pdb=" C   GLU C  19 "
            pdb=" CB  GLU C  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  PRO E  34 "
            pdb=" N   PRO E  34 "
            pdb=" C   PRO E  34 "
            pdb=" CB  PRO E  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CB  THR J 129 "
            pdb=" CA  THR J 129 "
            pdb=" OG1 THR J 129 "
            pdb=" CG2 THR J 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 1154 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  33 "   -0.056 5.00e-02 4.00e+02   8.17e-02 1.07e+01
        pdb=" N   PRO E  34 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO E  34 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO E  34 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 206 "    0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO F 207 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO F 207 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 207 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR I 206 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.44e+00
        pdb=" N   PRO I 207 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO I 207 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO I 207 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 83
        2.64 -     3.21: 6562
        3.21 -     3.77: 10971
        3.77 -     4.34: 14222
        4.34 -     4.90: 24985
  Nonbonded interactions: 56823
  Sorted by model distance:
  nonbonded pdb=" OG  SER I 218 "
            pdb=" OD1 ASP I 227 "
     model   vdw
     2.076 3.040
  nonbonded pdb=" OD1 ASN I 179 "
            pdb=" OG  SER I 200 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OD1 ASN I 149 "
            pdb=" NE2 GLN I 169 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OG  SER I 186 "
            pdb=" O   THR I 194 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NE2 GLN I 166 "
            pdb=" OE2 GLU I 168 "
     model   vdw
     2.221 3.120
  ... (remaining 56818 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 'B'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'I' and resid 49 through 373)
}

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:             2.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     20.890
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
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      :  0.004   0.059   7538  Z= 0.232
  Angle     :  0.717   9.239  10219  Z= 0.364
  Chirality :  0.043   0.237   1157
  Planarity :  0.005   0.082   1298
  Dihedral  : 17.116 111.328   2695
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 25.82 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.29), residues: 918
  helix:  2.28 (0.29), residues: 329
  sheet: -0.09 (0.26), residues: 406
  loop : -0.69 (0.49), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 260 
 HIS   0.002   0.001   HIS I 346 
 PHE   0.013   0.001   PHE E  50 
 TYR   0.020   0.001   TYR I 217 
 ARG   0.004   0.000   ARG F 310 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: K   23 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7942 (ptpt)
  outliers start: 7
  outliers final: 5
  residues processed: 118
  average time/residue: 0.2212
  time to fit residues: 34.1403
Evaluate side-chains
  103 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain L residue   56 MET
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  368 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.3980
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  26 ASN
I 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.188140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.171358 restraints weight = 7836.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.169358 restraints weight = 17662.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.169347 restraints weight = 17121.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.0745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7538  Z= 0.215
  Angle     :  0.658   7.161  10219  Z= 0.329
  Chirality :  0.043   0.154   1157
  Planarity :  0.004   0.054   1298
  Dihedral  :  7.965 109.186   1033
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 23.93 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.29), residues: 918
  helix:  2.43 (0.29), residues: 329
  sheet: -0.10 (0.26), residues: 410
  loop : -0.79 (0.49), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 260 
 HIS   0.008   0.001   HIS C  17 
 PHE   0.011   0.001   PHE E  50 
 TYR   0.015   0.001   TYR I 217 
 ARG   0.002   0.000   ARG F 261 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
  outliers start: 34
  outliers final: 20
  residues processed: 132
  average time/residue: 0.2196
  time to fit residues: 39.1261
Evaluate side-chains
  118 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0270
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** K  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  99 GLN
F 365 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.184964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.169503 restraints weight = 7990.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.167271 restraints weight = 17584.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.160381 restraints weight = 16939.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7538  Z= 0.227
  Angle     :  0.649   7.511  10219  Z= 0.323
  Chirality :  0.043   0.162   1157
  Planarity :  0.004   0.052   1298
  Dihedral  :  7.282 105.966   1025
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 23.43 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.29), residues: 918
  helix:  2.33 (0.29), residues: 331
  sheet: -0.11 (0.26), residues: 410
  loop : -0.70 (0.50), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I 260 
 HIS   0.008   0.001   HIS C  17 
 PHE   0.011   0.001   PHE I 340 
 TYR   0.011   0.001   TYR I 307 
 ARG   0.003   0.000   ARG M  47 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 100
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   28 LYS cc_start: 0.6527 (ptpp) cc_final: 0.5916 (mmtm)
REVERT: L   54 MET cc_start: 0.8417 (tmm) cc_final: 0.7969 (tpp)
REVERT: L   61 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.5049 (pt)
REVERT: M   26 ASN cc_start: 0.7590 (t0) cc_final: 0.7226 (p0)
REVERT: F  242 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8033 (t0)
  outliers start: 49
  outliers final: 34
  residues processed: 139
  average time/residue: 0.1927
  time to fit residues: 36.1891
Evaluate side-chains
  130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 GLN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   21 THR
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  242 ASP
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 26 optimal weight:    8.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
** K  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 321 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.184666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.168048 restraints weight = 7966.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.165384 restraints weight = 17666.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.165708 restraints weight = 17801.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7538  Z= 0.217
  Angle     :  0.635   8.049  10219  Z= 0.315
  Chirality :  0.042   0.163   1157
  Planarity :  0.004   0.051   1298
  Dihedral  :  7.071 102.257   1025
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 24.56 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.29), residues: 918
  helix:  2.35 (0.29), residues: 333
  sheet: -0.09 (0.26), residues: 410
  loop : -0.63 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 260 
 HIS   0.010   0.001   HIS C  17 
 PHE   0.024   0.001   PHE L  42 
 TYR   0.017   0.001   TYR I 217 
 ARG   0.003   0.000   ARG F 310 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 92
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: L   28 LYS cc_start: 0.5735 (ptpp) cc_final: 0.5530 (mmtm)
REVERT: L   61 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.5127 (pt)
REVERT: F  242 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8102 (t0)
REVERT: I  158 SER cc_start: 0.6755 (OUTLIER) cc_final: 0.6441 (p)
  outliers start: 48
  outliers final: 35
  residues processed: 128
  average time/residue: 0.1975
  time to fit residues: 33.9504
Evaluate side-chains
  128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 90
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  242 ASP
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  158 SER
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  164 MET
Chi-restraints excluded: chain I residue  180 VAL
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0970
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0970
   overall best weight:    0.5576

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

Flipped N/Q/H residues before XYZ refinement:
** K  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 321 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.184873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.169897 restraints weight = 7953.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.156845 restraints weight = 16634.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.156032 restraints weight = 16973.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7538  Z= 0.204
  Angle     :  0.622   7.974  10219  Z= 0.310
  Chirality :  0.041   0.163   1157
  Planarity :  0.004   0.050   1298
  Dihedral  :  6.906  97.499   1025
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 25.19 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.29), residues: 918
  helix:  2.44 (0.29), residues: 321
  sheet: -0.09 (0.26), residues: 410
  loop : -0.19 (0.51), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 260 
 HIS   0.006   0.001   HIS C  17 
 PHE   0.010   0.001   PHE I 340 
 TYR   0.008   0.001   TYR I 307 
 ARG   0.003   0.000   ARG F 310 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 98
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  113 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8160 (tp)
REVERT: J  128 LYS cc_start: 0.8512 (mptt) cc_final: 0.8265 (mmtp)
REVERT: L   28 LYS cc_start: 0.6459 (ptpp) cc_final: 0.5837 (mmtm)
REVERT: L   61 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5102 (pt)
REVERT: F  242 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8120 (t0)
  outliers start: 48
  outliers final: 32
  residues processed: 135
  average time/residue: 0.1904
  time to fit residues: 34.7269
Evaluate side-chains
  126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   20 GLN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  242 ASP
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  216 LEU
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Chi-restraints excluded: chain I residue  368 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 56 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
I 321 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.182204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.167023 restraints weight = 7977.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.154181 restraints weight = 17858.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.151918 restraints weight = 17045.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7538  Z= 0.278
  Angle     :  0.666  10.473  10219  Z= 0.332
  Chirality :  0.043   0.163   1157
  Planarity :  0.004   0.051   1298
  Dihedral  :  6.935  94.639   1025
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 24.56 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 918
  helix:  2.39 (0.29), residues: 321
  sheet: -0.13 (0.26), residues: 410
  loop : -0.19 (0.51), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I 260 
 HIS   0.007   0.001   HIS C  17 
 PHE   0.015   0.002   PHE L  42 
 TYR   0.008   0.001   TYR I 307 
 ARG   0.003   0.001   ARG I 315 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 89
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  113 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8541 (tp)
REVERT: J  128 LYS cc_start: 0.8533 (mptt) cc_final: 0.8281 (mmtp)
REVERT: L   61 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5219 (pt)
REVERT: M   38 TYR cc_start: 0.7023 (t80) cc_final: 0.6803 (t80)
REVERT: F  275 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7072 (pp)
  outliers start: 53
  outliers final: 40
  residues processed: 131
  average time/residue: 0.1829
  time to fit residues: 32.7521
Evaluate side-chains
  129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 86
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   20 GLN
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   17 HIS
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  275 LEU
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue   51 HIS
Chi-restraints excluded: chain I residue   89 ASN
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  216 LEU
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
I 156 GLN
I 321 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.181250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.164580 restraints weight = 7986.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.162482 restraints weight = 17360.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.162490 restraints weight = 17818.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7538  Z= 0.294
  Angle     :  0.673   9.531  10219  Z= 0.336
  Chirality :  0.043   0.164   1157
  Planarity :  0.004   0.054   1298
  Dihedral  :  6.860  92.186   1025
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 24.43 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.29), residues: 918
  helix:  2.28 (0.28), residues: 333
  sheet: -0.19 (0.26), residues: 410
  loop : -0.57 (0.52), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I 260 
 HIS   0.009   0.001   HIS C  17 
 PHE   0.015   0.002   PHE L  42 
 TYR   0.009   0.001   TYR I 307 
 ARG   0.003   0.000   ARG I 315 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 90
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  113 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8739 (tp)
REVERT: L   54 MET cc_start: 0.8474 (tmm) cc_final: 0.8086 (tpp)
REVERT: F  275 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7027 (pp)
REVERT: I   94 MET cc_start: 0.7642 (tpp) cc_final: 0.7319 (tpt)
  outliers start: 56
  outliers final: 45
  residues processed: 135
  average time/residue: 0.1882
  time to fit residues: 34.6234
Evaluate side-chains
  134 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 87
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   20 GLN
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain J residue  113 LEU
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   17 HIS
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain F residue  275 LEU
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue   51 HIS
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   89 ASN
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  216 LEU
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  303 ILE
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  339 LEU
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0270
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7438

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

Flipped N/Q/H residues before XYZ refinement:
J 121 GLN
I 321 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.166190 restraints weight = 7992.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.163976 restraints weight = 18511.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.164059 restraints weight = 17879.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7538  Z= 0.239
  Angle     :  0.660   8.851  10219  Z= 0.326
  Chirality :  0.042   0.165   1157
  Planarity :  0.004   0.053   1298
  Dihedral  :  6.582  85.859   1025
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 25.82 %
    Favored  : 67.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.29), residues: 918
  helix:  2.32 (0.28), residues: 333
  sheet: -0.17 (0.26), residues: 410
  loop : -0.46 (0.52), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I 260 
 HIS   0.009   0.001   HIS C  17 
 PHE   0.011   0.001   PHE L  42 
 TYR   0.009   0.001   TYR I 307 
 ARG   0.003   0.000   ARG I 310 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 91
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   36 TRP cc_start: 0.6655 (t60) cc_final: 0.6391 (t60)
REVERT: L   54 MET cc_start: 0.8512 (tmm) cc_final: 0.8075 (tpp)
REVERT: F  275 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7069 (pp)
REVERT: I   94 MET cc_start: 0.7663 (tpp) cc_final: 0.7389 (tpt)
  outliers start: 51
  outliers final: 44
  residues processed: 129
  average time/residue: 0.1786
  time to fit residues: 31.9418
Evaluate side-chains
  132 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 87
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   20 GLN
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   17 HIS
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain F residue  275 LEU
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue   51 HIS
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   89 ASN
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  216 LEU
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  339 LEU
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Chi-restraints excluded: chain I residue  368 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4158 r_free = 0.4158 target = 0.181709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.165482 restraints weight = 8060.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.163086 restraints weight = 18580.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.162842 restraints weight = 17903.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7538  Z= 0.254
  Angle     :  0.673   9.133  10219  Z= 0.334
  Chirality :  0.043   0.163   1157
  Planarity :  0.004   0.052   1298
  Dihedral  :  6.372  81.766   1023
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 26.32 %
    Favored  : 67.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.29), residues: 918
  helix:  2.25 (0.28), residues: 333
  sheet: -0.18 (0.26), residues: 410
  loop : -0.49 (0.52), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I 260 
 HIS   0.008   0.001   HIS C  17 
 PHE   0.011   0.001   PHE L  42 
 TYR   0.015   0.001   TYR I 217 
 ARG   0.003   0.000   ARG I 310 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 91
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   36 TRP cc_start: 0.6638 (t60) cc_final: 0.6356 (t60)
REVERT: L   54 MET cc_start: 0.8521 (tmm) cc_final: 0.8069 (tpp)
REVERT: F  275 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6977 (pp)
REVERT: I   94 MET cc_start: 0.7632 (tpp) cc_final: 0.7387 (tpt)
  outliers start: 48
  outliers final: 43
  residues processed: 127
  average time/residue: 0.1859
  time to fit residues: 32.6639
Evaluate side-chains
  133 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 89
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain K residue   17 HIS
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   51 HIS
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain F residue  275 LEU
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue   51 HIS
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  216 LEU
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  339 LEU
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Chi-restraints excluded: chain I residue  368 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 80 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.181624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.164873 restraints weight = 8091.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.162983 restraints weight = 18327.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.162258 restraints weight = 17501.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7538  Z= 0.278
  Angle     :  0.692   9.594  10219  Z= 0.343
  Chirality :  0.043   0.162   1157
  Planarity :  0.004   0.053   1298
  Dihedral  :  6.419  82.423   1023
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 26.83 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.29), residues: 918
  helix:  2.22 (0.28), residues: 333
  sheet: -0.20 (0.26), residues: 410
  loop : -0.53 (0.52), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I 260 
 HIS   0.008   0.001   HIS C  17 
 PHE   0.012   0.001   PHE L  42 
 TYR   0.008   0.001   TYR I 307 
 ARG   0.004   0.000   ARG I 310 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 90
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: K   36 TRP cc_start: 0.6644 (t60) cc_final: 0.6337 (t60)
REVERT: L   54 MET cc_start: 0.8531 (tmm) cc_final: 0.8071 (tpp)
REVERT: F  175 ASP cc_start: 0.8133 (t0) cc_final: 0.7802 (t0)
REVERT: F  275 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7143 (pp)
REVERT: I   94 MET cc_start: 0.7674 (tpp) cc_final: 0.7409 (tpt)
  outliers start: 45
  outliers final: 42
  residues processed: 124
  average time/residue: 0.1811
  time to fit residues: 30.9079
Evaluate side-chains
  131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 88
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain E residue   29 HIS
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain K residue   17 HIS
Chi-restraints excluded: chain L residue   32 LEU
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain M residue   25 HIS
Chi-restraints excluded: chain M residue   45 SER
Chi-restraints excluded: chain M residue   54 LEU
Chi-restraints excluded: chain F residue   94 MET
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  153 VAL
Chi-restraints excluded: chain F residue  157 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  273 THR
Chi-restraints excluded: chain F residue  275 LEU
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain F residue  340 PHE
Chi-restraints excluded: chain I residue   51 HIS
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   89 ASN
Chi-restraints excluded: chain I residue  100 THR
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain I residue  153 VAL
Chi-restraints excluded: chain I residue  163 THR
Chi-restraints excluded: chain I residue  181 LYS
Chi-restraints excluded: chain I residue  182 THR
Chi-restraints excluded: chain I residue  200 SER
Chi-restraints excluded: chain I residue  216 LEU
Chi-restraints excluded: chain I residue  259 LEU
Chi-restraints excluded: chain I residue  267 VAL
Chi-restraints excluded: chain I residue  326 CYS
Chi-restraints excluded: chain I residue  337 SER
Chi-restraints excluded: chain I residue  339 LEU
Chi-restraints excluded: chain I residue  347 PHE
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain I residue  367 LEU
Chi-restraints excluded: chain I residue  368 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9980
   chunk 61 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9990
   chunk 73 optimal weight:    0.2980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** C  17 HIS ** 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 = 0.4160 r_free = 0.4160 target = 0.182010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.165452 restraints weight = 7979.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.163603 restraints weight = 18280.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.163611 restraints weight = 16637.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7538  Z= 0.231
  Angle     :  0.685   9.640  10219  Z= 0.339
  Chirality :  0.043   0.209   1157
  Planarity :  0.004   0.052   1298
  Dihedral  :  6.335  80.066   1023
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 27.46 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.29), residues: 918
  helix:  2.23 (0.28), residues: 333
  sheet: -0.16 (0.26), residues: 410
  loop : -0.48 (0.52), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I 260 
 HIS   0.014   0.001   HIS C  17 
 PHE   0.011   0.001   PHE L  42 
 TYR   0.021   0.001   TYR I 217 
 ARG   0.004   0.001   ARG I 310 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2323.85 seconds
wall clock time: 42 minutes 37.60 seconds (2557.60 seconds total)