Starting phenix.real_space_refine
on Fri Aug 22 19:45:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5j_37294/08_2025/8w5j_37294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5j_37294/08_2025/8w5j_37294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5j_37294/08_2025/8w5j_37294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5j_37294/08_2025/8w5j_37294.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5j_37294/08_2025/8w5j_37294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5j_37294/08_2025/8w5j_37294.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.023
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    4718      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 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7356
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      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: {'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    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: "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: {'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    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: "I"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'46E': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 23
  Time building chain proxies: 1.99, per 1000 atoms: 0.27
  Number of scatterers: 7356
  At special positions: 0
  Unit cell: (94.16, 104.86, 138.03, 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    4718      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 401.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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, 35.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 55
      removed outlier: 3.671A  pdb=" N   GLN A  53 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 66
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 364 through 373
    Processing helix  chain 'B' and resid 87 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 52 through 58
    Processing helix  chain 'E' and resid 20 through 44
      removed outlier: 3.809A  pdb=" N   ASN E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL E  27 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   HIS E  29 " --> pdb=" O   HIS E  25 " (cutoff:3.500A)
      removed outlier: 5.498A  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 'I' and resid 50 through 56
      removed outlier: 3.953A  pdb=" N   GLU I  56 " --> pdb=" O   ARG I  52 " (cutoff:3.500A)
    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: 3.575A  pdb=" N   GLN I 372 " --> pdb=" O   LEU I 368 " (cutoff:3.500A)
    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: 4.019A  pdb=" N   ASP L  55 " --> pdb=" O   SER L  51 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 20 through 31
      removed outlier: 3.558A  pdb=" N   ALA M  28 " --> pdb=" O   THR M  24 " (cutoff:3.500A)
      removed outlier: 3.945A  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 sheet with id=AA1, first strand: chain 'A' and resid 83 through 93
      removed outlier: 6.930A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 209 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 261 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL A 263 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A 267 " --> pdb=" O   VAL A 263 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   THR A 302 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A 313 " --> pdb=" O   GLU A 329 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A 317 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LYS A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU A 357 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 84 through 93
      removed outlier: 7.274A  pdb=" N   PHE I  98 " --> pdb=" O   PHE I  92 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   MET I 164 " --> pdb=" O   GLN I 156 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL I 196 " --> pdb=" O   LEU I 183 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU I 209 " --> pdb=" O   VAL I 205 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU I 255 " --> pdb=" O   LEU I 275 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLU I 268 " --> pdb=" O   LYS I 306 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LYS I 323 " --> pdb=" O   ASP I 319 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER I 337 " --> pdb=" O   GLN I 358 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ARG I  85 " --> pdb=" O   LEU I 357 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   PHE I 359 " --> pdb=" O   ARG I  85 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP I  87 " --> pdb=" O   PHE I 359 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   THR I 361 " --> pdb=" O   ASP I  87 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ASN I  89 " --> pdb=" O   THR I 361 " (cutoff:3.500A)

    518 hydrogen bonds defined for protein.
    1500 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 0.82 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: 1306
        1.33 -     1.45: 1978
        1.45 -     1.57: 4192
        1.57 -     1.69: 3
        1.69 -     1.81: 36
  Bond restraints: 7515
  Sorted by residual:
  bond pdb=" CA  ASP A 134 "
       pdb=" CB  ASP A 134 "
    ideal  model  delta    sigma   weight residual
    1.532  1.548 -0.016 1.33e-02 5.65e+03 1.40e+00
  bond pdb=" CB  ASP I 134 "
       pdb=" CG  ASP I 134 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.22e+00
  bond pdb=" CA  VAL E  60 "
       pdb=" CB  VAL E  60 "
    ideal  model  delta    sigma   weight residual
    1.540  1.569 -0.029 2.70e-02 1.37e+03 1.17e+00
  bond pdb=" CA  VAL M  60 "
       pdb=" CB  VAL M  60 "
    ideal  model  delta    sigma   weight residual
    1.540  1.568 -0.028 2.70e-02 1.37e+03 1.08e+00
  bond pdb=" CB  ASP A 134 "
       pdb=" CG  ASP A 134 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.01e+00
  ... (remaining 7510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 9929
        1.59 -     3.19: 205
        3.19 -     4.78: 40
        4.78 -     6.38: 12
        6.38 -     7.97: 10
  Bond angle restraints: 10196
  Sorted by residual:
  angle pdb=" CA  PRO I 185 "
        pdb=" N   PRO I 185 "
        pdb=" CD  PRO I 185 "
      ideal   model   delta    sigma   weight residual
     112.00  107.38    4.62 1.40e+00 5.10e-01 1.09e+01
  angle pdb=" C   ASN A 133 "
        pdb=" N   ASP A 134 "
        pdb=" CA  ASP A 134 "
      ideal   model   delta    sigma   weight residual
     124.82  130.42   -5.60 1.78e+00 3.16e-01 9.90e+00
  angle pdb=" C   ASN I 133 "
        pdb=" N   ASP I 134 "
        pdb=" CA  ASP I 134 "
      ideal   model   delta    sigma   weight residual
     125.66  130.23   -4.57 1.85e+00 2.92e-01 6.11e+00
  angle pdb=" CA  LEU D  57 "
        pdb=" CB  LEU D  57 "
        pdb=" CG  LEU D  57 "
      ideal   model   delta    sigma   weight residual
     116.30  124.27   -7.97 3.50e+00 8.16e-02 5.19e+00
  angle pdb=" C   SER E  59 "
        pdb=" N   VAL E  60 "
        pdb=" CA  VAL E  60 "
      ideal   model   delta    sigma   weight residual
     121.70  125.78   -4.08 1.80e+00 3.09e-01 5.13e+00
  ... (remaining 10191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 4069
       17.28 -    34.56: 307
       34.56 -    51.84: 43
       51.84 -    69.12: 11
       69.12 -    86.40: 2
  Dihedral angle restraints: 4432
    sinusoidal: 1714
      harmonic: 2718
  Sorted by residual:
  dihedral pdb=" CA  ASN A  95 "
           pdb=" C   ASN A  95 "
           pdb=" N   PRO A  96 "
           pdb=" CA  PRO A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.93   28.07     0      5.00e+00 4.00e-02 3.15e+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  155.14   24.86     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  ASN A 133 "
           pdb=" C   ASN A 133 "
           pdb=" N   ASP A 134 "
           pdb=" CA  ASP A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.25  -20.75     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 4429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 701
       0.029 -    0.058: 314
       0.058 -    0.087: 85
       0.087 -    0.116: 50
       0.116 -    0.145: 7
  Chirality restraints: 1157
  Sorted by residual:
  chirality pdb=" CA  ILE I 353 "
            pdb=" N   ILE I 353 "
            pdb=" C   ILE I 353 "
            pdb=" CB  ILE I 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.27e-01
  chirality pdb=" CA  ILE I 344 "
            pdb=" N   ILE I 344 "
            pdb=" C   ILE I 344 "
            pdb=" CB  ILE I 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE A 303 "
            pdb=" N   ILE A 303 "
            pdb=" C   ILE A 303 "
            pdb=" CB  ILE A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 1154 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN I 184 "   -0.073 5.00e-02 4.00e+02   1.09e-01 1.91e+01
        pdb=" N   PRO I 185 "    0.189 5.00e-02 4.00e+02
        pdb=" CA  PRO I 185 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO I 185 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 206 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO A 207 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 207 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 207 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  33 "    0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO E  34 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO E  34 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E  34 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 302
        2.72 -     3.26: 7779
        3.26 -     3.81: 12230
        3.81 -     4.35: 13958
        4.35 -     4.90: 24143
  Nonbonded interactions: 58412
  Sorted by model distance:
  nonbonded pdb=" OG  SER I 218 "
            pdb=" OD1 ASP I 227 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OD1 ASN A 179 "
            pdb=" OG  SER A 200 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG  SER I 151 "
            pdb=" OE1 GLN I 169 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OD1 ASN I 179 "
            pdb=" OG  SER I 200 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG1 THR A  62 "
            pdb=" OD1 ASN A  65 "
     model   vdw
     2.231 3.040
  ... (remaining 58407 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 'A'
  selection = (chain 'I' and resid 49 through 373)
}
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'
}

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:             3.100
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.340
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7515  Z= 0.118
  Angle     :  0.631   7.970  10196  Z= 0.310
  Chirality :  0.039   0.145   1157
  Planarity :  0.005   0.109   1298
  Dihedral  : 12.495  86.405   2672
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.29), residues: 918
  helix:  2.12 (0.28), residues: 324
  sheet:  0.18 (0.27), residues: 378
  loop : -0.30 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 315 
 TYR   0.018   0.001   TYR I 314 
 PHE   0.016   0.001   PHE I 340 
 TRP   0.008   0.001   TRP K  42 
 HIS   0.004   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7515)
  covalent geometry    : angle       0.63060 (10196)
  hydrogen bonds       : bond        0.21990 (  518)
  hydrogen bonds       : angle       8.02147 ( 1500)

*********************** 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
  74 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: D   54 MET cc_start: 0.8156 (ptt) cc_final: 0.7902 (ptt)
REVERT: I  352 LYS cc_start: 0.9468 (mttp) cc_final: 0.9231 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0580
  time to fit residues: 6.6880
Evaluate side-chains
  56 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
I 133 ASN
** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 248 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.045374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.037343 restraints weight = 73150.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.038338 restraints weight = 44871.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.039082 restraints weight = 31832.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.039587 restraints weight = 24364.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.040004 restraints weight = 20149.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7515  Z= 0.135
  Angle     :  0.627   7.173  10196  Z= 0.323
  Chirality :  0.042   0.197   1157
  Planarity :  0.005   0.075   1298
  Dihedral  :  6.827  78.124   1000
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.53 %
    Favored  : 95.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.29), residues: 918
  helix:  2.19 (0.28), residues: 328
  sheet: -0.01 (0.25), residues: 400
  loop :  0.21 (0.57), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 330 
 TYR   0.013   0.002   TYR I 307 
 PHE   0.012   0.001   PHE A 201 
 TRP   0.010   0.001   TRP A 260 
 HIS   0.005   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7515)
  covalent geometry    : angle       0.62691 (10196)
  hydrogen bonds       : bond        0.03777 (  518)
  hydrogen bonds       : angle       5.95129 ( 1500)

*********************** 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
  78 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ARG cc_start: 0.8978 (tmm-80) cc_final: 0.8777 (ttm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0502
  time to fit residues: 6.1698
Evaluate side-chains
  50 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0970
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.044487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.036494 restraints weight = 75177.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.037482 restraints weight = 46560.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.038178 restraints weight = 33010.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.038661 restraints weight = 25595.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.038828 restraints weight = 21336.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7515  Z= 0.177
  Angle     :  0.624   9.613  10196  Z= 0.322
  Chirality :  0.041   0.172   1157
  Planarity :  0.005   0.059   1298
  Dihedral  :  6.780  75.434   1000
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.67 %
    Favored  : 94.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.29), residues: 918
  helix:  2.07 (0.27), residues: 328
  sheet: -0.01 (0.26), residues: 374
  loop : -0.28 (0.50), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.016   0.002   TYR I 314 
 PHE   0.013   0.001   PHE A 359 
 TRP   0.009   0.001   TRP A 260 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7515)
  covalent geometry    : angle       0.62378 (10196)
  hydrogen bonds       : bond        0.03422 (  518)
  hydrogen bonds       : angle       5.57981 ( 1500)

*********************** 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
  69 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8740 (m-80) cc_final: 0.8327 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0473
  time to fit residues: 5.3835
Evaluate side-chains
  53 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 86 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 GLN
I  99 GLN
I 133 ASN
I 248 GLN
I 266 ASN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.044115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.035918 restraints weight = 74690.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.036957 restraints weight = 44938.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.037682 restraints weight = 31315.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.038157 restraints weight = 24055.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.038589 restraints weight = 19998.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7515  Z= 0.165
  Angle     :  0.618  10.029  10196  Z= 0.316
  Chirality :  0.041   0.168   1157
  Planarity :  0.004   0.054   1298
  Dihedral  :  6.798  72.912   1000
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.28 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.29), residues: 918
  helix:  2.17 (0.27), residues: 328
  sheet: -0.19 (0.25), residues: 400
  loop : -0.04 (0.54), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.013   0.002   TYR I 114 
 PHE   0.014   0.001   PHE A 359 
 TRP   0.008   0.001   TRP K  42 
 HIS   0.005   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7515)
  covalent geometry    : angle       0.61798 (10196)
  hydrogen bonds       : bond        0.03135 (  518)
  hydrogen bonds       : angle       5.36164 ( 1500)

*********************** 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
  70 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8806 (m-80) cc_final: 0.8350 (m-10)
REVERT: I  259 LEU cc_start: 0.9290 (tp) cc_final: 0.9069 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0494
  time to fit residues: 5.6444
Evaluate side-chains
  52 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 88 optimal weight:    0.0070
   chunk 25 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   overall best weight:    2.6004

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

Flipped N/Q/H residues before XYZ refinement:
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.043872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.035922 restraints weight = 74876.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.036953 restraints weight = 45067.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.037679 restraints weight = 31485.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.038040 restraints weight = 24107.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.038492 restraints weight = 20482.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
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      :  0.004   0.048   7515  Z= 0.181
  Angle     :  0.620  11.409  10196  Z= 0.318
  Chirality :  0.041   0.166   1157
  Planarity :  0.004   0.059   1298
  Dihedral  :  6.807  71.521   1000
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.29), residues: 918
  helix:  2.16 (0.27), residues: 324
  sheet: -0.30 (0.25), residues: 400
  loop : -0.25 (0.54), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 140 
 TYR   0.015   0.002   TYR I 143 
 PHE   0.015   0.001   PHE A 359 
 TRP   0.007   0.001   TRP K  42 
 HIS   0.005   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7515)
  covalent geometry    : angle       0.62025 (10196)
  hydrogen bonds       : bond        0.03094 (  518)
  hydrogen bonds       : angle       5.32630 ( 1500)

*********************** 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
  66 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8852 (m-80) cc_final: 0.8516 (m-10)
REVERT: I  259 LEU cc_start: 0.9337 (tp) cc_final: 0.9105 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0502
  time to fit residues: 5.4516
Evaluate side-chains
  50 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    0.0370
   chunk 23 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   overall best weight:    0.7658

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.044484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.036299 restraints weight = 72731.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.037359 restraints weight = 43305.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.038118 restraints weight = 30221.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.038640 restraints weight = 23077.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.039007 restraints weight = 18952.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7515  Z= 0.112
  Angle     :  0.621   8.019  10196  Z= 0.305
  Chirality :  0.042   0.170   1157
  Planarity :  0.004   0.057   1298
  Dihedral  :  6.595  70.297   1000
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.29), residues: 918
  helix:  2.21 (0.28), residues: 328
  sheet: -0.25 (0.25), residues: 402
  loop :  0.05 (0.56), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 330 
 TYR   0.013   0.001   TYR D  33 
 PHE   0.016   0.001   PHE D  42 
 TRP   0.007   0.001   TRP K  42 
 HIS   0.006   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7515)
  covalent geometry    : angle       0.62063 (10196)
  hydrogen bonds       : bond        0.02838 (  518)
  hydrogen bonds       : angle       5.17264 ( 1500)

*********************** 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
  76 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8802 (m-80) cc_final: 0.8561 (m-10)
REVERT: I  259 LEU cc_start: 0.9298 (tp) cc_final: 0.9081 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0595
  time to fit residues: 7.0233
Evaluate side-chains
  52 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 36 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 86 optimal weight:   20.0000
   chunk 2 optimal weight:    0.1980
   chunk 22 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.043525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.035574 restraints weight = 75676.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.036556 restraints weight = 45431.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.037291 restraints weight = 32070.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.037783 restraints weight = 24383.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.038162 restraints weight = 20193.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7515  Z= 0.196
  Angle     :  0.647  11.549  10196  Z= 0.328
  Chirality :  0.041   0.171   1157
  Planarity :  0.005   0.080   1298
  Dihedral  :  6.725  69.676   1000
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.29), residues: 918
  helix:  2.05 (0.27), residues: 328
  sheet: -0.28 (0.25), residues: 406
  loop : -0.09 (0.56), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 140 
 TYR   0.012   0.002   TYR I 143 
 PHE   0.034   0.001   PHE D  42 
 TRP   0.009   0.001   TRP I 243 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7515)
  covalent geometry    : angle       0.64674 (10196)
  hydrogen bonds       : bond        0.03061 (  518)
  hydrogen bonds       : angle       5.25040 ( 1500)

*********************** 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
  68 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8908 (m-80) cc_final: 0.8636 (m-10)
REVERT: I  164 MET cc_start: 0.9082 (pmm) cc_final: 0.8869 (pmm)
REVERT: I  259 LEU cc_start: 0.9349 (tp) cc_final: 0.9110 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0520
  time to fit residues: 5.7059
Evaluate side-chains
  50 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
A  99 GLN
** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
I 133 ASN
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.044006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.035840 restraints weight = 74584.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.036875 restraints weight = 44028.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.037636 restraints weight = 30559.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.038174 restraints weight = 23282.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.038505 restraints weight = 19070.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7515  Z= 0.120
  Angle     :  0.616   8.564  10196  Z= 0.306
  Chirality :  0.041   0.164   1157
  Planarity :  0.005   0.065   1298
  Dihedral  :  6.553  68.109   1000
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.64 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.29), residues: 918
  helix:  2.19 (0.28), residues: 328
  sheet: -0.29 (0.25), residues: 402
  loop : -0.02 (0.56), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 330 
 TYR   0.011   0.001   TYR I 314 
 PHE   0.022   0.001   PHE D  42 
 TRP   0.007   0.001   TRP K  42 
 HIS   0.004   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7515)
  covalent geometry    : angle       0.61618 (10196)
  hydrogen bonds       : bond        0.02761 (  518)
  hydrogen bonds       : angle       5.01152 ( 1500)

*********************** 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
  71 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8839 (m-80) cc_final: 0.8587 (m-10)
REVERT: I  259 LEU cc_start: 0.9298 (tp) cc_final: 0.9070 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 71
  average time/residue: 0.0580
  time to fit residues: 6.7249
Evaluate side-chains
  54 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 48 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 33 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
I 133 ASN
I 169 GLN
I 248 GLN
I 321 ASN
K  43 HIS
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.042689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.034834 restraints weight = 75114.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.035838 restraints weight = 44528.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.036525 restraints weight = 30781.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.037028 restraints weight = 23586.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.037251 restraints weight = 19535.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7515  Z= 0.249
  Angle     :  0.702  14.068  10196  Z= 0.357
  Chirality :  0.042   0.145   1157
  Planarity :  0.005   0.063   1298
  Dihedral  :  6.980  67.359   1000
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.13 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.28), residues: 918
  helix:  1.80 (0.27), residues: 330
  sheet: -0.32 (0.25), residues: 406
  loop : -0.45 (0.53), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 140 
 TYR   0.016   0.002   TYR I 114 
 PHE   0.027   0.002   PHE D  42 
 TRP   0.011   0.002   TRP A 243 
 HIS   0.006   0.002   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 7515)
  covalent geometry    : angle       0.70231 (10196)
  hydrogen bonds       : bond        0.03224 (  518)
  hydrogen bonds       : angle       5.37853 ( 1500)

*********************** 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
  65 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8887 (m-80) cc_final: 0.8269 (m-80)
REVERT: A  307 TYR cc_start: 0.9170 (m-80) cc_final: 0.8589 (m-80)
REVERT: I   79 TYR cc_start: 0.8701 (m-80) cc_final: 0.8414 (m-10)
REVERT: I  259 LEU cc_start: 0.9314 (tp) cc_final: 0.9075 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0556
  time to fit residues: 5.8704
Evaluate side-chains
  51 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
I 133 ASN
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.042617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.034808 restraints weight = 75746.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.035813 restraints weight = 44359.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.036481 restraints weight = 30529.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.036980 restraints weight = 23630.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.037306 restraints weight = 19450.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7515  Z= 0.195
  Angle     :  0.646  11.473  10196  Z= 0.331
  Chirality :  0.042   0.150   1157
  Planarity :  0.005   0.058   1298
  Dihedral  :  6.939  69.561   1000
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.63 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.29), residues: 918
  helix:  1.93 (0.27), residues: 329
  sheet: -0.38 (0.25), residues: 402
  loop : -0.34 (0.53), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 315 
 TYR   0.017   0.002   TYR D  33 
 PHE   0.021   0.002   PHE D  42 
 TRP   0.018   0.001   TRP K  42 
 HIS   0.005   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 7515)
  covalent geometry    : angle       0.64630 (10196)
  hydrogen bonds       : bond        0.03053 (  518)
  hydrogen bonds       : angle       5.25937 ( 1500)

********************** 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
  68 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8855 (m-80) cc_final: 0.8241 (m-80)
REVERT: A  213 LEU cc_start: 0.9445 (tp) cc_final: 0.9214 (tp)
REVERT: B  126 MET cc_start: 0.9665 (ppp) cc_final: 0.9399 (ppp)
REVERT: I  164 MET cc_start: 0.9191 (pmm) cc_final: 0.8944 (pmm)
REVERT: I  259 LEU cc_start: 0.9331 (tp) cc_final: 0.9092 (tp)
REVERT: L   61 LEU cc_start: 0.8818 (pt) cc_final: 0.8473 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 68
  average time/residue: 0.0566
  time to fit residues: 6.2367
Evaluate side-chains
  54 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 45 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  99 GLN
I 133 ASN
I 248 GLN
** M  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.043100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.035279 restraints weight = 73696.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.036275 restraints weight = 43903.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.036978 restraints weight = 30464.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.037428 restraints weight = 23268.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.037792 restraints weight = 19404.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7515  Z= 0.146
  Angle     :  0.644  10.268  10196  Z= 0.321
  Chirality :  0.042   0.156   1157
  Planarity :  0.005   0.056   1298
  Dihedral  :  6.820  70.745   1000
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.76 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.29), residues: 918
  helix:  2.04 (0.27), residues: 327
  sheet: -0.37 (0.25), residues: 402
  loop : -0.19 (0.53), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I 315 
 TYR   0.014   0.002   TYR A 314 
 PHE   0.021   0.001   PHE D  42 
 TRP   0.012   0.001   TRP K  42 
 HIS   0.005   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7515)
  covalent geometry    : angle       0.64441 (10196)
  hydrogen bonds       : bond        0.02926 (  518)
  hydrogen bonds       : angle       5.16084 ( 1500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1119.03 seconds
wall clock time: 20 minutes 11.69 seconds (1211.69 seconds total)