Starting phenix.real_space_refine
on Wed Jan 15 10:24:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xdh_38278/01_2025/8xdh_38278_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xdh_38278/01_2025/8xdh_38278.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xdh_38278/01_2025/8xdh_38278.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xdh_38278/01_2025/8xdh_38278.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xdh_38278/01_2025/8xdh_38278_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xdh_38278/01_2025/8xdh_38278_neut.cif"
  }
  resolution = 3.1
  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=   0.211
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    5511      2.51       5
     N    1344      2.21       5
     O    1383      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8310
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2750
          Classifications: {'peptide': 358}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 14, 'TRANS': 343}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 3
      Conformer: "B"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
      Conformer: "C"
        Number of residues, atoms: 1, 4
          Unusual residues: {'URE': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B
  Residues with excluded nonbonded symmetry interactions: 15
    residue:
      pdb=" C  BURE A 501 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 BURE A 501 " occ=0.25
    residue:
      pdb=" C  AURE A 502 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE A 502 " occ=0.25
    residue:
      pdb=" C  CURE A 503 " occ=0.50
      ... (2 atoms not shown)
      pdb=" N2 CURE A 503 " occ=0.50
    residue:
      pdb=" C  AURE A 504 " occ=0.50
      ... (2 atoms not shown)
      pdb=" N2 AURE A 504 " occ=0.50
    residue:
      pdb=" C  BURE A 505 " occ=0.50
      ... (2 atoms not shown)
      pdb=" N2 BURE A 505 " occ=0.50
    residue:
      pdb=" C  BURE B 501 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 BURE B 501 " occ=0.25
    residue:
      pdb=" C  AURE B 502 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE B 502 " occ=0.25
    residue:
      pdb=" C  CURE B 503 " occ=0.50
      ... (2 atoms not shown)
      pdb=" N2 CURE B 503 " occ=0.50
    residue:
      pdb=" C  AURE B 504 " occ=0.50
      ... (2 atoms not shown)
      pdb=" N2 AURE B 504 " occ=0.50
    residue:
      pdb=" C  BURE B 505 " occ=0.50
      ... (2 atoms not shown)
      pdb=" N2 BURE B 505 " occ=0.50
    residue:
      pdb=" C  BURE C 501 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 BURE C 501 " occ=0.25
    residue:
      pdb=" C  AURE C 502 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE C 502 " occ=0.25
    ... (remaining 3 not shown)
  Time building chain proxies: 4.89, per 1000 atoms: 0.59
  Number of scatterers: 8310
  At special positions: 0
  Unit cell: (105.8, 103.96, 76.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    1383      8.00
     N    1344      7.00
     C    5511      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 0 sheets defined
      78.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 38
    Processing helix  chain 'A' and resid 41 through 49
    Processing helix  chain 'A' and resid 52 through 67
    Processing helix  chain 'A' and resid 68 through 70
      No H-bonds generated for 'chain 'A' and resid 68 through 70'
    Processing helix  chain 'A' and resid 73 through 88
    Processing helix  chain 'A' and resid 88 through 109
    Processing helix  chain 'A' and resid 122 through 135
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 145 through 168
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 176 through 191
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 4.730A  pdb=" N   ILE A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 232 through 234
      No H-bonds generated for 'chain 'A' and resid 232 through 234'
    Processing helix  chain 'A' and resid 237 through 252
    Processing helix  chain 'A' and resid 252 through 273
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 286 through 297
    Processing helix  chain 'A' and resid 304 through 330
    Processing helix  chain 'A' and resid 338 through 351
      removed outlier: 3.619A  pdb=" N   ILE A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
    Processing helix  chain 'A' and resid 368 through 385
    Processing helix  chain 'B' and resid 29 through 38
    Processing helix  chain 'B' and resid 41 through 49
    Processing helix  chain 'B' and resid 52 through 67
    Processing helix  chain 'B' and resid 68 through 70
      No H-bonds generated for 'chain 'B' and resid 68 through 70'
    Processing helix  chain 'B' and resid 73 through 88
    Processing helix  chain 'B' and resid 88 through 109
    Processing helix  chain 'B' and resid 122 through 135
    Processing helix  chain 'B' and resid 142 through 144
      No H-bonds generated for 'chain 'B' and resid 142 through 144'
    Processing helix  chain 'B' and resid 145 through 168
      Proline residue:  B 157  - end of helix
    Processing helix  chain 'B' and resid 169 through 171
      No H-bonds generated for 'chain 'B' and resid 169 through 171'
    Processing helix  chain 'B' and resid 176 through 191
    Processing helix  chain 'B' and resid 212 through 216
    Processing helix  chain 'B' and resid 217 through 231
      removed outlier: 4.729A  pdb=" N   ILE B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      Proline residue:  B 226  - end of helix
    Processing helix  chain 'B' and resid 232 through 234
      No H-bonds generated for 'chain 'B' and resid 232 through 234'
    Processing helix  chain 'B' and resid 237 through 252
    Processing helix  chain 'B' and resid 252 through 273
    Processing helix  chain 'B' and resid 276 through 282
    Processing helix  chain 'B' and resid 286 through 297
    Processing helix  chain 'B' and resid 304 through 330
    Processing helix  chain 'B' and resid 338 through 351
      removed outlier: 3.620A  pdb=" N   ILE B 351 " --> pdb=" O   THR B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 366
    Processing helix  chain 'B' and resid 368 through 385
    Processing helix  chain 'C' and resid 29 through 38
    Processing helix  chain 'C' and resid 41 through 49
    Processing helix  chain 'C' and resid 52 through 67
    Processing helix  chain 'C' and resid 68 through 70
      No H-bonds generated for 'chain 'C' and resid 68 through 70'
    Processing helix  chain 'C' and resid 73 through 88
    Processing helix  chain 'C' and resid 88 through 109
    Processing helix  chain 'C' and resid 122 through 135
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 145 through 168
      Proline residue:  C 157  - end of helix
    Processing helix  chain 'C' and resid 169 through 171
      No H-bonds generated for 'chain 'C' and resid 169 through 171'
    Processing helix  chain 'C' and resid 176 through 191
    Processing helix  chain 'C' and resid 212 through 216
    Processing helix  chain 'C' and resid 217 through 231
      removed outlier: 4.729A  pdb=" N   ILE C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      Proline residue:  C 226  - end of helix
    Processing helix  chain 'C' and resid 232 through 234
      No H-bonds generated for 'chain 'C' and resid 232 through 234'
    Processing helix  chain 'C' and resid 237 through 252
    Processing helix  chain 'C' and resid 252 through 273
    Processing helix  chain 'C' and resid 276 through 282
    Processing helix  chain 'C' and resid 286 through 297
    Processing helix  chain 'C' and resid 304 through 330
    Processing helix  chain 'C' and resid 338 through 351
      removed outlier: 3.621A  pdb=" N   ILE C 351 " --> pdb=" O   THR C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 362 through 366
    Processing helix  chain 'C' and resid 368 through 385

    571 hydrogen bonds defined for protein.
    1677 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: 2.48

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1233
        1.31 -     1.43: 2566
        1.43 -     1.56: 4640
        1.56 -     1.68: 0
        1.68 -     1.81: 114
  Bond restraints: 8553
  Sorted by residual:
  bond pdb=" CA  PHE B 175 "
       pdb=" C   PHE B 175 "
    ideal  model  delta    sigma   weight residual
    1.532  1.476  0.056 1.12e-02 7.97e+03 2.54e+01
  bond pdb=" CA  PHE A 175 "
       pdb=" C   PHE A 175 "
    ideal  model  delta    sigma   weight residual
    1.532  1.476  0.056 1.12e-02 7.97e+03 2.53e+01
  bond pdb=" CA  PHE C 175 "
       pdb=" C   PHE C 175 "
    ideal  model  delta    sigma   weight residual
    1.532  1.476  0.056 1.12e-02 7.97e+03 2.49e+01
  bond pdb=" C  AURE C 504 "
       pdb=" N1 AURE C 504 "
    ideal  model  delta    sigma   weight residual
    1.363  1.454 -0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C  AURE C 502 "
       pdb=" N2 AURE C 502 "
    ideal  model  delta    sigma   weight residual
    1.363  1.454 -0.091 2.00e-02 2.50e+03 2.05e+01
  ... (remaining 8548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 11232
        2.14 -     4.27: 337
        4.27 -     6.41: 74
        6.41 -     8.54: 24
        8.54 -    10.68: 9
  Bond angle restraints: 11676
  Sorted by residual:
  angle pdb=" N   VAL C 232 "
        pdb=" CA  VAL C 232 "
        pdb=" C   VAL C 232 "
      ideal   model   delta    sigma   weight residual
     110.72  103.42    7.30 1.01e+00 9.80e-01 5.22e+01
  angle pdb=" N   VAL B 232 "
        pdb=" CA  VAL B 232 "
        pdb=" C   VAL B 232 "
      ideal   model   delta    sigma   weight residual
     110.72  103.46    7.26 1.01e+00 9.80e-01 5.17e+01
  angle pdb=" N   VAL A 232 "
        pdb=" CA  VAL A 232 "
        pdb=" C   VAL A 232 "
      ideal   model   delta    sigma   weight residual
     110.72  103.46    7.26 1.01e+00 9.80e-01 5.17e+01
  angle pdb=" N   CYS C 337 "
        pdb=" CA  CYS C 337 "
        pdb=" C   CYS C 337 "
      ideal   model   delta    sigma   weight residual
     111.07  117.43   -6.36 1.07e+00 8.73e-01 3.53e+01
  angle pdb=" N   CYS A 337 "
        pdb=" CA  CYS A 337 "
        pdb=" C   CYS A 337 "
      ideal   model   delta    sigma   weight residual
     111.07  117.40   -6.33 1.07e+00 8.73e-01 3.50e+01
  ... (remaining 11671 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.92: 4110
       11.92 -    23.85: 445
       23.85 -    35.77: 164
       35.77 -    47.69: 36
       47.69 -    59.61: 18
  Dihedral angle restraints: 4773
    sinusoidal: 1692
      harmonic: 3081
  Sorted by residual:
  dihedral pdb=" CA  GLY A 114 "
           pdb=" C   GLY A 114 "
           pdb=" N   ALA A 115 "
           pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.61   15.39     0      5.00e+00 4.00e-02 9.47e+00
  dihedral pdb=" CA  GLY B 114 "
           pdb=" C   GLY B 114 "
           pdb=" N   ALA B 115 "
           pdb=" CA  ALA B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.65   15.35     0      5.00e+00 4.00e-02 9.43e+00
  dihedral pdb=" CA  GLY C 114 "
           pdb=" C   GLY C 114 "
           pdb=" N   ALA C 115 "
           pdb=" CA  ALA C 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.68   15.32     0      5.00e+00 4.00e-02 9.39e+00
  ... (remaining 4770 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1137
       0.073 -    0.146: 133
       0.146 -    0.219: 24
       0.219 -    0.292: 14
       0.292 -    0.365: 9
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  TRP C  33 "
            pdb=" N   TRP C  33 "
            pdb=" C   TRP C  33 "
            pdb=" CB  TRP C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.37 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  TRP B  33 "
            pdb=" N   TRP B  33 "
            pdb=" C   TRP B  33 "
            pdb=" CB  TRP B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  TRP A  33 "
            pdb=" N   TRP A  33 "
            pdb=" C   TRP A  33 "
            pdb=" CB  TRP A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.31e+00
  ... (remaining 1314 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 334 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.39e+00
        pdb=" N   PRO C 335 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO C 335 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 335 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 334 "   -0.035 5.00e-02 4.00e+02   5.23e-02 4.37e+00
        pdb=" N   PRO A 335 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 334 "   -0.035 5.00e-02 4.00e+02   5.22e-02 4.35e+00
        pdb=" N   PRO B 335 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 335 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 335 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2621
        2.82 -     3.34: 8536
        3.34 -     3.86: 14636
        3.86 -     4.38: 17523
        4.38 -     4.90: 28852
  Nonbonded interactions: 72168
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 367 "
            pdb=" ND2 ASN C 372 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   ALA B 367 "
            pdb=" ND2 ASN B 372 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   ALA A 367 "
            pdb=" ND2 ASN A 372 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   TRP B  47 "
            pdb=" NE2 GLN B  51 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   TRP A  47 "
            pdb=" NE2 GLN A  51 "
     model   vdw
     2.309 3.120
  ... (remaining 72163 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.340
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.050
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
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      :  0.010   0.091   8553  Z= 0.634
  Angle     :  0.938  10.681  11676  Z= 0.554
  Chirality :  0.064   0.365   1317
  Planarity :  0.005   0.052   1431
  Dihedral  : 12.346  59.613   2805
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  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:  1.08 (0.26), residues: 1068
  helix:  0.99 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  0.23 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  33 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.031   0.002   PHE B 179 
 TYR   0.025   0.003   TYR C 320 
 ARG   0.006   0.001   ARG C  89 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8203 (mtp) cc_final: 0.7843 (mtm)
REVERT: A  176 THR cc_start: 0.7563 (m) cc_final: 0.7296 (p)
REVERT: A  327 ASN cc_start: 0.8042 (m-40) cc_final: 0.7735 (m110)
REVERT: A  365 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7646 (mmmt)
REVERT: B   41 MET cc_start: 0.8247 (mtp) cc_final: 0.7926 (mtm)
REVERT: B  224 SER cc_start: 0.7183 (t) cc_final: 0.6864 (m)
REVERT: B  365 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7566 (mmmt)
REVERT: C   40 ASP cc_start: 0.7654 (m-30) cc_final: 0.7415 (m-30)
REVERT: C   41 MET cc_start: 0.8082 (mtp) cc_final: 0.7830 (mtp)
REVERT: C  176 THR cc_start: 0.7786 (m) cc_final: 0.7390 (p)
REVERT: C  224 SER cc_start: 0.7008 (t) cc_final: 0.6751 (m)
REVERT: C  365 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7526 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1496
  time to fit residues: 26.5911
Evaluate side-chains
  96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
B 180 ASN
B 327 ASN
C  94 ASN
C 180 ASN
C 327 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.115545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.101375 restraints weight = 8969.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 0.73
r_work: 0.2796 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2578 r_free = 0.2578    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8553  Z= 0.258
  Angle     :  0.584   6.032  11676  Z= 0.308
  Chirality :  0.040   0.124   1317
  Planarity :  0.004   0.029   1431
  Dihedral  :  4.427  15.454   1131
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  6.69 %
    Favored  : 91.88 %
  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:  1.60 (0.27), residues: 1068
  helix:  1.37 (0.18), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.39 (0.43), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  90 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.013   0.001   PHE B 341 
 TYR   0.024   0.002   TYR B 320 
 ARG   0.003   0.000   ARG C  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8711 (mtp) cc_final: 0.8417 (mtp)
REVERT: A  154 MET cc_start: 0.9071 (mtp) cc_final: 0.8724 (mtp)
REVERT: A  365 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8299 (mmmt)
REVERT: B   41 MET cc_start: 0.8801 (mtp) cc_final: 0.8409 (mtp)
REVERT: B  224 SER cc_start: 0.8722 (t) cc_final: 0.8455 (m)
REVERT: B  267 MET cc_start: 0.8581 (ptm) cc_final: 0.8272 (ptm)
REVERT: B  365 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8213 (mmmt)
REVERT: C  199 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8349 (mm-40)
REVERT: C  267 MET cc_start: 0.8631 (ptm) cc_final: 0.8425 (ptt)
  outliers start: 12
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1615
  time to fit residues: 24.1600
Evaluate side-chains
  94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 101 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.110115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.094955 restraints weight = 9226.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 0.78
r_work: 0.2743 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2646 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8553  Z= 0.241
  Angle     :  0.552   6.024  11676  Z= 0.289
  Chirality :  0.039   0.123   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.327  14.705   1131
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  8.96 %
    Favored  : 89.25 %
  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:  1.75 (0.26), residues: 1068
  helix:  1.54 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.28 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 305 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.015   0.001   PHE B 341 
 TYR   0.015   0.001   TYR C 368 
 ARG   0.003   0.000   ARG B  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8740 (mtp) cc_final: 0.8462 (mtp)
REVERT: A  154 MET cc_start: 0.9110 (mtp) cc_final: 0.8758 (mtp)
REVERT: A  365 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8181 (mmmt)
REVERT: B   41 MET cc_start: 0.8744 (mtp) cc_final: 0.8297 (mtp)
REVERT: B  267 MET cc_start: 0.8414 (ptm) cc_final: 0.8054 (ptm)
REVERT: B  355 THR cc_start: 0.8173 (t) cc_final: 0.7900 (t)
REVERT: B  365 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8122 (mmmt)
REVERT: C   41 MET cc_start: 0.8371 (mtp) cc_final: 0.8153 (mtp)
REVERT: C  208 MET cc_start: 0.7990 (tpp) cc_final: 0.7763 (tpt)
  outliers start: 15
  outliers final: 14
  residues processed: 92
  average time/residue: 0.1638
  time to fit residues: 22.9615
Evaluate side-chains
  97 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  379 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 79 optimal weight:    0.3980
   chunk 30 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0970
   chunk 95 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0270
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.3836

-------------------------------------------------------------------------------
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 = 0.3099 r_free = 0.3099 target = 0.112247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.096878 restraints weight = 9166.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 0.83
r_work: 0.2777 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8553  Z= 0.192
  Angle     :  0.506   5.959  11676  Z= 0.265
  Chirality :  0.038   0.122   1317
  Planarity :  0.004   0.030   1431
  Dihedral  :  4.134  14.463   1131
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  9.08 %
    Favored  : 88.77 %
  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:  1.95 (0.26), residues: 1068
  helix:  1.74 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.16 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  90 
 HIS   0.002   0.000   HIS C 258 
 PHE   0.014   0.001   PHE B 341 
 TYR   0.012   0.001   TYR C 368 
 ARG   0.002   0.000   ARG B  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8718 (mtp) cc_final: 0.8427 (mtp)
REVERT: A  154 MET cc_start: 0.8973 (mtp) cc_final: 0.8588 (mtp)
REVERT: A  365 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8207 (mmmt)
REVERT: B   41 MET cc_start: 0.8672 (mtp) cc_final: 0.8257 (mtp)
REVERT: B  267 MET cc_start: 0.8419 (ptm) cc_final: 0.8015 (ptm)
REVERT: B  365 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8155 (mmmt)
REVERT: C  208 MET cc_start: 0.7915 (tpp) cc_final: 0.7683 (tpt)
  outliers start: 18
  outliers final: 15
  residues processed: 98
  average time/residue: 0.2060
  time to fit residues: 28.7656
Evaluate side-chains
  99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 99 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 69 optimal weight:    0.7980
   chunk 81 optimal weight:    0.3980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3065 r_free = 0.3065 target = 0.109921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.094434 restraints weight = 9127.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 0.81
r_work: 0.2785 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8553  Z= 0.216
  Angle     :  0.520   5.986  11676  Z= 0.275
  Chirality :  0.038   0.123   1317
  Planarity :  0.004   0.031   1431
  Dihedral  :  4.142  16.556   1131
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.92 %
    Favored  : 88.05 %
  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:  1.97 (0.26), residues: 1068
  helix:  1.76 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.12 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  90 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.015   0.001   PHE B 341 
 TYR   0.014   0.001   TYR C 368 
 ARG   0.005   0.000   ARG A  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8743 (mtp) cc_final: 0.8418 (mtp)
REVERT: A  154 MET cc_start: 0.9080 (mtp) cc_final: 0.8740 (mtp)
REVERT: A  365 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8080 (mmmt)
REVERT: B   41 MET cc_start: 0.8722 (mtp) cc_final: 0.8227 (mtp)
REVERT: B  365 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8084 (mmmt)
  outliers start: 17
  outliers final: 17
  residues processed: 99
  average time/residue: 0.1561
  time to fit residues: 23.4940
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3075 r_free = 0.3075 target = 0.109752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.094740 restraints weight = 9159.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 0.79
r_work: 0.2740 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8553  Z= 0.263
  Angle     :  0.547   6.020  11676  Z= 0.288
  Chirality :  0.040   0.141   1317
  Planarity :  0.004   0.033   1431
  Dihedral  :  4.302  18.374   1131
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 10.27 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 1068
  helix:  1.71 (0.19), residues: 777
  sheet:  None (None), residues: 0
  loop :  0.46 (0.41), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 141 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.017   0.001   PHE B 341 
 TYR   0.017   0.001   TYR B 368 
 ARG   0.005   0.001   ARG A  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8811 (mtp) cc_final: 0.8550 (mtp)
REVERT: A  154 MET cc_start: 0.9228 (mtp) cc_final: 0.8938 (mtp)
REVERT: A  365 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8035 (mmmt)
REVERT: B  154 MET cc_start: 0.9099 (mtp) cc_final: 0.8865 (mtt)
REVERT: B  267 MET cc_start: 0.8409 (ptm) cc_final: 0.8109 (ptm)
REVERT: B  365 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8150 (mmmt)
  outliers start: 23
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1552
  time to fit residues: 25.0869
Evaluate side-chains
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  379 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0370
   chunk 89 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
C  51 GLN
C 195 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.110642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.094988 restraints weight = 9154.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 0.87
r_work: 0.2742 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2646 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8553  Z= 0.237
  Angle     :  0.526   5.991  11676  Z= 0.277
  Chirality :  0.039   0.129   1317
  Planarity :  0.004   0.033   1431
  Dihedral  :  4.256  17.686   1131
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 10.87 %
    Favored  : 86.38 %
  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:  2.03 (0.27), residues: 1068
  helix:  1.73 (0.19), residues: 783
  sheet:  None (None), residues: 0
  loop :  0.44 (0.42), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  90 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.013   0.001   PHE B 341 
 TYR   0.015   0.001   TYR C 368 
 ARG   0.004   0.000   ARG A  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8784 (mtp) cc_final: 0.8452 (mtp)
REVERT: A  154 MET cc_start: 0.9207 (mtp) cc_final: 0.8917 (mtp)
REVERT: A  365 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8092 (mmmt)
REVERT: B  267 MET cc_start: 0.8413 (ptm) cc_final: 0.8103 (ptm)
REVERT: B  355 THR cc_start: 0.8149 (t) cc_final: 0.7843 (t)
REVERT: B  365 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8169 (mmmt)
  outliers start: 23
  outliers final: 18
  residues processed: 101
  average time/residue: 0.1746
  time to fit residues: 26.1379
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0170
   chunk 103 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.3061 r_free = 0.3061 target = 0.109388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.095311 restraints weight = 9229.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 0.74
r_work: 0.2681 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2565 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2488 r_free = 0.2488    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2488 r_free = 0.2488    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8553  Z= 0.199
  Angle     :  0.502   5.946  11676  Z= 0.265
  Chirality :  0.038   0.124   1317
  Planarity :  0.003   0.032   1431
  Dihedral  :  4.115  16.664   1131
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.43 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.26), residues: 1068
  helix:  2.00 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.11 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  90 
 HIS   0.002   0.000   HIS C 258 
 PHE   0.012   0.001   PHE B 341 
 TYR   0.012   0.001   TYR C 368 
 ARG   0.003   0.000   ARG A  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8824 (p) cc_final: 0.8500 (m)
REVERT: A   41 MET cc_start: 0.8799 (mtp) cc_final: 0.8501 (mtp)
REVERT: A  154 MET cc_start: 0.9107 (mtp) cc_final: 0.8842 (mtp)
REVERT: A  365 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8221 (mmmt)
REVERT: B  267 MET cc_start: 0.8488 (ptm) cc_final: 0.8179 (ptm)
REVERT: B  355 THR cc_start: 0.8133 (t) cc_final: 0.7840 (t)
REVERT: B  365 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8276 (mmmt)
  outliers start: 16
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1631
  time to fit residues: 24.2248
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3089 r_free = 0.3089 target = 0.110771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.095497 restraints weight = 9336.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 0.80
r_work: 0.2757 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8553  Z= 0.232
  Angle     :  0.523   5.985  11676  Z= 0.275
  Chirality :  0.039   0.151   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.194  16.936   1131
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.66 %
    Favored  : 85.30 %
  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:  2.00 (0.27), residues: 1068
  helix:  1.76 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.25 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  90 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.015   0.001   PHE B 341 
 TYR   0.016   0.001   TYR B 368 
 ARG   0.004   0.000   ARG A  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8805 (mtp) cc_final: 0.8515 (mtp)
REVERT: A  154 MET cc_start: 0.9160 (mtp) cc_final: 0.8877 (mtp)
REVERT: A  167 ASN cc_start: 0.8750 (m-40) cc_final: 0.8476 (m110)
REVERT: A  365 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8149 (mmmt)
REVERT: B  167 ASN cc_start: 0.8912 (m-40) cc_final: 0.8591 (m110)
REVERT: B  267 MET cc_start: 0.8394 (ptm) cc_final: 0.8068 (ptm)
REVERT: B  355 THR cc_start: 0.8048 (t) cc_final: 0.7742 (t)
REVERT: B  365 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8162 (mmmt)
  outliers start: 17
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1584
  time to fit residues: 23.1826
Evaluate side-chains
  104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3098 r_free = 0.3098 target = 0.111027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.095983 restraints weight = 9127.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 0.79
r_work: 0.2755 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2618 r_free = 0.2618    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8553  Z= 0.240
  Angle     :  0.527   5.990  11676  Z= 0.278
  Chirality :  0.039   0.148   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.226  18.058   1131
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.90 %
    Favored  : 85.07 %
  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:  1.98 (0.27), residues: 1068
  helix:  1.73 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.28 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.015   0.001   PHE B 341 
 TYR   0.017   0.001   TYR B 368 
 ARG   0.004   0.000   ARG A  63 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8833 (p) cc_final: 0.8504 (m)
REVERT: A   41 MET cc_start: 0.8842 (mtp) cc_final: 0.8550 (mtp)
REVERT: A  154 MET cc_start: 0.9174 (mtp) cc_final: 0.8906 (mtp)
REVERT: A  167 ASN cc_start: 0.8773 (m-40) cc_final: 0.8496 (m110)
REVERT: A  365 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8150 (mmmt)
REVERT: B  167 ASN cc_start: 0.8930 (m-40) cc_final: 0.8616 (m110)
REVERT: B  267 MET cc_start: 0.8404 (ptm) cc_final: 0.8077 (ptm)
REVERT: B  355 THR cc_start: 0.8031 (t) cc_final: 0.7738 (t)
REVERT: B  365 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8187 (mmmt)
  outliers start: 17
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1575
  time to fit residues: 22.6196
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3073 r_free = 0.3073 target = 0.109655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.094362 restraints weight = 9268.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 0.84
r_work: 0.2746 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8553  Z= 0.239
  Angle     :  0.527   5.992  11676  Z= 0.277
  Chirality :  0.039   0.143   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.228  18.035   1131
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.14 %
    Favored  : 84.71 %
  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:  1.98 (0.27), residues: 1068
  helix:  1.73 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.29 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.026   0.001   PHE B  36 
 TYR   0.016   0.001   TYR B 368 
 ARG   0.004   0.000   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3952.95 seconds
wall clock time: 70 minutes 53.77 seconds (4253.77 seconds total)