Starting phenix.real_space_refine
on Wed Mar 12 20:36:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xdh_38278/03_2025/8xdh_38278_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xdh_38278/03_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_38278/03_2025/8xdh_38278.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xdh_38278/03_2025/8xdh_38278.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xdh_38278/03_2025/8xdh_38278_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xdh_38278/03_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-5624/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: 5.29, per 1000 atoms: 0.64
  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: 2.11
  Conformation dependent library (CDL) restraints added in 1.6 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: 0.92
  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: 2.51

  Time building geometry restraints manager: 2.49 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: 0.06
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:             2.010
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.050
  Find NCS groups from input model:        0.170
  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:3.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.100
-------------------------------------------------------------------------------
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  : 0.856 
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: 0.1515
  time to fit residues: 26.7782
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  : 0.827 
-------------------------------------------------------------------------------
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 = 0.101377 restraints weight = 8969.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 0.73
r_work: 0.2785 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    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 = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
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  : 0.968 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8708 (mtp) cc_final: 0.8417 (mtp)
REVERT: A  154 MET cc_start: 0.9070 (mtp) cc_final: 0.8723 (mtp)
REVERT: A  365 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8293 (mmmt)
REVERT: B   41 MET cc_start: 0.8801 (mtp) cc_final: 0.8412 (mtp)
REVERT: B  224 SER cc_start: 0.8718 (t) cc_final: 0.8452 (m)
REVERT: B  267 MET cc_start: 0.8578 (ptm) cc_final: 0.8272 (ptm)
REVERT: B  365 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8213 (mmmt)
REVERT: C  199 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8349 (mm-40)
REVERT: C  267 MET cc_start: 0.8628 (ptm) cc_final: 0.8427 (ptt)
  outliers start: 12
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1643
  time to fit residues: 25.4551
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  : 0.898 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 101 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0470
   overall best weight:    0.5278

-------------------------------------------------------------------------------
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 = 0.3089 r_free = 0.3089 target = 0.111257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.096246 restraints weight = 9197.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 0.79
r_work: 0.2767 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2030

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= 0.219
  Angle     :  0.538   5.967  11676  Z= 0.282
  Chirality :  0.038   0.123   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.271  14.503   1131
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.08 %
    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:  1.78 (0.26), residues: 1068
  helix:  1.58 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.24 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 305 
 HIS   0.002   0.001   HIS B 258 
 PHE   0.014   0.001   PHE B 341 
 TYR   0.014   0.001   TYR C 368 
 ARG   0.002   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
  100 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8718 (mtp) cc_final: 0.8434 (mtp)
REVERT: A  154 MET cc_start: 0.9063 (mtp) cc_final: 0.8702 (mtp)
REVERT: A  365 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8249 (mmmt)
REVERT: B   41 MET cc_start: 0.8701 (mtp) cc_final: 0.8275 (mtp)
REVERT: B  224 SER cc_start: 0.8706 (t) cc_final: 0.8500 (m)
REVERT: B  267 MET cc_start: 0.8422 (ptm) cc_final: 0.8052 (ptm)
REVERT: B  355 THR cc_start: 0.8105 (t) cc_final: 0.7833 (t)
REVERT: B  365 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8122 (mmmt)
REVERT: C  208 MET cc_start: 0.7921 (tpp) cc_final: 0.7714 (tpt)
  outliers start: 14
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1747
  time to fit residues: 24.2496
Evaluate side-chains
  96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
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  250 ILE
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0170
   chunk 65 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    0.2980
   chunk 95 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 92 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.4618

-------------------------------------------------------------------------------
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 = 0.3086 r_free = 0.3086 target = 0.111290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.096095 restraints weight = 9179.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 0.79
r_work: 0.2773 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    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 = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2270

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= 0.205
  Angle     :  0.513   5.975  11676  Z= 0.270
  Chirality :  0.038   0.122   1317
  Planarity :  0.004   0.031   1431
  Dihedral  :  4.168  16.755   1131
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.96 %
    Favored  : 88.89 %
  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:  1.92 (0.26), residues: 1068
  helix:  1.72 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.15 (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   0.015   0.001   PHE B 341 
 TYR   0.013   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
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8737 (mtp) cc_final: 0.8456 (mtp)
REVERT: A  154 MET cc_start: 0.9051 (mtp) cc_final: 0.8679 (mtp)
REVERT: A  365 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8173 (mmmt)
REVERT: B   41 MET cc_start: 0.8684 (mtp) cc_final: 0.8257 (mtp)
REVERT: B  267 MET cc_start: 0.8394 (ptm) cc_final: 0.8003 (ptm)
REVERT: B  365 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8135 (mmmt)
REVERT: C  208 MET cc_start: 0.7885 (tpp) cc_final: 0.7648 (tpt)
  outliers start: 18
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1864
  time to fit residues: 26.2632
Evaluate side-chains
  97 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   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 = 0.3044 r_free = 0.3044 target = 0.108274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.092937 restraints weight = 9128.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 0.80
r_work: 0.2759 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2403

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= 0.241
  Angle     :  0.541   6.010  11676  Z= 0.287
  Chirality :  0.039   0.124   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.245  19.054   1131
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.80 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.99 (0.27), residues: 1068
  helix:  1.71 (0.19), residues: 783
  sheet:  None (None), residues: 0
  loop :  0.39 (0.42), residues: 285

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   0.005   0.001   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
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8768 (mtp) cc_final: 0.8437 (mtp)
REVERT: A   47 TRP cc_start: 0.8626 (t60) cc_final: 0.8404 (t60)
REVERT: A  154 MET cc_start: 0.9182 (mtp) cc_final: 0.8870 (mtp)
REVERT: A  365 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8139 (mmmt)
REVERT: B   41 MET cc_start: 0.8742 (mtp) cc_final: 0.8239 (mtp)
REVERT: B  154 MET cc_start: 0.9005 (mtp) cc_final: 0.8800 (mtt)
REVERT: B  365 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8113 (mmmt)
  outliers start: 17
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1534
  time to fit residues: 22.5139
Evaluate side-chains
  103 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 96 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.111665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.096153 restraints weight = 9132.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 0.86
r_work: 0.2753 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    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 = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8553  Z= 0.222
  Angle     :  0.523   5.973  11676  Z= 0.277
  Chirality :  0.038   0.123   1317
  Planarity :  0.004   0.032   1431
  Dihedral  :  4.192  17.224   1131
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.27 %
    Favored  : 87.46 %
  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:  1.73 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.17 (0.40), residues: 282

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   0.012   0.001   PHE B 341 
 TYR   0.014   0.001   TYR C 368 
 ARG   0.004   0.000   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
  109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8800 (mtp) cc_final: 0.8502 (mtp)
REVERT: A  154 MET cc_start: 0.9147 (mtp) cc_final: 0.8831 (mtp)
REVERT: A  365 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8115 (mmmt)
REVERT: B  267 MET cc_start: 0.8405 (ptm) cc_final: 0.8095 (ptm)
REVERT: B  355 THR cc_start: 0.8071 (t) cc_final: 0.7777 (t)
REVERT: B  365 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8144 (mmmt)
  outliers start: 19
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1634
  time to fit residues: 24.5376
Evaluate side-chains
  104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0040
   chunk 71 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0070
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0070
   chunk 89 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.2628

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.113166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.098271 restraints weight = 9111.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 0.77
r_work: 0.2801 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8553  Z= 0.170
  Angle     :  0.487   5.897  11676  Z= 0.257
  Chirality :  0.037   0.140   1317
  Planarity :  0.003   0.030   1431
  Dihedral  :  3.968  14.320   1131
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.59 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.26 (0.26), residues: 1068
  helix:  2.01 (0.19), residues: 777
  sheet:  None (None), residues: 0
  loop :  0.19 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 339 
 HIS   0.001   0.000   HIS C 258 
 PHE   0.012   0.001   PHE B 341 
 TYR   0.011   0.001   TYR C 368 
 ARG   0.003   0.000   ARG B  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
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8580 (p) cc_final: 0.8312 (m)
REVERT: A   41 MET cc_start: 0.8582 (mtp) cc_final: 0.8257 (mtp)
REVERT: A  365 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8098 (mmmt)
REVERT: B  267 MET cc_start: 0.8267 (ptm) cc_final: 0.7922 (ptm)
REVERT: B  365 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8115 (mmmt)
  outliers start: 14
  outliers final: 11
  residues processed: 99
  average time/residue: 0.1550
  time to fit residues: 23.3345
Evaluate side-chains
  99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
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 B residue  174 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  290 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
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:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 103 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
B 331 ASN
C  51 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.106949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.091529 restraints weight = 9271.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 0.82
r_work: 0.2701 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2563 r_free = 0.2563    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2563 r_free = 0.2563    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2563
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2635

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= 0.253
  Angle     :  0.540   6.000  11676  Z= 0.284
  Chirality :  0.040   0.159   1317
  Planarity :  0.004   0.033   1431
  Dihedral  :  4.199  17.127   1131
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.23 %
    Favored  : 86.62 %
  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:  1.78 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.20 (0.40), residues: 282

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   0.015   0.001   PHE B 341 
 TYR   0.017   0.001   TYR B 368 
 ARG   0.004   0.001   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
  109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8873 (p) cc_final: 0.8516 (m)
REVERT: A   41 MET cc_start: 0.8741 (mtp) cc_final: 0.8468 (mtp)
REVERT: A  365 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8080 (mmmt)
REVERT: B  267 MET cc_start: 0.8372 (ptm) cc_final: 0.8029 (ptm)
REVERT: B  365 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8093 (mmmt)
  outliers start: 18
  outliers final: 15
  residues processed: 98
  average time/residue: 0.1666
  time to fit residues: 24.6892
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  : 0.862 
-------------------------------------------------------------------------------
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  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  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 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:    0.3980
   chunk 82 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3039 r_free = 0.3039 target = 0.107986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.093626 restraints weight = 9367.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 0.78
r_work: 0.2657 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8553  Z= 0.225
  Angle     :  0.519   5.966  11676  Z= 0.273
  Chirality :  0.039   0.144   1317
  Planarity :  0.004   0.033   1431
  Dihedral  :  4.158  16.270   1131
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.19 %
    Favored  : 86.14 %
  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 (0.26), residues: 1068
  helix:  1.80 (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   0.007   0.001   TRP B  90 
 HIS   0.003   0.001   HIS B 258 
 PHE   0.013   0.001   PHE B 341 
 TYR   0.014   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
  102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8778 (mtp) cc_final: 0.8503 (mtp)
REVERT: A  365 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8225 (mmmt)
REVERT: B  267 MET cc_start: 0.8514 (ptm) cc_final: 0.8190 (ptm)
REVERT: B  355 THR cc_start: 0.8064 (t) cc_final: 0.7750 (t)
REVERT: B  365 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8205 (mmmt)
  outliers start: 14
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1589
  time to fit residues: 22.8761
Evaluate side-chains
  99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
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 C residue   40 ASP
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 69 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3060 r_free = 0.3060 target = 0.109664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.095385 restraints weight = 9127.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 0.75
r_work: 0.2660 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    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 = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2707

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= 0.202
  Angle     :  0.503   5.945  11676  Z= 0.265
  Chirality :  0.038   0.143   1317
  Planarity :  0.003   0.032   1431
  Dihedral  :  4.068  15.702   1131
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.31 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.26), residues: 1068
  helix:  2.03 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.01 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  47 
 HIS   0.002   0.000   HIS C 258 
 PHE   0.013   0.001   PHE B 341 
 TYR   0.012   0.001   TYR C 368 
 ARG   0.003   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
  102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8816 (p) cc_final: 0.8493 (m)
REVERT: A   41 MET cc_start: 0.8789 (mtp) cc_final: 0.8507 (mtp)
REVERT: A  365 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8188 (mmmt)
REVERT: B  267 MET cc_start: 0.8352 (ptm) cc_final: 0.8010 (ptm)
REVERT: B  355 THR cc_start: 0.8029 (t) cc_final: 0.7725 (t)
REVERT: B  365 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8192 (mmmt)
  outliers start: 14
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1629
  time to fit residues: 23.5668
Evaluate side-chains
  99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
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 C residue  250 ILE
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  304 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 44 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3092 r_free = 0.3092 target = 0.111144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.095917 restraints weight = 9242.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 0.80
r_work: 0.2758 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    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 = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2705

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= 0.231
  Angle     :  0.523   5.985  11676  Z= 0.275
  Chirality :  0.039   0.145   1317
  Planarity :  0.004   0.033   1431
  Dihedral  :  4.166  16.289   1131
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.19 %
    Favored  : 86.14 %
  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:  2.02 (0.26), residues: 1068
  helix:  1.79 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.17 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 258 
 PHE   0.025   0.001   PHE B  36 
 TYR   0.015   0.001   TYR B 368 
 ARG   0.003   0.000   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4357.64 seconds
wall clock time: 75 minutes 47.02 seconds (4547.02 seconds total)