Starting phenix.real_space_refine
on Wed Sep 17 09:28:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xdd_38274/09_2025/8xdd_38274_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xdd_38274/09_2025/8xdd_38274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xdd_38274/09_2025/8xdd_38274_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xdd_38274/09_2025/8xdd_38274_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xdd_38274/09_2025/8xdd_38274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xdd_38274/09_2025/8xdd_38274.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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      57      5.16       5
     C    5151      2.51       5
     N    1158      2.21       5
     O    1302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7668
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2533
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 331, 2525
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
      Conformer: "B"
        Number of residues, atoms: 331, 2525
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 2594
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'8HC': 1, 'SZ4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'8HC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.55, per 1000 atoms: 0.33
  Number of scatterers: 7668
  At special positions: 0
  Unit cell: (94.3, 92.66, 72.98, 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      57     16.00
     O    1302      8.00
     N    1158      7.00
     C    5151      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 801.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      78.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    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 112 through 119
    Processing helix  chain 'A' and resid 124 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
      removed outlier: 3.735A  pdb=" N   SER A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   CYS A 156 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
      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
      removed outlier: 3.543A  pdb=" N   VAL A 216 " --> pdb=" O   TRP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 4.417A  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 237 through 252
      removed outlier: 3.784A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 273
      removed outlier: 3.823A  pdb=" N   ILE A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 286 through 298
      removed outlier: 4.185A  pdb=" N   GLY A 298 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 330
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.725A  pdb=" N   VAL A 366 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 381
    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 112 through 119
    Processing helix  chain 'B' and resid 124 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
      removed outlier: 3.735A  pdb=" N   SER B 155 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   CYS B 156 " --> pdb=" O   MET B 152 " (cutoff:3.500A)
      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
      removed outlier: 3.543A  pdb=" N   VAL B 216 " --> pdb=" O   TRP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 231
      removed outlier: 4.417A  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 237 through 252
      removed outlier: 3.784A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 273
      removed outlier: 3.822A  pdb=" N   ILE B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 282
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 4.185A  pdb=" N   GLY B 298 " --> pdb=" O   ILE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 330
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'B' and resid 362 through 366
      removed outlier: 3.725A  pdb=" N   VAL B 366 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 381
    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 112 through 119
    Processing helix  chain 'C' and resid 124 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
      removed outlier: 3.736A  pdb=" N   SER C 155 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   CYS C 156 " --> pdb=" O   MET C 152 " (cutoff:3.500A)
      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
      removed outlier: 3.542A  pdb=" N   VAL C 216 " --> pdb=" O   TRP C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 231
      removed outlier: 4.417A  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 237 through 252
      removed outlier: 3.783A  pdb=" N   SER C 251 " --> pdb=" O   ALA C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 273
      removed outlier: 3.824A  pdb=" N   ILE C 273 " --> pdb=" O   ALA C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 282
    Processing helix  chain 'C' and resid 286 through 298
      removed outlier: 4.186A  pdb=" N   GLY C 298 " --> pdb=" O   ILE C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 330
    Processing helix  chain 'C' and resid 338 through 350
    Processing helix  chain 'C' and resid 362 through 366
      removed outlier: 3.725A  pdb=" N   VAL C 366 " --> pdb=" O   LEU C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 381

    513 hydrogen bonds defined for protein.
    1521 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 1.03 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: 1113
        1.31 -     1.43: 2331
        1.43 -     1.56: 4380
        1.56 -     1.68: 3
        1.68 -     1.81: 87
  Bond restraints: 7914
  Sorted by residual:
  bond pdb=" C   THR B 275 "
       pdb=" N   PRO B 276 "
    ideal  model  delta    sigma   weight residual
    1.331  1.372 -0.041 1.27e-02 6.20e+03 1.05e+01
  bond pdb=" C   THR A 275 "
       pdb=" N   PRO A 276 "
    ideal  model  delta    sigma   weight residual
    1.331  1.372 -0.041 1.27e-02 6.20e+03 1.04e+01
  bond pdb=" C   THR C 275 "
       pdb=" N   PRO C 276 "
    ideal  model  delta    sigma   weight residual
    1.331  1.372 -0.041 1.27e-02 6.20e+03 1.04e+01
  bond pdb=" CA  THR B 275 "
       pdb=" C   THR B 275 "
    ideal  model  delta    sigma   weight residual
    1.528  1.565 -0.037 1.18e-02 7.18e+03 9.93e+00
  bond pdb=" CA  THR A 275 "
       pdb=" C   THR A 275 "
    ideal  model  delta    sigma   weight residual
    1.528  1.565 -0.037 1.18e-02 7.18e+03 9.82e+00
  ... (remaining 7909 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 10263
        1.33 -     2.66: 451
        2.66 -     3.99: 104
        3.99 -     5.33: 39
        5.33 -     6.66: 6
  Bond angle restraints: 10863
  Sorted by residual:
  angle pdb=" N   GLY B 119 "
        pdb=" CA  GLY B 119 "
        pdb=" C   GLY B 119 "
      ideal   model   delta    sigma   weight residual
     115.63  111.25    4.38 1.49e+00 4.50e-01 8.63e+00
  angle pdb=" N   GLY A 119 "
        pdb=" CA  GLY A 119 "
        pdb=" C   GLY A 119 "
      ideal   model   delta    sigma   weight residual
     115.63  111.26    4.37 1.49e+00 4.50e-01 8.59e+00
  angle pdb=" N   GLY C 119 "
        pdb=" CA  GLY C 119 "
        pdb=" C   GLY C 119 "
      ideal   model   delta    sigma   weight residual
     115.63  111.29    4.34 1.49e+00 4.50e-01 8.50e+00
  angle pdb=" N   THR C 176 "
        pdb=" CA  THR C 176 "
        pdb=" C   THR C 176 "
      ideal   model   delta    sigma   weight residual
     113.31  107.85    5.46 2.04e+00 2.40e-01 7.17e+00
  angle pdb=" N   THR B 176 "
        pdb=" CA  THR B 176 "
        pdb=" C   THR B 176 "
      ideal   model   delta    sigma   weight residual
     113.31  107.89    5.42 2.04e+00 2.40e-01 7.06e+00
  ... (remaining 10858 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4170
       17.97 -    35.93: 261
       35.93 -    53.90: 27
       53.90 -    71.87: 12
       71.87 -    89.83: 6
  Dihedral angle restraints: 4476
    sinusoidal: 1599
      harmonic: 2877
  Sorted by residual:
  dihedral pdb=" CA  LEU C 131 "
           pdb=" C   LEU C 131 "
           pdb=" N   MET C 132 "
           pdb=" CA  MET C 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.00   17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  LEU A 131 "
           pdb=" C   LEU A 131 "
           pdb=" N   MET A 132 "
           pdb=" CA  MET A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.03   16.97     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  LEU B 131 "
           pdb=" C   LEU B 131 "
           pdb=" N   MET B 132 "
           pdb=" CA  MET B 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.04   16.96     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 4473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 626
       0.027 -    0.054: 374
       0.054 -    0.082: 200
       0.082 -    0.109: 65
       0.109 -    0.136: 16
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" CA  PRO C 369 "
            pdb=" N   PRO C 369 "
            pdb=" C   PRO C 369 "
            pdb=" CB  PRO C 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  PRO A 369 "
            pdb=" N   PRO A 369 "
            pdb=" C   PRO A 369 "
            pdb=" CB  PRO A 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  PRO B 369 "
            pdb=" N   PRO B 369 "
            pdb=" C   PRO B 369 "
            pdb=" CB  PRO B 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1278 not shown)

  Planarity restraints: 1311
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 147 "    0.051 5.00e-02 4.00e+02   7.78e-02 9.68e+00
        pdb=" N   PRO B 148 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 148 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 148 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 147 "    0.051 5.00e-02 4.00e+02   7.77e-02 9.67e+00
        pdb=" N   PRO A 148 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 148 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 148 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 147 "   -0.051 5.00e-02 4.00e+02   7.77e-02 9.65e+00
        pdb=" N   PRO C 148 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C 148 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 148 "   -0.043 5.00e-02 4.00e+02
  ... (remaining 1308 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1238
        2.75 -     3.29: 8063
        3.29 -     3.83: 13542
        3.83 -     4.36: 16051
        4.36 -     4.90: 27316
  Nonbonded interactions: 66210
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 180 "
            pdb=" O   CYS A 337 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" ND2 ASN C 180 "
            pdb=" O   CYS C 337 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" ND2 ASN B 180 "
            pdb=" O   CYS B 337 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OG  SER C 102 "
            pdb=" O   HIS C 121 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG  SER A 102 "
            pdb=" O   HIS A 121 "
     model   vdw
     2.302 3.040
  ... (remaining 66205 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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=0.50 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:             2.020
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.560
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
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      :  0.006   0.062   7917  Z= 0.277
  Angle     :  0.697   6.657  10863  Z= 0.359
  Chirality :  0.043   0.136   1281
  Planarity :  0.007   0.078   1311
  Dihedral  : 12.324  89.833   2634
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.28), residues: 990
  helix:  1.50 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.73 (0.43), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 373 
 TYR   0.012   0.002   TYR B 123 
 PHE   0.020   0.002   PHE A 300 
 TRP   0.008   0.001   TRP B 305 
 HIS   0.003   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 7914)
  covalent geometry    : angle       0.69687 (10863)
  hydrogen bonds       : bond        0.13591 (  513)
  hydrogen bonds       : angle       5.43256 ( 1521)
  Misc. bond           : bond        0.01917 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.278 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.5227
  time to fit residues: 70.6805
Evaluate side-chains
  95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.076624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.063507 restraints weight = 38739.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2714 rms_B_bonded: 3.96
r_work: 0.2544 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2552 r_free = 0.2552    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2552 r_free = 0.2552    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7917  Z= 0.143
  Angle     :  0.637   9.095  10863  Z= 0.314
  Chirality :  0.042   0.128   1281
  Planarity :  0.006   0.059   1311
  Dihedral  :  5.172  57.771   1053
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.56 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.27), residues: 990
  helix:  1.85 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.71 (0.43), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 373 
 TYR   0.011   0.001   TYR A 123 
 PHE   0.017   0.001   PHE B 175 
 TRP   0.010   0.001   TRP C 305 
 HIS   0.001   0.000   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7914)
  covalent geometry    : angle       0.63651 (10863)
  hydrogen bonds       : bond        0.04016 (  513)
  hydrogen bonds       : angle       3.73574 ( 1521)
  Misc. bond           : bond        0.00039 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  169 LYS cc_start: 0.9400 (mptp) cc_final: 0.9053 (mmtp)
REVERT: A  250 ILE cc_start: 0.9159 (tp) cc_final: 0.8830 (pp)
REVERT: B   82 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8362 (tm)
REVERT: B  250 ILE cc_start: 0.9146 (tp) cc_final: 0.8828 (pp)
REVERT: C  250 ILE cc_start: 0.9172 (tp) cc_final: 0.8859 (pp)
REVERT: C  299 MET cc_start: 0.7869 (ttm) cc_final: 0.7645 (ttp)
  outliers start: 11
  outliers final: 1
  residues processed: 114
  average time/residue: 0.5726
  time to fit residues: 69.2332
Evaluate side-chains
  101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.074976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.062686 restraints weight = 27164.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.2696 rms_B_bonded: 3.32
r_work: 0.2546 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7917  Z= 0.164
  Angle     :  0.630   9.123  10863  Z= 0.309
  Chirality :  0.042   0.130   1281
  Planarity :  0.005   0.052   1311
  Dihedral  :  4.945  53.109   1053
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.76 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.27), residues: 990
  helix:  1.94 (0.19), residues: 717
  sheet:  None (None), residues: 0
  loop :  0.83 (0.44), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 373 
 TYR   0.012   0.001   TYR A 123 
 PHE   0.019   0.001   PHE A 175 
 TRP   0.008   0.001   TRP C 305 
 HIS   0.001   0.000   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 7914)
  covalent geometry    : angle       0.62964 (10863)
  hydrogen bonds       : bond        0.03958 (  513)
  hydrogen bonds       : angle       3.56646 ( 1521)
  Misc. bond           : bond        0.00048 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  250 ILE cc_start: 0.9166 (tp) cc_final: 0.8861 (pp)
REVERT: B   82 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8395 (tm)
REVERT: B  250 ILE cc_start: 0.9144 (tp) cc_final: 0.8859 (pp)
REVERT: C  169 LYS cc_start: 0.9399 (mmtp) cc_final: 0.9082 (mmtp)
REVERT: C  250 ILE cc_start: 0.9171 (tp) cc_final: 0.8882 (pp)
  outliers start: 13
  outliers final: 2
  residues processed: 109
  average time/residue: 0.6283
  time to fit residues: 72.2790
Evaluate side-chains
  102 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 68 optimal weight:    0.1980
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.077530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.065549 restraints weight = 23889.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.2746 rms_B_bonded: 3.14
r_work: 0.2602 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7917  Z= 0.127
  Angle     :  0.606   8.345  10863  Z= 0.295
  Chirality :  0.040   0.123   1281
  Planarity :  0.005   0.048   1311
  Dihedral  :  4.588  44.493   1053
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.48 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.27), residues: 990
  helix:  2.07 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.88 (0.44), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 373 
 TYR   0.011   0.001   TYR A 123 
 PHE   0.013   0.001   PHE C 300 
 TRP   0.008   0.001   TRP C 305 
 HIS   0.001   0.000   HIS A 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7914)
  covalent geometry    : angle       0.60582 (10863)
  hydrogen bonds       : bond        0.03603 (  513)
  hydrogen bonds       : angle       3.36155 ( 1521)
  Misc. bond           : bond        0.00032 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  169 LYS cc_start: 0.9404 (mptp) cc_final: 0.9091 (mmtp)
REVERT: A  250 ILE cc_start: 0.9128 (tp) cc_final: 0.8879 (pp)
REVERT: B   82 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8372 (tm)
REVERT: B  132 MET cc_start: 0.8801 (mmm) cc_final: 0.8402 (mtt)
REVERT: B  250 ILE cc_start: 0.9084 (tp) cc_final: 0.8854 (pp)
REVERT: C  169 LYS cc_start: 0.9414 (mmtp) cc_final: 0.9079 (mmtp)
REVERT: C  250 ILE cc_start: 0.9111 (tp) cc_final: 0.8844 (pp)
  outliers start: 10
  outliers final: 2
  residues processed: 103
  average time/residue: 0.6286
  time to fit residues: 68.3970
Evaluate side-chains
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0070
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.078530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.065223 restraints weight = 45242.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 4.26
r_work: 0.2563 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7917  Z= 0.124
  Angle     :  0.596   7.682  10863  Z= 0.290
  Chirality :  0.040   0.127   1281
  Planarity :  0.005   0.045   1311
  Dihedral  :  4.175  32.673   1053
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.20 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.27), residues: 990
  helix:  2.15 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.86 (0.44), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 373 
 TYR   0.011   0.001   TYR C 123 
 PHE   0.011   0.001   PHE B 287 
 TRP   0.007   0.001   TRP A 305 
 HIS   0.001   0.000   HIS C 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7914)
  covalent geometry    : angle       0.59576 (10863)
  hydrogen bonds       : bond        0.03508 (  513)
  hydrogen bonds       : angle       3.29134 ( 1521)
  Misc. bond           : bond        0.00031 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8432 (tm)
REVERT: A  250 ILE cc_start: 0.9098 (tp) cc_final: 0.8871 (pp)
REVERT: B   82 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8348 (tm)
REVERT: B  132 MET cc_start: 0.8817 (mmm) cc_final: 0.8486 (mtt)
REVERT: B  250 ILE cc_start: 0.9064 (tp) cc_final: 0.8856 (pp)
REVERT: C   69 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8464 (mpp)
REVERT: C  169 LYS cc_start: 0.9400 (mmtp) cc_final: 0.9071 (mmtp)
REVERT: C  250 ILE cc_start: 0.9060 (tp) cc_final: 0.8823 (pp)
  outliers start: 10
  outliers final: 3
  residues processed: 104
  average time/residue: 0.6391
  time to fit residues: 70.1979
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.074611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.061527 restraints weight = 44134.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 4.11
r_work: 0.2494 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2520 r_free = 0.2520    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2520 r_free = 0.2520    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7917  Z= 0.174
  Angle     :  0.630   8.380  10863  Z= 0.306
  Chirality :  0.042   0.142   1281
  Planarity :  0.005   0.045   1311
  Dihedral  :  4.169  27.380   1053
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.44 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.27), residues: 990
  helix:  2.11 (0.19), residues: 717
  sheet:  None (None), residues: 0
  loop :  0.86 (0.43), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 373 
 TYR   0.012   0.001   TYR C 123 
 PHE   0.015   0.001   PHE C 175 
 TRP   0.006   0.001   TRP C 305 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 7914)
  covalent geometry    : angle       0.62981 (10863)
  hydrogen bonds       : bond        0.03909 (  513)
  hydrogen bonds       : angle       3.46291 ( 1521)
  Misc. bond           : bond        0.00061 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8516 (tm)
REVERT: A  250 ILE cc_start: 0.9176 (tp) cc_final: 0.8905 (pp)
REVERT: B   82 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8411 (tm)
REVERT: B  250 ILE cc_start: 0.9118 (tp) cc_final: 0.8860 (pp)
REVERT: B  299 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8100 (ttp)
REVERT: C  169 LYS cc_start: 0.9424 (mmtp) cc_final: 0.9134 (mmtp)
REVERT: C  250 ILE cc_start: 0.9128 (tp) cc_final: 0.8860 (pp)
  outliers start: 13
  outliers final: 2
  residues processed: 108
  average time/residue: 0.6181
  time to fit residues: 70.5397
Evaluate side-chains
  101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0010
   chunk 89 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.077887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.065213 restraints weight = 31694.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 3.63
r_work: 0.2581 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7917  Z= 0.127
  Angle     :  0.610   7.966  10863  Z= 0.296
  Chirality :  0.040   0.127   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  4.010  21.746   1053
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 16.54 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.27), residues: 990
  helix:  2.19 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.84 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 373 
 TYR   0.013   0.001   TYR C 123 
 PHE   0.011   0.001   PHE B 287 
 TRP   0.007   0.001   TRP A 339 
 HIS   0.001   0.000   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7914)
  covalent geometry    : angle       0.61002 (10863)
  hydrogen bonds       : bond        0.03500 (  513)
  hydrogen bonds       : angle       3.27518 ( 1521)
  Misc. bond           : bond        0.00028 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8497 (tm)
REVERT: A  154 MET cc_start: 0.8870 (mtm) cc_final: 0.8386 (mmm)
REVERT: A  250 ILE cc_start: 0.9129 (tp) cc_final: 0.8900 (pp)
REVERT: B   82 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8363 (tm)
REVERT: B  250 ILE cc_start: 0.9063 (tp) cc_final: 0.8848 (pp)
REVERT: C  169 LYS cc_start: 0.9388 (mmtp) cc_final: 0.9098 (mmtp)
REVERT: C  250 ILE cc_start: 0.9074 (tp) cc_final: 0.8831 (pp)
  outliers start: 7
  outliers final: 3
  residues processed: 100
  average time/residue: 0.6422
  time to fit residues: 67.6918
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 94 optimal weight:   50.0000
   chunk 86 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.076923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.063689 restraints weight = 45582.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 4.23
r_work: 0.2538 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7917  Z= 0.138
  Angle     :  0.612   8.788  10863  Z= 0.298
  Chirality :  0.041   0.129   1281
  Planarity :  0.005   0.044   1311
  Dihedral  :  3.949  17.546   1053
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.67 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.27), residues: 990
  helix:  2.20 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.74 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 373 
 TYR   0.013   0.001   TYR C 123 
 PHE   0.011   0.001   PHE C 287 
 TRP   0.006   0.001   TRP A 305 
 HIS   0.001   0.000   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7914)
  covalent geometry    : angle       0.61240 (10863)
  hydrogen bonds       : bond        0.03597 (  513)
  hydrogen bonds       : angle       3.31673 ( 1521)
  Misc. bond           : bond        0.00036 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8660 (mpp)
REVERT: A   82 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8510 (tm)
REVERT: A  250 ILE cc_start: 0.9133 (tp) cc_final: 0.8912 (pp)
REVERT: B   82 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (tm)
REVERT: B  250 ILE cc_start: 0.9063 (tp) cc_final: 0.8850 (pp)
REVERT: C  169 LYS cc_start: 0.9382 (mmtp) cc_final: 0.9115 (mmtp)
REVERT: C  250 ILE cc_start: 0.9092 (tp) cc_final: 0.8854 (pp)
  outliers start: 9
  outliers final: 3
  residues processed: 101
  average time/residue: 0.6176
  time to fit residues: 65.8348
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 78 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 76 optimal weight:    0.0870
   chunk 16 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.079277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.066513 restraints weight = 34730.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 3.80
r_work: 0.2603 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7917  Z= 0.124
  Angle     :  0.613   9.263  10863  Z= 0.297
  Chirality :  0.040   0.124   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.832  15.419   1053
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.54 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.27), residues: 990
  helix:  2.26 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.68 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 373 
 TYR   0.013   0.001   TYR C 123 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.008   0.001   TRP C 339 
 HIS   0.001   0.000   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7914)
  covalent geometry    : angle       0.61264 (10863)
  hydrogen bonds       : bond        0.03379 (  513)
  hydrogen bonds       : angle       3.22364 ( 1521)
  Misc. bond           : bond        0.00015 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8606 (mpp)
REVERT: A  154 MET cc_start: 0.8879 (mtm) cc_final: 0.8357 (mmm)
REVERT: B   82 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (tm)
REVERT: C  250 ILE cc_start: 0.9038 (tp) cc_final: 0.8835 (pp)
  outliers start: 9
  outliers final: 4
  residues processed: 103
  average time/residue: 0.6207
  time to fit residues: 67.7084
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN
** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.078291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.065764 restraints weight = 32860.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 3.70
r_work: 0.2586 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7917  Z= 0.135
  Angle     :  0.631   9.140  10863  Z= 0.303
  Chirality :  0.042   0.260   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.831  15.346   1053
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.91 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.74 (0.27), residues: 990
  helix:  2.29 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.63 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 373 
 TYR   0.013   0.001   TYR C 123 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.007   0.001   TRP C 339 
 HIS   0.001   0.000   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7914)
  covalent geometry    : angle       0.63076 (10863)
  hydrogen bonds       : bond        0.03469 (  513)
  hydrogen bonds       : angle       3.27277 ( 1521)
  Misc. bond           : bond        0.00031 (    3)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   69 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.8613 (mpp)
REVERT: B   82 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8374 (tm)
  outliers start: 8
  outliers final: 4
  residues processed: 98
  average time/residue: 0.6228
  time to fit residues: 64.3434
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0170
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN
** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.078067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.065500 restraints weight = 33681.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2738 rms_B_bonded: 3.73
r_work: 0.2579 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7917  Z= 0.136
  Angle     :  0.637   9.135  10863  Z= 0.307
  Chirality :  0.042   0.232   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.846  16.205   1053
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 17.03 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.27), residues: 990
  helix:  2.32 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.63 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 373 
 TYR   0.014   0.001   TYR C 123 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.006   0.001   TRP A 339 
 HIS   0.001   0.000   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7914)
  covalent geometry    : angle       0.63713 (10863)
  hydrogen bonds       : bond        0.03469 (  513)
  hydrogen bonds       : angle       3.28125 ( 1521)
  Misc. bond           : bond        0.00030 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2428.73 seconds
wall clock time: 42 minutes 20.40 seconds (2540.40 seconds total)