Starting phenix.real_space_refine
on Wed Mar 12 09:27:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xdd_38274/03_2025/8xdd_38274_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xdd_38274/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xdd_38274/03_2025/8xdd_38274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xdd_38274/03_2025/8xdd_38274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xdd_38274/03_2025/8xdd_38274_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xdd_38274/03_2025/8xdd_38274_neut.cif"
  }
  resolution = 3.0
  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=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 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:
    C, B
  Time building chain proxies: 6.26, per 1000 atoms: 0.82
  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: 2.43
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  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: 0.71
  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: 2.26

  Time building geometry restraints manager: 2.63 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.700
  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:16.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.640
-------------------------------------------------------------------------------
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   7914  Z= 0.386
  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 (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:  1.83 (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
 TRP   0.008   0.001   TRP B 305 
 HIS   0.003   0.001   HIS B 121 
 PHE   0.020   0.002   PHE A 300 
 TYR   0.012   0.002   TYR B 123 
 ARG   0.001   0.000   ARG C 373 

*********************** 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  : 0.842 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 1.0684
  time to fit residues: 144.6973
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  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 89 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:
** 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 = 0.2966 r_free = 0.2966 target = 0.076366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.064170 restraints weight = 24656.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 3.21
r_work: 0.2581 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2593 r_free = 0.2593    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7914  Z= 0.216
  Angle     :  0.638   9.239  10863  Z= 0.314
  Chirality :  0.042   0.128   1281
  Planarity :  0.006   0.060   1311
  Dihedral  :  5.177  57.805   1053
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.56 %
    Favored  : 89.22 %
  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 (0.27), residues: 990
  helix:  1.86 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.72 (0.43), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 305 
 HIS   0.001   0.000   HIS C 121 
 PHE   0.018   0.001   PHE B 175 
 TYR   0.011   0.001   TYR A 123 
 ARG   0.004   0.001   ARG B 373 

*********************** 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: 10
    poor density    : 109
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A  169 LYS cc_start: 0.9402 (mptp) cc_final: 0.9050 (mmtp)
REVERT: A  250 ILE cc_start: 0.9154 (tp) cc_final: 0.8831 (pp)
REVERT: B   82 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8367 (tm)
REVERT: B  250 ILE cc_start: 0.9142 (tp) cc_final: 0.8829 (pp)
REVERT: C  250 ILE cc_start: 0.9170 (tp) cc_final: 0.8861 (pp)
REVERT: C  299 MET cc_start: 0.7881 (ttm) cc_final: 0.7665 (ttp)
  outliers start: 10
  outliers final: 1
  residues processed: 115
  average time/residue: 1.1865
  time to fit residues: 145.0404
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  : 0.906 
-------------------------------------------------------------------------------
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 16 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.2955 r_free = 0.2955 target = 0.075780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.063175 restraints weight = 32186.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 3.62
r_work: 0.2547 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    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 = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7914  Z= 0.228
  Angle     :  0.624   9.304  10863  Z= 0.306
  Chirality :  0.041   0.129   1281
  Planarity :  0.005   0.052   1311
  Dihedral  :  4.869  51.635   1053
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.52 %
    Favored  : 86.52 %
  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:  2.45 (0.27), residues: 990
  helix:  1.98 (0.19), residues: 717
  sheet:  None (None), residues: 0
  loop :  0.84 (0.44), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 305 
 HIS   0.001   0.000   HIS A 121 
 PHE   0.018   0.001   PHE A 175 
 TYR   0.012   0.001   TYR A 123 
 ARG   0.004   0.001   ARG B 373 

*********************** 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
  118 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  250 ILE cc_start: 0.9159 (tp) cc_final: 0.8865 (pp)
REVERT: B   82 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8387 (tm)
REVERT: B  250 ILE cc_start: 0.9120 (tp) cc_final: 0.8851 (pp)
REVERT: C  169 LYS cc_start: 0.9410 (mmtp) cc_final: 0.9079 (mmtp)
REVERT: C  250 ILE cc_start: 0.9142 (tp) cc_final: 0.8853 (pp)
  outliers start: 16
  outliers final: 2
  residues processed: 107
  average time/residue: 1.2408
  time to fit residues: 140.4381
Evaluate side-chains
  100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain B residue   82 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 88 optimal weight:    0.0470
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.076572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.063665 restraints weight = 38996.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 3.97
r_work: 0.2546 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    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 = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7914  Z= 0.203
  Angle     :  0.608   8.430  10863  Z= 0.295
  Chirality :  0.041   0.122   1281
  Planarity :  0.005   0.048   1311
  Dihedral  :  4.586  44.241   1053
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.85 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.27), residues: 990
  helix:  2.08 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.76 (0.43), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 305 
 HIS   0.001   0.000   HIS A 308 
 PHE   0.013   0.001   PHE C 300 
 TYR   0.011   0.001   TYR A 123 
 ARG   0.004   0.001   ARG C 373 

*********************** 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
  105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A  169 LYS cc_start: 0.9415 (mptp) cc_final: 0.9130 (mmtp)
REVERT: A  250 ILE cc_start: 0.9142 (tp) cc_final: 0.8875 (pp)
REVERT: B   82 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8373 (tm)
REVERT: B  250 ILE cc_start: 0.9095 (tp) cc_final: 0.8856 (pp)
REVERT: C  169 LYS cc_start: 0.9420 (mmtp) cc_final: 0.9085 (mmtp)
REVERT: C  250 ILE cc_start: 0.9120 (tp) cc_final: 0.8844 (pp)
  outliers start: 9
  outliers final: 3
  residues processed: 100
  average time/residue: 1.2627
  time to fit residues: 133.6361
Evaluate side-chains
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.077420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.065045 restraints weight = 28624.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.2738 rms_B_bonded: 3.42
r_work: 0.2584 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2606 r_free = 0.2606    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 = 0.2606 r_free = 0.2606    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7914  Z= 0.203
  Angle     :  0.602   7.590  10863  Z= 0.292
  Chirality :  0.040   0.126   1281
  Planarity :  0.005   0.046   1311
  Dihedral  :  4.270  35.051   1053
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.44 %
    Favored  : 83.70 %
  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:  2.62 (0.27), residues: 990
  helix:  2.12 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.86 (0.43), residues: 270

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

*********************** 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
  100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.042 
Fit side-chains
REVERT: A  250 ILE cc_start: 0.9127 (tp) cc_final: 0.8890 (pp)
REVERT: B   82 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8364 (tm)
REVERT: B  250 ILE cc_start: 0.9084 (tp) cc_final: 0.8853 (pp)
REVERT: C  169 LYS cc_start: 0.9413 (mmtp) cc_final: 0.9109 (mmtp)
REVERT: C  250 ILE cc_start: 0.9088 (tp) cc_final: 0.8841 (pp)
  outliers start: 7
  outliers final: 3
  residues processed: 98
  average time/residue: 1.9228
  time to fit residues: 198.5476
Evaluate side-chains
  96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 96 optimal weight:    0.2980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.076746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.064002 restraints weight = 34663.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 3.73
r_work: 0.2553 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2578 r_free = 0.2578    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 = 0.2578 r_free = 0.2578    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7914  Z= 0.217
  Angle     :  0.607   8.593  10863  Z= 0.293
  Chirality :  0.041   0.125   1281
  Planarity :  0.005   0.044   1311
  Dihedral  :  4.099  27.037   1053
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.20 %
    Favored  : 83.46 %
  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:  2.66 (0.27), residues: 990
  helix:  2.15 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.85 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 305 
 HIS   0.001   0.000   HIS C 308 
 PHE   0.011   0.001   PHE C 300 
 TYR   0.013   0.001   TYR C 123 
 ARG   0.004   0.001   ARG B 373 

*********************** 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
  105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A  169 LYS cc_start: 0.9421 (mptp) cc_final: 0.9147 (mmtp)
REVERT: A  250 ILE cc_start: 0.9141 (tp) cc_final: 0.8898 (pp)
REVERT: B   82 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8385 (tm)
REVERT: B  250 ILE cc_start: 0.9080 (tp) cc_final: 0.8851 (pp)
REVERT: C  169 LYS cc_start: 0.9399 (mmtp) cc_final: 0.9103 (mmtp)
REVERT: C  250 ILE cc_start: 0.9104 (tp) cc_final: 0.8854 (pp)
  outliers start: 11
  outliers final: 4
  residues processed: 102
  average time/residue: 1.4960
  time to fit residues: 162.2084
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  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.2946 r_free = 0.2946 target = 0.075504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.063090 restraints weight = 28164.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2699 rms_B_bonded: 3.38
r_work: 0.2547 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2547
-------------------------------------------------------------------------------
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 = 0.46   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: 0.8476
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7914  Z= 0.250
  Angle     :  0.624   7.838  10863  Z= 0.305
  Chirality :  0.041   0.130   1281
  Planarity :  0.005   0.044   1311
  Dihedral  :  4.089  23.270   1053
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.93 %
    Favored  : 83.21 %
  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:  2.61 (0.27), residues: 990
  helix:  2.12 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.83 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 305 
 HIS   0.001   0.000   HIS C 258 
 PHE   0.012   0.001   PHE C 300 
 TYR   0.013   0.001   TYR C 123 
 ARG   0.004   0.001   ARG B 373 

*********************** 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
  108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 1.317 
Fit side-chains
REVERT: A  250 ILE cc_start: 0.9157 (tp) cc_final: 0.8891 (pp)
REVERT: B   82 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8386 (tm)
REVERT: B  250 ILE cc_start: 0.9101 (tp) cc_final: 0.8852 (pp)
REVERT: C  169 LYS cc_start: 0.9413 (mmtp) cc_final: 0.9143 (mmtp)
REVERT: C  250 ILE cc_start: 0.9126 (tp) cc_final: 0.8856 (pp)
  outliers start: 7
  outliers final: 2
  residues processed: 105
  average time/residue: 1.3798
  time to fit residues: 153.7736
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  : 1.012 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0030
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 217 GLN
C 258 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.077541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.064309 restraints weight = 44163.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 4.16
r_work: 0.2547 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    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 = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7914  Z= 0.202
  Angle     :  0.610   7.715  10863  Z= 0.297
  Chirality :  0.040   0.127   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.982  19.065   1053
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.54 %
    Favored  : 82.48 %
  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:  2.66 (0.27), residues: 990
  helix:  2.21 (0.19), residues: 717
  sheet:  None (None), residues: 0
  loop :  0.68 (0.43), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 339 
 HIS   0.001   0.000   HIS B 308 
 PHE   0.011   0.001   PHE A 287 
 TYR   0.013   0.001   TYR C 123 
 ARG   0.005   0.001   ARG C 373 

*********************** 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
  102 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  169 LYS cc_start: 0.9378 (mptp) cc_final: 0.9024 (mmtp)
REVERT: A  250 ILE cc_start: 0.9118 (tp) cc_final: 0.8888 (pp)
REVERT: B   82 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8371 (tm)
REVERT: B  169 LYS cc_start: 0.9347 (mmtp) cc_final: 0.9059 (mmtp)
REVERT: B  250 ILE cc_start: 0.9068 (tp) cc_final: 0.8841 (pp)
REVERT: C  250 ILE cc_start: 0.9100 (tp) cc_final: 0.8856 (pp)
  outliers start: 8
  outliers final: 3
  residues processed: 99
  average time/residue: 2.1164
  time to fit residues: 221.4994
Evaluate side-chains
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    0.4980
   chunk 23 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 217 GLN
C 258 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.076797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.063806 restraints weight = 39931.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 3.95
r_work: 0.2546 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7914  Z= 0.220
  Angle     :  0.622   7.512  10863  Z= 0.304
  Chirality :  0.041   0.126   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.958  16.499   1053
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 16.79 %
    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 (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:  2.66 (0.27), residues: 990
  helix:  2.18 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.74 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 305 
 HIS   0.002   0.000   HIS A 258 
 PHE   0.011   0.001   PHE C 287 
 TYR   0.013   0.001   TYR C 123 
 ARG   0.004   0.001   ARG C 373 

*********************** 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
  104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  250 ILE cc_start: 0.9123 (tp) cc_final: 0.8891 (pp)
REVERT: B   82 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8402 (tm)
REVERT: B  250 ILE cc_start: 0.9054 (tp) cc_final: 0.8842 (pp)
REVERT: C  250 ILE cc_start: 0.9102 (tp) cc_final: 0.8860 (pp)
  outliers start: 7
  outliers final: 3
  residues processed: 102
  average time/residue: 1.3154
  time to fit residues: 142.0286
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0570
   chunk 27 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 217 GLN
C 258 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.077027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.064322 restraints weight = 33198.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 3.65
r_work: 0.2564 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7914  Z= 0.213
  Angle     :  0.617   7.431  10863  Z= 0.301
  Chirality :  0.041   0.126   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.954  16.654   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 :  0.61 %
    Allowed  : 16.79 %
    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 (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:  2.67 (0.27), residues: 990
  helix:  2.21 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.68 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 305 
 HIS   0.002   0.000   HIS A 258 
 PHE   0.011   0.001   PHE A 300 
 TYR   0.014   0.001   TYR C 123 
 ARG   0.004   0.001   ARG A 373 

********************** 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
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  250 ILE cc_start: 0.9107 (tp) cc_final: 0.8887 (pp)
REVERT: B   82 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8383 (tm)
REVERT: B  250 ILE cc_start: 0.9050 (tp) cc_final: 0.8834 (pp)
REVERT: C  250 ILE cc_start: 0.9092 (tp) cc_final: 0.8858 (pp)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 1.3181
  time to fit residues: 136.4105
Evaluate side-chains
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 15 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0370
   chunk 13 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.077152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.064684 restraints weight = 29627.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 3.45
r_work: 0.2578 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    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 = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7914  Z= 0.213
  Angle     :  0.623   7.377  10863  Z= 0.304
  Chirality :  0.041   0.128   1281
  Planarity :  0.005   0.043   1311
  Dihedral  :  3.945  16.270   1053
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.91 %
    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 (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:  2.68 (0.27), residues: 990
  helix:  2.22 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.67 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 305 
 HIS   0.002   0.000   HIS A 258 
 PHE   0.011   0.001   PHE A 300 
 TYR   0.014   0.001   TYR C 123 
 ARG   0.005   0.001   ARG C 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5205.12 seconds
wall clock time: 92 minutes 56.08 seconds (5576.08 seconds total)