Starting phenix.real_space_refine
on Thu Mar  6 02:14:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uaq_26430/03_2025/7uaq_26430.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uaq_26430/03_2025/7uaq_26430.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2025/7uaq_26430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2025/7uaq_26430.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2025/7uaq_26430.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2025/7uaq_26430.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.035
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      16      5.16       5
     C    2773      2.51       5
     N     723      2.21       5
     O     850      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4362
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2392
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 15, 'TRANS': 279}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 997
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 833
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "L"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.65, per 1000 atoms: 0.84
  Number of scatterers: 4362
  At special positions: 0
  Unit cell: (96.82, 64.89, 89.61, 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      16     16.00
     O     850      8.00
     N     723      7.00
     C    2773      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 165 "
      " NAG A1303 " - " ASN A 282 "
      " NAG B   1 " - " ASN A 122 "
      " NAG C   1 " - " ASN A 149 "
      " NAG D   1 " - " ASN A 234 "
      " NAG L 301 " - " ASN L  20 "
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 529.7 milliseconds
  

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 12 sheets defined
      4.9% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.625A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 26 through 29
      removed outlier: 3.625A  pdb=" N   ASN L  29 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.628A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLU L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 4.319A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS A 206 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55
      removed outlier: 3.501A  pdb=" N   LYS A 278 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104
      removed outlier: 6.301A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117
    Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.693A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER H   7 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 34 through 39
      removed outlier: 7.162A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89
      removed outlier: 3.612A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 119 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 93 through 95
      removed outlier: 3.936A  pdb=" N   ILE H 112 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23
      removed outlier: 3.524A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER L  67 " --> pdb=" O   GLU L  70 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 44 through 50
      removed outlier: 6.653A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   SER L  49 " --> pdb=" O   ILE L  33 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE L  33 " --> pdb=" O   SER L  49 " (cutoff:3.500A)

    91 hydrogen bonds defined for protein.
    231 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: 1.14

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1293
        1.34 -     1.46: 1224
        1.46 -     1.59: 1933
        1.59 -     1.72: 0
        1.72 -     1.84: 22
  Bond restraints: 4472
  Sorted by residual:
  bond pdb=" N   ILE A 233 "
       pdb=" CA  ILE A 233 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.15e-02 7.56e+03 1.02e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.467 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" N   ILE A 197 "
       pdb=" CA  ILE A 197 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.18e-02 7.18e+03 8.87e+00
  bond pdb=" N   ILE A  68 "
       pdb=" CA  ILE A  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 6.85e+00
  bond pdb=" N   GLY L 101 "
       pdb=" CA  GLY L 101 "
    ideal  model  delta    sigma   weight residual
    1.447  1.474 -0.027 1.09e-02 8.42e+03 6.11e+00
  ... (remaining 4467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 5766
        2.49 -     4.99: 266
        4.99 -     7.48: 28
        7.48 -     9.98: 11
        9.98 -    12.47: 2
  Bond angle restraints: 6073
  Sorted by residual:
  angle pdb=" C   ASN A 165 "
        pdb=" CA  ASN A 165 "
        pdb=" CB  ASN A 165 "
      ideal   model   delta    sigma   weight residual
     110.42  122.89  -12.47 1.99e+00 2.53e-01 3.93e+01
  angle pdb=" N   ASN A 122 "
        pdb=" CA  ASN A 122 "
        pdb=" CB  ASN A 122 "
      ideal   model   delta    sigma   weight residual
     110.45  101.66    8.79 1.44e+00 4.82e-01 3.73e+01
  angle pdb=" CA  GLY L 101 "
        pdb=" C   GLY L 101 "
        pdb=" O   GLY L 101 "
      ideal   model   delta    sigma   weight residual
     122.29  117.98    4.31 8.10e-01 1.52e+00 2.83e+01
  angle pdb=" N   ASN A 165 "
        pdb=" CA  ASN A 165 "
        pdb=" CB  ASN A 165 "
      ideal   model   delta    sigma   weight residual
     110.49  101.68    8.81 1.69e+00 3.50e-01 2.72e+01
  angle pdb=" N   ASN L  20 "
        pdb=" CA  ASN L  20 "
        pdb=" CB  ASN L  20 "
      ideal   model   delta    sigma   weight residual
     110.84  104.20    6.64 1.52e+00 4.33e-01 1.91e+01
  ... (remaining 6068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.78: 2435
       14.78 -    29.56: 219
       29.56 -    44.34: 53
       44.34 -    59.13: 28
       59.13 -    73.91: 4
  Dihedral angle restraints: 2739
    sinusoidal: 1197
      harmonic: 1542
  Sorted by residual:
  dihedral pdb=" N   ASN A 122 "
           pdb=" C   ASN A 122 "
           pdb=" CA  ASN A 122 "
           pdb=" CB  ASN A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  110.48   12.32     0      2.50e+00 1.60e-01 2.43e+01
  dihedral pdb=" CA  GLN H  81 "
           pdb=" C   GLN H  81 "
           pdb=" N   MET H  82 "
           pdb=" CA  MET H  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.77  -23.23     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  HIS L  54B"
           pdb=" C   HIS L  54B"
           pdb=" N   THR L  54C"
           pdb=" CA  THR L  54C"
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.31   19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 2736 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 537
       0.078 -    0.155: 128
       0.155 -    0.233: 15
       0.233 -    0.310: 3
       0.310 -    0.388: 4
  Chirality restraints: 687
  Sorted by residual:
  chirality pdb=" C4  NAG C   1 "
            pdb=" C3  NAG C   1 "
            pdb=" C5  NAG C   1 "
            pdb=" O4  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.14   -0.39 2.00e-01 2.50e+01 3.76e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 149 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.75    0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.97e+00
  ... (remaining 684 not shown)

  Planarity restraints: 773
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 165 "    0.010 2.00e-02 2.50e+03   7.50e-02 7.02e+01
        pdb=" CG  ASN A 165 "   -0.093 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 165 "    0.089 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 165 "   -0.078 2.00e-02 2.50e+03
        pdb=" C1  NAG A1302 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 224 "    0.085 5.00e-02 4.00e+02   1.29e-01 2.64e+01
        pdb=" N   PRO A 225 "   -0.222 5.00e-02 4.00e+02
        pdb=" CA  PRO A 225 "    0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO A 225 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 165 "    0.023 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" CG  ASN A 165 "   -0.079 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 165 "    0.030 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 165 "    0.026 2.00e-02 2.50e+03
  ... (remaining 770 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 125
        2.66 -     3.22: 4192
        3.22 -     3.78: 6567
        3.78 -     4.34: 9038
        4.34 -     4.90: 14761
  Nonbonded interactions: 34683
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN L   6 "
            pdb=" OG1 THR L 102 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OG1 THR L  22 "
            pdb=" OE2 GLU L  70 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OE2 GLU A  96 "
            pdb=" N   ASN A  99 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" O   SER H  30 "
            pdb=" OG1 THR H  52A"
     model   vdw
     2.174 3.040
  nonbonded pdb=" OE1 GLN A  14 "
            pdb=" NH1 ARG A 158 "
     model   vdw
     2.210 3.120
  ... (remaining 34678 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.630
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
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   0.061   4472  Z= 0.399
  Angle     :  1.187  12.470   6073  Z= 0.662
  Chirality :  0.071   0.388    687
  Planarity :  0.008   0.129    766
  Dihedral  : 13.129  73.906   1740
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 25.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.86 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.41 %
  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: -2.56 (0.35), residues: 523
  helix: -0.03 (1.56), residues: 11
  sheet: -0.76 (0.46), residues: 139
  loop : -2.30 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 152 
 HIS   0.008   0.002   HIS H 106 
 PHE   0.032   0.003   PHE L  72 
 TYR   0.032   0.002   TYR A 144 
 ARG   0.007   0.001   ARG A 319 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8027 (tm-30)
REVERT: A  158 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8067 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8320 (p0) cc_final: 0.8032 (p0)
REVERT: A  314 GLN cc_start: 0.6398 (tp40) cc_final: 0.6067 (tp40)
REVERT: H   38 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.6051 (ttm-80)
REVERT: H   67 PHE cc_start: 0.7819 (m-80) cc_final: 0.7310 (m-80)
REVERT: H   97 TYR cc_start: 0.7891 (t80) cc_final: 0.7566 (t80)
REVERT: L   72 PHE cc_start: 0.7263 (m-10) cc_final: 0.6951 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1557
  time to fit residues: 26.1523
Evaluate side-chains
  87 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.117200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.093274 restraints weight = 10770.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 4.97
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   4472  Z= 0.297
  Angle     :  0.868  11.775   6073  Z= 0.442
  Chirality :  0.055   0.355    687
  Planarity :  0.006   0.067    766
  Dihedral  :  8.570  57.436    794
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.74 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.41 (0.34), residues: 523
  helix:  0.89 (1.65), residues: 11
  sheet: -0.70 (0.43), residues: 145
  loop : -2.23 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  35 
 HIS   0.006   0.002   HIS H  98 
 PHE   0.025   0.002   PHE A 238 
 TYR   0.026   0.002   TYR H  50 
 ARG   0.007   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8222 (tm-30)
REVERT: A  190 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7470 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8689 (p0) cc_final: 0.8454 (p0)
REVERT: A  298 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6341 (pt0)
REVERT: A  314 GLN cc_start: 0.6844 (tp40) cc_final: 0.6337 (tp40)
REVERT: H  107 SER cc_start: 0.7248 (p) cc_final: 0.6807 (p)
REVERT: L    4 LEU cc_start: 0.7529 (pt) cc_final: 0.7153 (pt)
REVERT: L   85 ASP cc_start: 0.7640 (m-30) cc_final: 0.7005 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 107
  average time/residue: 0.2075
  time to fit residues: 27.7666
Evaluate side-chains
  101 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 GLN
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.115610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.091542 restraints weight = 10900.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 5.00
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4472  Z= 0.259
  Angle     :  0.781   9.286   6073  Z= 0.396
  Chirality :  0.051   0.324    687
  Planarity :  0.005   0.051    766
  Dihedral  :  7.888  57.063    792
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 14.25 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.22 (0.35), residues: 523
  helix:  1.36 (1.85), residues: 11
  sheet: -0.50 (0.44), residues: 147
  loop : -2.15 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  36 
 HIS   0.005   0.001   HIS H  98 
 PHE   0.013   0.002   PHE A 238 
 TYR   0.021   0.002   TYR H  50 
 ARG   0.015   0.001   ARG L 103 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8222 (tm-30)
REVERT: A  132 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: A  153 MET cc_start: 0.7532 (ptt) cc_final: 0.7227 (ptt)
REVERT: A  185 ASN cc_start: 0.8626 (p0) cc_final: 0.8123 (p0)
REVERT: A  190 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7472 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8813 (p0) cc_final: 0.8605 (p0)
REVERT: A  298 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6291 (pt0)
REVERT: A  314 GLN cc_start: 0.6882 (tp40) cc_final: 0.6607 (tp40)
REVERT: H   45 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8009 (pp)
REVERT: H  107 SER cc_start: 0.7290 (p) cc_final: 0.6893 (p)
REVERT: L    4 LEU cc_start: 0.7558 (pt) cc_final: 0.7213 (pt)
REVERT: L   39 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7569 (tm-30)
REVERT: L   42 LYS cc_start: 0.8531 (mppt) cc_final: 0.7926 (mmtm)
REVERT: L   70 GLU cc_start: 0.7797 (pp20) cc_final: 0.7220 (pp20)
REVERT: L   72 PHE cc_start: 0.7311 (m-80) cc_final: 0.6721 (t80)
REVERT: L   85 ASP cc_start: 0.7681 (m-30) cc_final: 0.7467 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.3561
  time to fit residues: 50.3188
Evaluate side-chains
  109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  106 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** 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 = 0.3959 r_free = 0.3959 target = 0.114000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.089712 restraints weight = 11000.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 5.15
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4472  Z= 0.257
  Angle     :  0.738   9.313   6073  Z= 0.372
  Chirality :  0.050   0.327    687
  Planarity :  0.005   0.049    766
  Dihedral  :  7.476  56.792    792
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.37 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 13.82 %
    Favored  : 80.78 %
  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: -2.13 (0.35), residues: 523
  helix:  1.43 (1.85), residues: 11
  sheet: -0.49 (0.44), residues: 147
  loop : -2.05 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  36 
 HIS   0.006   0.002   HIS H  98 
 PHE   0.012   0.002   PHE A 238 
 TYR   0.022   0.002   TYR H  50 
 ARG   0.005   0.001   ARG L 103 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: A  132 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7608 (tm-30)
REVERT: A  190 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7559 (mtt-85)
REVERT: A  298 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6275 (pt0)
REVERT: A  314 GLN cc_start: 0.6961 (tp40) cc_final: 0.6669 (tp40)
REVERT: H   45 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7814 (pp)
REVERT: H   57 ARG cc_start: 0.8361 (mmt-90) cc_final: 0.7898 (mmt-90)
REVERT: H   72 ASP cc_start: 0.7233 (p0) cc_final: 0.6988 (p0)
REVERT: L    4 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7265 (pt)
REVERT: L   39 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7637 (tm-30)
REVERT: L   45 ARG cc_start: 0.7398 (mtm110) cc_final: 0.7142 (ttp-110)
REVERT: L   70 GLU cc_start: 0.7845 (pp20) cc_final: 0.6947 (pp20)
REVERT: L  103 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8249 (mmm160)
  outliers start: 25
  outliers final: 15
  residues processed: 112
  average time/residue: 0.2406
  time to fit residues: 34.8495
Evaluate side-chains
  113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 41 optimal weight:    0.4980
   chunk 1 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 GLN
** H   3 GLN ** 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 = 0.3951 r_free = 0.3951 target = 0.114084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.089787 restraints weight = 10991.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 5.05
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4472  Z= 0.233
  Angle     :  0.716   9.351   6073  Z= 0.363
  Chirality :  0.049   0.334    687
  Planarity :  0.005   0.048    766
  Dihedral  :  7.216  56.621    792
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 15.77 %
    Favored  : 79.48 %
  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: -2.07 (0.35), residues: 523
  helix:  1.55 (1.89), residues: 11
  sheet: -0.53 (0.44), residues: 147
  loop : -1.97 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 258 
 HIS   0.006   0.001   HIS H  98 
 PHE   0.010   0.002   PHE A 238 
 TYR   0.019   0.002   TYR H  50 
 ARG   0.004   0.000   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: A   69 HIS cc_start: 0.8082 (t-90) cc_final: 0.7830 (t-90)
REVERT: A  115 GLN cc_start: 0.8787 (mm110) cc_final: 0.8542 (mm-40)
REVERT: A  132 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7683 (tm-30)
REVERT: A  190 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7670 (mtt-85)
REVERT: A  294 ASP cc_start: 0.8093 (m-30) cc_final: 0.7885 (t0)
REVERT: A  298 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6160 (pt0)
REVERT: A  314 GLN cc_start: 0.7040 (tp40) cc_final: 0.6751 (tp40)
REVERT: H   57 ARG cc_start: 0.8408 (mmt-90) cc_final: 0.7920 (mmt-90)
REVERT: L    4 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7305 (pt)
REVERT: L   39 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7605 (tm-30)
REVERT: L   45 ARG cc_start: 0.7453 (mtm110) cc_final: 0.7178 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8090 (pp20) cc_final: 0.7474 (pp20)
REVERT: L  103 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8139 (mmm160)
  outliers start: 22
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1951
  time to fit residues: 26.5931
Evaluate side-chains
  110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** 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 = 0.3866 r_free = 0.3866 target = 0.108055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.083412 restraints weight = 10897.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 4.98
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074   4472  Z= 0.489
  Angle     :  0.809   9.293   6073  Z= 0.414
  Chirality :  0.051   0.309    687
  Planarity :  0.005   0.050    766
  Dihedral  :  7.671  55.817    792
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.33 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 16.20 %
    Favored  : 79.48 %
  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: -2.26 (0.35), residues: 523
  helix:  1.54 (1.88), residues: 11
  sheet: -0.80 (0.42), residues: 156
  loop : -2.06 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 258 
 HIS   0.007   0.002   HIS A  66 
 PHE   0.011   0.002   PHE A 238 
 TYR   0.020   0.002   TYR H  50 
 ARG   0.006   0.001   ARG A 319 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8336 (tm-30)
REVERT: A   53 ASP cc_start: 0.8583 (t0) cc_final: 0.8374 (t70)
REVERT: A  115 GLN cc_start: 0.8832 (mm110) cc_final: 0.8578 (mm-40)
REVERT: A  190 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7504 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8633 (p0) cc_final: 0.8421 (p0)
REVERT: A  314 GLN cc_start: 0.7278 (tp40) cc_final: 0.7029 (tp40)
REVERT: H   57 ARG cc_start: 0.8446 (mmt-90) cc_final: 0.7876 (mmt-90)
REVERT: H   82 MET cc_start: 0.7492 (tpt) cc_final: 0.7159 (tpt)
REVERT: L    4 LEU cc_start: 0.7757 (pt) cc_final: 0.7468 (pt)
REVERT: L   39 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7776 (tm-30)
REVERT: L   45 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7463 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8141 (pp20) cc_final: 0.7445 (pp20)
REVERT: L  103 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8177 (mmm160)
  outliers start: 20
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1886
  time to fit residues: 23.6400
Evaluate side-chains
  112 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   79 TYR
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0570
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:    0.1980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** 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 = 0.3924 r_free = 0.3924 target = 0.111933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.087310 restraints weight = 10842.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 5.07
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4472  Z= 0.216
  Angle     :  0.728   9.405   6073  Z= 0.368
  Chirality :  0.049   0.329    687
  Planarity :  0.004   0.051    766
  Dihedral  :  7.345  56.704    792
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.99 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.93 %
    Favored  : 78.40 %
  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: -2.12 (0.36), residues: 523
  helix:  1.41 (1.85), residues: 11
  sheet: -0.71 (0.43), residues: 153
  loop : -1.94 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  36 
 HIS   0.006   0.001   HIS H  98 
 PHE   0.019   0.002   PHE H  67 
 TYR   0.018   0.002   TYR H  50 
 ARG   0.004   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: A  115 GLN cc_start: 0.8903 (mm110) cc_final: 0.8628 (mm-40)
REVERT: A  132 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: A  190 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7494 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8664 (p0) cc_final: 0.8413 (p0)
REVERT: A  314 GLN cc_start: 0.7128 (tp40) cc_final: 0.6869 (tp40)
REVERT: H   57 ARG cc_start: 0.8259 (mmt-90) cc_final: 0.7799 (mmt-90)
REVERT: H   76 ASN cc_start: 0.7856 (t0) cc_final: 0.7594 (t0)
REVERT: H   99 TYR cc_start: 0.8997 (t80) cc_final: 0.8725 (t80)
REVERT: H  115 GLN cc_start: 0.8786 (mp10) cc_final: 0.8554 (mp10)
REVERT: L    4 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7156 (pt)
REVERT: L   39 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7715 (tm-30)
REVERT: L   45 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7338 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8181 (pp20) cc_final: 0.7549 (pp20)
REVERT: L  103 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8157 (mmm160)
  outliers start: 17
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2005
  time to fit residues: 27.7521
Evaluate side-chains
  109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   79 TYR
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.111450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.086922 restraints weight = 10691.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 5.03
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4472  Z= 0.227
  Angle     :  0.708   9.428   6073  Z= 0.357
  Chirality :  0.049   0.343    687
  Planarity :  0.004   0.049    766
  Dihedral  :  7.184  56.218    792
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.56 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 19.01 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.36), residues: 523
  helix:  1.57 (1.87), residues: 11
  sheet: -0.65 (0.43), residues: 153
  loop : -1.86 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  36 
 HIS   0.005   0.001   HIS H  98 
 PHE   0.010   0.001   PHE A 318 
 TYR   0.017   0.002   TYR H  50 
 ARG   0.004   0.000   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: A  115 GLN cc_start: 0.8929 (mm110) cc_final: 0.8669 (mm-40)
REVERT: A  132 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7747 (tm-30)
REVERT: A  173 GLN cc_start: 0.8508 (tp40) cc_final: 0.8066 (tp40)
REVERT: A  190 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7493 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8696 (p0) cc_final: 0.8473 (p0)
REVERT: A  314 GLN cc_start: 0.7125 (tp40) cc_final: 0.6884 (tp40)
REVERT: H   57 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7850 (mmt-90)
REVERT: H   76 ASN cc_start: 0.7701 (t0) cc_final: 0.7432 (t0)
REVERT: H   99 TYR cc_start: 0.9016 (t80) cc_final: 0.8705 (t80)
REVERT: H  115 GLN cc_start: 0.8746 (mp10) cc_final: 0.8506 (mp10)
REVERT: L    4 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7056 (pt)
REVERT: L   39 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7712 (tm-30)
REVERT: L   45 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7388 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8201 (pp20) cc_final: 0.7621 (pp20)
  outliers start: 18
  outliers final: 13
  residues processed: 106
  average time/residue: 0.2048
  time to fit residues: 27.5551
Evaluate side-chains
  108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   79 TYR
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** 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 = 0.3891 r_free = 0.3891 target = 0.109990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.085312 restraints weight = 10887.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 5.06
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4472  Z= 0.302
  Angle     :  0.744   9.436   6073  Z= 0.378
  Chirality :  0.049   0.345    687
  Planarity :  0.005   0.050    766
  Dihedral  :  7.283  56.060    792
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.94 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.52 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.36), residues: 523
  helix:  1.58 (1.88), residues: 11
  sheet: -0.67 (0.42), residues: 158
  loop : -1.83 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 258 
 HIS   0.006   0.001   HIS H  98 
 PHE   0.019   0.002   PHE H  67 
 TYR   0.020   0.002   TYR H  50 
 ARG   0.004   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: A  115 GLN cc_start: 0.8935 (mm110) cc_final: 0.8672 (mm-40)
REVERT: A  173 GLN cc_start: 0.8575 (tp40) cc_final: 0.8141 (tp40)
REVERT: A  190 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7707 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8750 (p0) cc_final: 0.8526 (p0)
REVERT: A  314 GLN cc_start: 0.7163 (tp40) cc_final: 0.6936 (tp40)
REVERT: H   69 ILE cc_start: 0.8415 (tp) cc_final: 0.7788 (tt)
REVERT: H   72 ASP cc_start: 0.8143 (p0) cc_final: 0.7589 (p0)
REVERT: H   76 ASN cc_start: 0.7865 (t0) cc_final: 0.7533 (t0)
REVERT: H   99 TYR cc_start: 0.9012 (t80) cc_final: 0.8666 (t80)
REVERT: H  115 GLN cc_start: 0.8745 (mp10) cc_final: 0.8421 (mp10)
REVERT: L    4 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7138 (pt)
REVERT: L   39 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7790 (tm-30)
REVERT: L   45 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7444 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8220 (pp20) cc_final: 0.7570 (pp20)
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1635
  time to fit residues: 22.0175
Evaluate side-chains
  108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 49 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 25 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** 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 = 0.3888 r_free = 0.3888 target = 0.110741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.086099 restraints weight = 10556.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 4.98
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.5073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4472  Z= 0.246
  Angle     :  0.745   9.434   6073  Z= 0.379
  Chirality :  0.049   0.340    687
  Planarity :  0.005   0.050    766
  Dihedral  :  7.268  56.269    792
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.38 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.36), residues: 523
  helix:  1.47 (1.87), residues: 11
  sheet: -0.81 (0.42), residues: 144
  loop : -1.77 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  36 
 HIS   0.005   0.001   HIS H 106 
 PHE   0.011   0.001   PHE A 318 
 TYR   0.019   0.002   TYR H 100 
 ARG   0.004   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: A  115 GLN cc_start: 0.8947 (mm110) cc_final: 0.8661 (mm-40)
REVERT: A  173 GLN cc_start: 0.8530 (tp40) cc_final: 0.8137 (tp40)
REVERT: A  190 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7672 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8801 (p0) cc_final: 0.8551 (p0)
REVERT: A  314 GLN cc_start: 0.7140 (tp40) cc_final: 0.6906 (tp40)
REVERT: H   57 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.8271 (mmt-90)
REVERT: H   58 TYR cc_start: 0.8282 (m-80) cc_final: 0.7884 (m-80)
REVERT: H   72 ASP cc_start: 0.8168 (p0) cc_final: 0.7633 (p0)
REVERT: H   76 ASN cc_start: 0.7806 (t0) cc_final: 0.7545 (t0)
REVERT: H   97 TYR cc_start: 0.8602 (t80) cc_final: 0.8076 (t80)
REVERT: H   99 TYR cc_start: 0.8994 (t80) cc_final: 0.8621 (t80)
REVERT: L    4 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7042 (pt)
REVERT: L   39 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7776 (tm-30)
REVERT: L   45 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7431 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8234 (pp20) cc_final: 0.7727 (pp20)
  outliers start: 15
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1716
  time to fit residues: 22.2125
Evaluate side-chains
  105 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** 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 = 0.3893 r_free = 0.3893 target = 0.109811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.085504 restraints weight = 10799.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 4.98
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.5191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4472  Z= 0.289
  Angle     :  0.761   9.609   6073  Z= 0.383
  Chirality :  0.049   0.345    687
  Planarity :  0.005   0.051    766
  Dihedral  :  7.281  55.934    792
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.95 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.36), residues: 523
  helix:  1.70 (1.90), residues: 11
  sheet: -0.71 (0.42), residues: 153
  loop : -1.78 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  36 
 HIS   0.006   0.001   HIS H 106 
 PHE   0.010   0.002   PHE A 318 
 TYR   0.019   0.002   TYR H 100 
 ARG   0.005   0.001   ARG H  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2519.41 seconds
wall clock time: 46 minutes 27.86 seconds (2787.86 seconds total)