Starting phenix.real_space_refine
on Thu Jul 24 22:58:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bei_44479/07_2025/9bei_44479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bei_44479/07_2025/9bei_44479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bei_44479/07_2025/9bei_44479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bei_44479/07_2025/9bei_44479.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bei_44479/07_2025/9bei_44479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bei_44479/07_2025/9bei_44479.cif"
  }
  resolution = 4.16
  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=  -0.000 sd=   0.006
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      22      5.16       5
     C    4174      2.51       5
     N    1133      2.21       5
     O    1320      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6649
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1456
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 5, 'TRANS': 179}
    Chain: "B"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 942
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "H"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1694
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 11, 'TRANS': 214}
    Chain: "K"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 917
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1640
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 11, 'TRANS': 202}
  Time building chain proxies: 5.16, per 1000 atoms: 0.78
  Number of scatterers: 6649
  At special positions: 0
  Unit cell: (68.952, 91.936, 152.048, 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      22     16.00
     O    1320      8.00
     N    1133      7.00
     C    4174      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  64 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  48 " - pdb=" SG  CYS H 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 179 " - pdb=" SG  CYS H 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  48 " - pdb=" SG  CYS L 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 160 " - pdb=" SG  CYS L 220 " 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
  Time building additional restraints: 1.65
  Conformation dependent library (CDL) restraints added in 966.7 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 15 sheets defined
      18.6% alpha, 31.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 27
    Processing helix  chain 'A' and resid 74 through 101
    Processing helix  chain 'A' and resid 110 through 149
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 161 through 184
      removed outlier: 3.562A  pdb=" N   ALA A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 218
      removed outlier: 3.542A  pdb=" N   ASN B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 270
    Processing helix  chain 'H' and resid 225 through 231
      removed outlier: 3.686A  pdb=" N   THR H 230 " --> pdb=" O   SER H 226 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 240 through 243
    Processing helix  chain 'K' and resid 87 through 91
      removed outlier: 4.046A  pdb=" N   THR K  91 " --> pdb=" O   PRO K  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 147 through 154
    Processing helix  chain 'L' and resid 209 through 215
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66
    Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210
      removed outlier: 5.399A  pdb=" N   SER B 265 " --> pdb=" O   LYS B 273 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LYS B 273 " --> pdb=" O   SER B 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 227
    Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 33
      removed outlier: 4.089A  pdb=" N   GLN H  29 " --> pdb=" O   SER H  51 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER H  33 " --> pdb=" O   SER H  47 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   SER H  47 " --> pdb=" O   SER H  33 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 84 through 86
      removed outlier: 6.833A  pdb=" N   TRP H  62 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   SER H  76 " --> pdb=" O   ILE H  60 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   ILE H  60 " --> pdb=" O   SER H  76 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 163
      removed outlier: 3.630A  pdb=" N   SER H 159 " --> pdb=" O   LYS H 182 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   CYS H 179 " --> pdb=" O   SER H 219 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER H 219 " --> pdb=" O   CYS H 179 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL H 220 " --> pdb=" O   HIS H 203 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   HIS H 203 " --> pdb=" O   VAL H 220 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 159 through 163
      removed outlier: 3.630A  pdb=" N   SER H 159 " --> pdb=" O   LYS H 182 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   LYS H 182 " --> pdb=" O   LEU H 217 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   LEU H 217 " --> pdb=" O   LYS H 182 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR H 184 " --> pdb=" O   TYR H 215 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 190 through 194
      removed outlier: 3.839A  pdb=" N   ASN H 236 " --> pdb=" O   SER H 192 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ASN H 194 " --> pdb=" O   ILE H 234 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   ILE H 234 " --> pdb=" O   ASN H 194 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 3 through 8
    Processing sheet with id=AB1, first strand: chain 'K' and resid 59 through 60
      removed outlier: 5.418A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   MET K  34 " --> pdb=" O   ALA K  51 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 29 through 31
    Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37
      removed outlier: 6.269A  pdb=" N   LEU L  36 " --> pdb=" O   GLU L 131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'L' and resid 78 through 79
      removed outlier: 3.597A  pdb=" N   TYR L  74 " --> pdb=" O   SER L  78 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   TRP L  60 " --> pdb=" O   LEU L  72 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR L 123 " --> pdb=" O   GLN L 115 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 140 through 141
      removed outlier: 5.719A  pdb=" N   TYR L 199 " --> pdb=" O   ASN L 164 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 171 through 174
      removed outlier: 3.785A  pdb=" N   LYS L 171 " --> pdb=" O   THR L 223 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR L 223 " --> pdb=" O   LYS L 171 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN L 173 " --> pdb=" O   GLU L 221 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU L 221 " --> pdb=" O   GLN L 173 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL L 231 " --> pdb=" O   VAL L 222 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    774 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: 1.77

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2177
        1.34 -     1.46: 1660
        1.46 -     1.58: 2919
        1.58 -     1.70: 0
        1.70 -     1.82: 32
  Bond restraints: 6788
  Sorted by residual:
  bond pdb=" CA  CYS A  64 "
       pdb=" CB  CYS A  64 "
    ideal  model  delta    sigma   weight residual
    1.531  1.556 -0.025 1.83e-02 2.99e+03 1.85e+00
  bond pdb=" CB  CYS A  54 "
       pdb=" SG  CYS A  54 "
    ideal  model  delta    sigma   weight residual
    1.808  1.766  0.042 3.30e-02 9.18e+02 1.59e+00
  bond pdb=" C   CYS A  64 "
       pdb=" N   LYS A  65 "
    ideal  model  delta    sigma   weight residual
    1.331  1.348 -0.017 1.41e-02 5.03e+03 1.43e+00
  bond pdb=" CG  MET A  52 "
       pdb=" SD  MET A  52 "
    ideal  model  delta    sigma   weight residual
    1.803  1.776  0.027 2.50e-02 1.60e+03 1.13e+00
  bond pdb=" CG  LYS L  64 "
       pdb=" CD  LYS L  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.06e+00
  ... (remaining 6783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 9077
        2.60 -     5.21: 118
        5.21 -     7.81: 17
        7.81 -    10.41: 1
       10.41 -    13.01: 1
  Bond angle restraints: 9214
  Sorted by residual:
  angle pdb=" CA  CYS A  54 "
        pdb=" CB  CYS A  54 "
        pdb=" SG  CYS A  54 "
      ideal   model   delta    sigma   weight residual
     114.40  127.41  -13.01 2.30e+00 1.89e-01 3.20e+01
  angle pdb=" CG  MET A  52 "
        pdb=" SD  MET A  52 "
        pdb=" CE  MET A  52 "
      ideal   model   delta    sigma   weight residual
     100.90   93.69    7.21 2.20e+00 2.07e-01 1.07e+01
  angle pdb=" CB  LYS L  64 "
        pdb=" CG  LYS L  64 "
        pdb=" CD  LYS L  64 "
      ideal   model   delta    sigma   weight residual
     111.30  118.83   -7.53 2.30e+00 1.89e-01 1.07e+01
  angle pdb=" N   ALA L 109 "
        pdb=" CA  ALA L 109 "
        pdb=" C   ALA L 109 "
      ideal   model   delta    sigma   weight residual
     107.93  113.29   -5.36 1.65e+00 3.67e-01 1.05e+01
  angle pdb=" C   GLY K   8 "
        pdb=" N   GLY K   9 "
        pdb=" CA  GLY K   9 "
      ideal   model   delta    sigma   weight residual
     121.87  116.81    5.06 1.64e+00 3.72e-01 9.52e+00
  ... (remaining 9209 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 3651
       17.16 -    34.32: 336
       34.32 -    51.48: 55
       51.48 -    68.64: 12
       68.64 -    85.80: 13
  Dihedral angle restraints: 4067
    sinusoidal: 1565
      harmonic: 2502
  Sorted by residual:
  dihedral pdb=" CA  PHE H 185 "
           pdb=" C   PHE H 185 "
           pdb=" N   PRO H 186 "
           pdb=" CA  PRO H 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.35  -55.65     0      5.00e+00 4.00e-02 1.24e+02
  dihedral pdb=" CA  TYR H 129 "
           pdb=" C   TYR H 129 "
           pdb=" N   ASN H 130 "
           pdb=" CA  ASN H 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.89   44.11     0      5.00e+00 4.00e-02 7.78e+01
  dihedral pdb=" CA  ALA L 109 "
           pdb=" C   ALA L 109 "
           pdb=" N   THR L 110 "
           pdb=" CA  THR L 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.29   42.71     0      5.00e+00 4.00e-02 7.30e+01
  ... (remaining 4064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 868
       0.061 -    0.121: 141
       0.121 -    0.182: 13
       0.182 -    0.242: 1
       0.242 -    0.303: 1
  Chirality restraints: 1024
  Sorted by residual:
  chirality pdb=" CB  ILE B 258 "
            pdb=" CA  ILE B 258 "
            pdb=" CG1 ILE B 258 "
            pdb=" CG2 ILE B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  GLN L 225 "
            pdb=" N   GLN L 225 "
            pdb=" C   GLN L 225 "
            pdb=" CB  GLN L 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.36e-01
  chirality pdb=" CA  CYS A  54 "
            pdb=" N   CYS A  54 "
            pdb=" C   CYS A  54 "
            pdb=" CB  CYS A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.87e-01
  ... (remaining 1021 not shown)

  Planarity restraints: 1188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 185 "    0.086 5.00e-02 4.00e+02   1.31e-01 2.76e+01
        pdb=" N   PRO H 186 "   -0.227 5.00e-02 4.00e+02
        pdb=" CA  PRO H 186 "    0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO H 186 "    0.068 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 185 "    0.012 2.00e-02 2.50e+03   1.53e-02 4.10e+00
        pdb=" CG  PHE H 185 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 185 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 185 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 185 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 185 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 185 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 272 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.74e+00
        pdb=" C   VAL B 272 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   VAL B 272 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 273 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1185 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 108
        2.59 -     3.17: 6061
        3.17 -     3.75: 11137
        3.75 -     4.32: 14400
        4.32 -     4.90: 22832
  Nonbonded interactions: 54538
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN H 130 "
            pdb=" O   TYR H 134 "
     model   vdw
     2.016 3.120
  nonbonded pdb=" OG1 THR H 174 "
            pdb=" OG1 THR H 222 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ALA B 214 "
            pdb=" OG  SER B 217 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   GLY A  49 "
            pdb=" OH  TYR A  67 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR A  45 "
            pdb=" O   VAL A  56 "
     model   vdw
     2.257 3.040
  ... (remaining 54533 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.690
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.390
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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      :  0.003   0.042   6794  Z= 0.162
  Angle     :  0.785  13.013   9226  Z= 0.427
  Chirality :  0.046   0.303   1024
  Planarity :  0.006   0.131   1188
  Dihedral  : 14.426  85.803   2447
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.15 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.49 %

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: -1.93 (0.28), residues: 852
  helix:  1.66 (0.42), residues: 152
  sheet: -0.98 (0.30), residues: 293
  loop : -2.75 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  51 
 HIS   0.003   0.001   HIS L 224 
 PHE   0.035   0.002   PHE H 185 
 TYR   0.025   0.002   TYR A  67 
 ARG   0.006   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13694 (  281)
  hydrogen bonds       : angle       7.12199 (  774)
  SS BOND              : bond        0.00639 (    6)
  SS BOND              : angle       2.21915 (   12)
  covalent geometry    : bond        0.00317 ( 6788)
  covalent geometry    : angle       0.78165 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7921 (mm) cc_final: 0.7393 (tp)
REVERT: B  298 LEU cc_start: 0.8955 (tp) cc_final: 0.8117 (tp)
REVERT: L  112 TYR cc_start: 0.7623 (m-80) cc_final: 0.7209 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2402
  time to fit residues: 19.3565
Evaluate side-chains
  48 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 225 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 = 0.4013 r_free = 0.4013 target = 0.093513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.070144 restraints weight = 47930.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.070641 restraints weight = 33696.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.071209 restraints weight = 26433.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6794  Z= 0.146
  Angle     :  0.668   8.650   9226  Z= 0.349
  Chirality :  0.045   0.245   1024
  Planarity :  0.006   0.117   1188
  Dihedral  :  6.657  56.983    944
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.15 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.49 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.28), residues: 852
  helix:  1.76 (0.42), residues: 152
  sheet: -0.87 (0.28), residues: 309
  loop : -2.72 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  62 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.012   0.002   PHE H 185 
 TYR   0.019   0.002   TYR H 136 
 ARG   0.006   0.001   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  281)
  hydrogen bonds       : angle       6.02698 (  774)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       1.87504 (   12)
  covalent geometry    : bond        0.00314 ( 6788)
  covalent geometry    : angle       0.66528 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7957 (mm) cc_final: 0.7526 (tp)
REVERT: B  298 LEU cc_start: 0.8999 (tp) cc_final: 0.8085 (tp)
REVERT: L  112 TYR cc_start: 0.7712 (m-80) cc_final: 0.7270 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2112
  time to fit residues: 17.5447
Evaluate side-chains
  49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 80 optimal weight:    0.0470
   chunk 7 optimal weight:    0.0770
   chunk 15 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8038

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

Flipped N/Q/H residues before XYZ refinement:
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 225 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 = 0.4025 r_free = 0.4025 target = 0.093599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.070366 restraints weight = 48366.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.071251 restraints weight = 32760.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.071933 restraints weight = 25455.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6794  Z= 0.127
  Angle     :  0.640   7.950   9226  Z= 0.332
  Chirality :  0.044   0.217   1024
  Planarity :  0.005   0.111   1188
  Dihedral  :  6.314  53.738    944
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.51 %
    Favored  : 94.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.49 %

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: -1.63 (0.28), residues: 852
  helix:  1.91 (0.42), residues: 152
  sheet: -0.88 (0.28), residues: 328
  loop : -2.60 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  73 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.011   0.001   PHE L 108 
 TYR   0.012   0.001   TYR L  80 
 ARG   0.006   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03322 (  281)
  hydrogen bonds       : angle       5.78479 (  774)
  SS BOND              : bond        0.00559 (    6)
  SS BOND              : angle       1.70591 (   12)
  covalent geometry    : bond        0.00272 ( 6788)
  covalent geometry    : angle       0.63739 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7910 (mm) cc_final: 0.7482 (tp)
REVERT: B  298 LEU cc_start: 0.9039 (tp) cc_final: 0.8281 (tp)
REVERT: K   76 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7908 (mmmt)
REVERT: L  187 GLU cc_start: 0.8505 (pp20) cc_final: 0.8249 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 62
  average time/residue: 0.2158
  time to fit residues: 17.8569
Evaluate side-chains
  50 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.1744

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

Flipped N/Q/H residues before XYZ refinement:
B 218 ASN
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 130 ASN
** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 225 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 = 0.4014 r_free = 0.4014 target = 0.092937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.069501 restraints weight = 49043.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.070640 restraints weight = 33557.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071006 restraints weight = 26800.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6794  Z= 0.143
  Angle     :  0.671   9.188   9226  Z= 0.345
  Chirality :  0.045   0.256   1024
  Planarity :  0.006   0.128   1188
  Dihedral  :  6.411  55.757    944
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.49 %

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: -1.68 (0.28), residues: 852
  helix:  1.73 (0.42), residues: 152
  sheet: -0.98 (0.27), residues: 349
  loop : -2.55 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  73 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.045   0.002   PHE H 185 
 TYR   0.015   0.001   TYR B 306 
 ARG   0.006   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  281)
  hydrogen bonds       : angle       5.78543 (  774)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       1.74934 (   12)
  covalent geometry    : bond        0.00307 ( 6788)
  covalent geometry    : angle       0.66804 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  298 LEU cc_start: 0.9019 (tp) cc_final: 0.8266 (tp)
REVERT: K   76 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7871 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2303
  time to fit residues: 17.6618
Evaluate side-chains
  47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0470
   chunk 6 optimal weight:    4.9990
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.8682

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

Flipped N/Q/H residues before XYZ refinement:
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 103 ASN
** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 210 GLN
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 225 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 = 0.4031 r_free = 0.4031 target = 0.093683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.070516 restraints weight = 47671.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.071430 restraints weight = 32044.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.072100 restraints weight = 25261.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6794  Z= 0.127
  Angle     :  0.665   8.787   9226  Z= 0.340
  Chirality :  0.045   0.266   1024
  Planarity :  0.005   0.121   1188
  Dihedral  :  6.282  53.678    944
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.69 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.86 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.49 %

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: -1.61 (0.28), residues: 852
  helix:  1.78 (0.42), residues: 152
  sheet: -0.90 (0.28), residues: 326
  loop : -2.47 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  73 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.024   0.001   PHE H 185 
 TYR   0.018   0.001   TYR B 306 
 ARG   0.008   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  281)
  hydrogen bonds       : angle       5.60292 (  774)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       1.77628 (   12)
  covalent geometry    : bond        0.00270 ( 6788)
  covalent geometry    : angle       0.66192 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  298 LEU cc_start: 0.9049 (tp) cc_final: 0.8319 (tp)
REVERT: K   76 LYS cc_start: 0.8176 (mmpt) cc_final: 0.7874 (mmmt)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2155
  time to fit residues: 17.2260
Evaluate side-chains
  47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 74 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    0.4980
   chunk 64 optimal weight:    0.0010
   chunk 30 optimal weight:    0.0070
   chunk 40 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.3204

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

Flipped N/Q/H residues before XYZ refinement:
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 130 ASN
H 194 ASN
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 224 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.096430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.073102 restraints weight = 46663.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.073694 restraints weight = 32044.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.074614 restraints weight = 25221.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6794  Z= 0.114
  Angle     :  0.658   9.569   9226  Z= 0.336
  Chirality :  0.044   0.255   1024
  Planarity :  0.005   0.116   1188
  Dihedral  :  5.910  50.006    944
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.51 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.36 %

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: -1.44 (0.29), residues: 852
  helix:  2.19 (0.43), residues: 146
  sheet: -0.84 (0.28), residues: 332
  loop : -2.40 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 128 
 HIS   0.005   0.001   HIS B 241 
 PHE   0.019   0.001   PHE H 185 
 TYR   0.017   0.001   TYR H 136 
 ARG   0.004   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03008 (  281)
  hydrogen bonds       : angle       5.36450 (  774)
  SS BOND              : bond        0.00766 (    6)
  SS BOND              : angle       1.59041 (   12)
  covalent geometry    : bond        0.00237 ( 6788)
  covalent geometry    : angle       0.65574 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  298 LEU cc_start: 0.9026 (tp) cc_final: 0.8432 (tp)
REVERT: K   18 LEU cc_start: 0.8755 (tp) cc_final: 0.8489 (tt)
REVERT: K   76 LYS cc_start: 0.8124 (mmpt) cc_final: 0.7861 (mmmt)
REVERT: L  171 LYS cc_start: 0.7704 (ptpt) cc_final: 0.7420 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2427
  time to fit residues: 19.5359
Evaluate side-chains
  47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0570
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.1902

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

Flipped N/Q/H residues before XYZ refinement:
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 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 = 0.4037 r_free = 0.4037 target = 0.093559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.070814 restraints weight = 47662.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.071884 restraints weight = 32601.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.072663 restraints weight = 25723.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6794  Z= 0.139
  Angle     :  0.664   8.957   9226  Z= 0.338
  Chirality :  0.044   0.263   1024
  Planarity :  0.005   0.117   1188
  Dihedral  :  6.061  51.701    944
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.45 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.36 %

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: -1.44 (0.29), residues: 852
  helix:  1.89 (0.42), residues: 152
  sheet: -0.77 (0.28), residues: 336
  loop : -2.41 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  73 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.011   0.001   PHE H 185 
 TYR   0.016   0.001   TYR H 136 
 ARG   0.003   0.000   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03097 (  281)
  hydrogen bonds       : angle       5.47025 (  774)
  SS BOND              : bond        0.00570 (    6)
  SS BOND              : angle       1.83102 (   12)
  covalent geometry    : bond        0.00301 ( 6788)
  covalent geometry    : angle       0.66064 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  298 LEU cc_start: 0.9115 (tp) cc_final: 0.8483 (tp)
REVERT: K   34 MET cc_start: 0.7322 (mmp) cc_final: 0.7089 (mmm)
REVERT: K   76 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7923 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2235
  time to fit residues: 17.7013
Evaluate side-chains
  44 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 69 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 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 = 0.4033 r_free = 0.4033 target = 0.094281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.071766 restraints weight = 47821.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.072111 restraints weight = 35816.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.072741 restraints weight = 26923.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6794  Z= 0.135
  Angle     :  0.677  10.034   9226  Z= 0.344
  Chirality :  0.044   0.283   1024
  Planarity :  0.005   0.132   1188
  Dihedral  :  6.206  57.010    944
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.10 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.36 %

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: -1.45 (0.29), residues: 852
  helix:  1.89 (0.42), residues: 152
  sheet: -0.80 (0.28), residues: 338
  loop : -2.40 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 128 
 HIS   0.005   0.001   HIS L 224 
 PHE   0.058   0.002   PHE H 185 
 TYR   0.015   0.001   TYR H 136 
 ARG   0.003   0.000   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03121 (  281)
  hydrogen bonds       : angle       5.49043 (  774)
  SS BOND              : bond        0.00665 (    6)
  SS BOND              : angle       1.98914 (   12)
  covalent geometry    : bond        0.00287 ( 6788)
  covalent geometry    : angle       0.67410 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8524 (tt0)
REVERT: B  298 LEU cc_start: 0.9129 (tp) cc_final: 0.8506 (tp)
REVERT: K   34 MET cc_start: 0.7274 (mmp) cc_final: 0.7041 (mmm)
REVERT: K   76 LYS cc_start: 0.8187 (mmpt) cc_final: 0.7905 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2226
  time to fit residues: 18.1707
Evaluate side-chains
  46 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.1980
   chunk 68 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 215 HIS
** L 224 HIS ** 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 = 0.3958 r_free = 0.3958 target = 0.090081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.067582 restraints weight = 49206.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.068243 restraints weight = 34236.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.068968 restraints weight = 27175.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6794  Z= 0.249
  Angle     :  0.804  11.008   9226  Z= 0.413
  Chirality :  0.048   0.285   1024
  Planarity :  0.006   0.138   1188
  Dihedral  :  7.061  61.701    944
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 26.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.80 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.49 %

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: -1.77 (0.28), residues: 852
  helix:  1.46 (0.40), residues: 152
  sheet: -0.96 (0.28), residues: 332
  loop : -2.55 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H 128 
 HIS   0.006   0.002   HIS B 285 
 PHE   0.043   0.003   PHE H 185 
 TYR   0.019   0.002   TYR B 296 
 ARG   0.006   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  281)
  hydrogen bonds       : angle       6.06876 (  774)
  SS BOND              : bond        0.00853 (    6)
  SS BOND              : angle       2.19836 (   12)
  covalent geometry    : bond        0.00540 ( 6788)
  covalent geometry    : angle       0.80048 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8451 (tt0)
REVERT: A   27 LEU cc_start: 0.8925 (tt) cc_final: 0.8699 (tt)
REVERT: K   34 MET cc_start: 0.7803 (mmp) cc_final: 0.7453 (mmm)
REVERT: K   76 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7975 (mmmt)
REVERT: L  112 TYR cc_start: 0.7845 (m-80) cc_final: 0.7387 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2319
  time to fit residues: 17.4192
Evaluate side-chains
  43 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0270
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0040
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.5850

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 130 ASN
K  77 ASN
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 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 = 0.4034 r_free = 0.4034 target = 0.093423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.070521 restraints weight = 48129.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.071418 restraints weight = 32906.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.072286 restraints weight = 25914.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6794  Z= 0.122
  Angle     :  0.707  11.220   9226  Z= 0.358
  Chirality :  0.046   0.268   1024
  Planarity :  0.005   0.131   1188
  Dihedral  :  6.468  57.902    944
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.98 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.36 %

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: -1.56 (0.28), residues: 852
  helix:  1.68 (0.41), residues: 152
  sheet: -0.80 (0.29), residues: 307
  loop : -2.37 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 128 
 HIS   0.005   0.001   HIS L 224 
 PHE   0.049   0.002   PHE H 185 
 TYR   0.011   0.001   TYR H 136 
 ARG   0.004   0.000   ARG H  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03148 (  281)
  hydrogen bonds       : angle       5.64314 (  774)
  SS BOND              : bond        0.00513 (    6)
  SS BOND              : angle       2.16903 (   12)
  covalent geometry    : bond        0.00256 ( 6788)
  covalent geometry    : angle       0.70343 ( 9214)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8500 (tt0)
REVERT: B  298 LEU cc_start: 0.9076 (tp) cc_final: 0.8773 (tp)
REVERT: K   34 MET cc_start: 0.7202 (mmp) cc_final: 0.6966 (mmm)
REVERT: K   76 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7903 (mmmt)
REVERT: L  110 THR cc_start: 0.7979 (p) cc_final: 0.7443 (p)
REVERT: L  112 TYR cc_start: 0.7747 (m-80) cc_final: 0.7255 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2586
  time to fit residues: 21.7530
Evaluate side-chains
  49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0040
   chunk 75 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0000
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 224 HIS ** 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 = 0.4047 r_free = 0.4047 target = 0.094763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071025 restraints weight = 47490.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.071428 restraints weight = 33570.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.072431 restraints weight = 26829.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6794  Z= 0.119
  Angle     :  0.701  10.817   9226  Z= 0.353
  Chirality :  0.046   0.280   1024
  Planarity :  0.006   0.131   1188
  Dihedral  :  6.262  56.623    944
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.10 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.36 %

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: -1.46 (0.28), residues: 852
  helix:  2.04 (0.42), residues: 146
  sheet: -0.76 (0.29), residues: 319
  loop : -2.39 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H 128 
 HIS   0.003   0.001   HIS L 224 
 PHE   0.049   0.002   PHE H 185 
 TYR   0.010   0.001   TYR B 306 
 ARG   0.019   0.001   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (  281)
  hydrogen bonds       : angle       5.49674 (  774)
  SS BOND              : bond        0.00568 (    6)
  SS BOND              : angle       1.99892 (   12)
  covalent geometry    : bond        0.00254 ( 6788)
  covalent geometry    : angle       0.69744 ( 9214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3036.47 seconds
wall clock time: 53 minutes 19.78 seconds (3199.78 seconds total)