Starting phenix.real_space_refine
on Sat May 10 19:09:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bei_44479/05_2025/9bei_44479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bei_44479/05_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_44479/05_2025/9bei_44479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bei_44479/05_2025/9bei_44479.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bei_44479/05_2025/9bei_44479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bei_44479/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.37, per 1000 atoms: 0.81
  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: 1.63
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.86
  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: 1.95

  Time building geometry restraints manager: 1.92 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:             3.550
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.460
  Find NCS groups from input model:        0.080
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.400
-------------------------------------------------------------------------------
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  : 0.797 
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: 0.2324
  time to fit residues: 18.7563
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  : 0.779 
-------------------------------------------------------------------------------
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 = 0.070151 restraints weight = 47930.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.070620 restraints weight = 33670.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.071173 restraints weight = 26112.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
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       6.02696 (  774)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       1.87507 (   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  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7983 (mm) cc_final: 0.7547 (tp)
REVERT: B  298 LEU cc_start: 0.8997 (tp) cc_final: 0.8082 (tp)
REVERT: L  112 TYR cc_start: 0.7710 (m-80) cc_final: 0.7263 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2097
  time to fit residues: 17.6807
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  : 0.786 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.093716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.071104 restraints weight = 48305.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.071672 restraints weight = 34735.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.072554 restraints weight = 25621.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.1424

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= 0.128
  Angle     :  0.640   7.976   9226  Z= 0.332
  Chirality :  0.044   0.227   1024
  Planarity :  0.005   0.111   1188
  Dihedral  :  6.318  53.704    944
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  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:  1.92 (0.42), residues: 152
  sheet: -0.89 (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   0.011   0.001   TYR K  95 
 ARG   0.006   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  281)
  hydrogen bonds       : angle       5.78076 (  774)
  SS BOND              : bond        0.00575 (    6)
  SS BOND              : angle       1.67416 (   12)
  covalent geometry    : bond        0.00273 ( 6788)
  covalent geometry    : angle       0.63767 ( 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  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8557 (mm) cc_final: 0.8161 (tp)
REVERT: B  298 LEU cc_start: 0.9059 (tp) cc_final: 0.8293 (tp)
REVERT: K   76 LYS cc_start: 0.8192 (mmpt) cc_final: 0.7900 (mmmt)
REVERT: L  187 GLU cc_start: 0.8548 (pp20) cc_final: 0.8216 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 62
  average time/residue: 0.2090
  time to fit residues: 17.2284
Evaluate side-chains
  49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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  28 GLN ** 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 225 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.091898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.068378 restraints weight = 49207.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.069152 restraints weight = 34489.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.069726 restraints weight = 26571.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6794  Z= 0.196
  Angle     :  0.721  10.060   9226  Z= 0.373
  Chirality :  0.046   0.256   1024
  Planarity :  0.006   0.131   1188
  Dihedral  :  6.771  57.285    944
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 21.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.96 %
    Favored  : 94.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.61 %

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: -1.79 (0.28), residues: 852
  helix:  1.61 (0.41), residues: 152
  sheet: -1.08 (0.27), residues: 341
  loop : -2.54 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  73 
 HIS   0.005   0.002   HIS L 224 
 PHE   0.040   0.002   PHE H 185 
 TYR   0.017   0.002   TYR B 296 
 ARG   0.005   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  281)
  hydrogen bonds       : angle       6.00287 (  774)
  SS BOND              : bond        0.00519 (    6)
  SS BOND              : angle       1.83274 (   12)
  covalent geometry    : bond        0.00425 ( 6788)
  covalent geometry    : angle       0.71860 ( 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: 1
    poor density    : 56
  time to evaluate  : 0.829 
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: 0.9076 (tp) cc_final: 0.8288 (tp)
REVERT: K   34 MET cc_start: 0.7348 (mmp) cc_final: 0.7145 (mmm)
REVERT: K   76 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7888 (mmmt)
  outliers start: 1
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2185
  time to fit residues: 16.7933
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  : 0.791 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 66 optimal weight:    0.0980
   chunk 4 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.8188

-------------------------------------------------------------------------------
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  31 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 = 0.3974 r_free = 0.3974 target = 0.091062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.068319 restraints weight = 48733.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.069068 restraints weight = 33605.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.069806 restraints weight = 26106.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6794  Z= 0.179
  Angle     :  0.713   8.992   9226  Z= 0.367
  Chirality :  0.046   0.279   1024
  Planarity :  0.006   0.123   1188
  Dihedral  :  6.815  57.279    944
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 21.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.27 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.32 %
  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: -1.80 (0.28), residues: 852
  helix:  1.64 (0.41), residues: 152
  sheet: -1.07 (0.28), residues: 334
  loop : -2.56 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  73 
 HIS   0.005   0.001   HIS B 285 
 PHE   0.020   0.002   PHE H 185 
 TYR   0.022   0.002   TYR B 306 
 ARG   0.005   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03481 (  281)
  hydrogen bonds       : angle       5.92968 (  774)
  SS BOND              : bond        0.00535 (    6)
  SS BOND              : angle       1.88740 (   12)
  covalent geometry    : bond        0.00386 ( 6788)
  covalent geometry    : angle       0.71049 ( 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
  57 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.840 
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: B  298 LEU cc_start: 0.9078 (tp) cc_final: 0.8299 (tp)
REVERT: K   76 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7911 (mmmt)
REVERT: L  112 TYR cc_start: 0.7844 (m-80) cc_final: 0.7439 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 57
  average time/residue: 0.2014
  time to fit residues: 15.9060
Evaluate side-chains
  49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 69 optimal weight:    0.2980
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 130 ASN
** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  63 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.093565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.070410 restraints weight = 47390.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.071316 restraints weight = 32741.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.072025 restraints weight = 25868.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6794  Z= 0.122
  Angle     :  0.685   9.791   9226  Z= 0.349
  Chirality :  0.045   0.274   1024
  Planarity :  0.005   0.119   1188
  Dihedral  :  6.364  53.303    944
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.33 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  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: -1.67 (0.29), residues: 852
  helix:  1.74 (0.42), residues: 152
  sheet: -0.95 (0.28), residues: 326
  loop : -2.49 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H 128 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.016   0.001   PHE H 185 
 TYR   0.011   0.001   TYR B 306 
 ARG   0.008   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  281)
  hydrogen bonds       : angle       5.65003 (  774)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.73141 (   12)
  covalent geometry    : bond        0.00257 ( 6788)
  covalent geometry    : angle       0.68267 ( 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
  62 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.735 
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: 0.9034 (tp) cc_final: 0.8320 (tp)
REVERT: K   76 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7924 (mmmt)
REVERT: L  112 TYR cc_start: 0.7581 (m-80) cc_final: 0.7289 (m-80)
REVERT: L  171 LYS cc_start: 0.7614 (ptpt) cc_final: 0.7355 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2295
  time to fit residues: 18.8728
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  : 0.825 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 53 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  77 ASN
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.094024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.070611 restraints weight = 47305.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.071091 restraints weight = 32813.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.071864 restraints weight = 25892.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6794  Z= 0.126
  Angle     :  0.668   9.015   9226  Z= 0.340
  Chirality :  0.044   0.266   1024
  Planarity :  0.005   0.116   1188
  Dihedral  :  6.235  52.769    944
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.80 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  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:  1.73 (0.42), residues: 152
  sheet: -0.84 (0.28), residues: 328
  loop : -2.44 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 128 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.011   0.001   PHE H 185 
 TYR   0.021   0.001   TYR H 136 
 ARG   0.005   0.000   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03062 (  281)
  hydrogen bonds       : angle       5.61072 (  774)
  SS BOND              : bond        0.00613 (    6)
  SS BOND              : angle       1.89115 (   12)
  covalent geometry    : bond        0.00274 ( 6788)
  covalent geometry    : angle       0.66515 ( 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  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  298 LEU cc_start: 0.9041 (tp) cc_final: 0.8308 (tp)
REVERT: K   76 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7890 (mmmt)
REVERT: L  171 LYS cc_start: 0.7631 (ptpt) cc_final: 0.7340 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2440
  time to fit residues: 19.4275
Evaluate side-chains
  45 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 78 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 80 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 194 ASN
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.094008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.070704 restraints weight = 47717.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.071506 restraints weight = 33576.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.072114 restraints weight = 25575.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6794  Z= 0.132
  Angle     :  0.695   9.956   9226  Z= 0.353
  Chirality :  0.045   0.293   1024
  Planarity :  0.005   0.132   1188
  Dihedral  :  6.360  57.792    944
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.69 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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: -1.54 (0.29), residues: 852
  helix:  1.76 (0.42), residues: 152
  sheet: -0.83 (0.28), residues: 330
  loop : -2.44 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L  60 
 HIS   0.003   0.001   HIS B 285 
 PHE   0.062   0.002   PHE H 185 
 TYR   0.017   0.001   TYR H 136 
 ARG   0.009   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03175 (  281)
  hydrogen bonds       : angle       5.58175 (  774)
  SS BOND              : bond        0.00454 (    6)
  SS BOND              : angle       2.03766 (   12)
  covalent geometry    : bond        0.00285 ( 6788)
  covalent geometry    : angle       0.69108 ( 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
  58 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.741 
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: 0.9040 (tp) cc_final: 0.8326 (tp)
REVERT: K   76 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7891 (mmmt)
REVERT: L  171 LYS cc_start: 0.7516 (ptpt) cc_final: 0.7234 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2224
  time to fit residues: 17.3075
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  : 0.740 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0670
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    1.4922

-------------------------------------------------------------------------------
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 ** 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 = 0.4006 r_free = 0.4006 target = 0.091992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.069126 restraints weight = 48248.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.069854 restraints weight = 33812.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.070701 restraints weight = 26686.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2736

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= 0.159
  Angle     :  0.726  11.130   9226  Z= 0.368
  Chirality :  0.046   0.285   1024
  Planarity :  0.006   0.131   1188
  Dihedral  :  6.623  59.607    944
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 20.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.62 %
    Favored  : 90.26 %
  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: -1.63 (0.28), residues: 852
  helix:  1.75 (0.41), residues: 152
  sheet: -0.89 (0.28), residues: 322
  loop : -2.48 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  60 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.050   0.002   PHE H 185 
 TYR   0.014   0.002   TYR B 306 
 ARG   0.008   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  281)
  hydrogen bonds       : angle       5.72934 (  774)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       2.19432 (   12)
  covalent geometry    : bond        0.00343 ( 6788)
  covalent geometry    : angle       0.72213 ( 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  : 0.735 
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: 0.8735 (mm-30) cc_final: 0.8496 (pt0)
REVERT: A   27 LEU cc_start: 0.8909 (tt) cc_final: 0.8698 (tt)
REVERT: B  298 LEU cc_start: 0.9052 (tp) cc_final: 0.8392 (tp)
REVERT: K   34 MET cc_start: 0.7464 (mmp) cc_final: 0.7194 (mmm)
REVERT: K   76 LYS cc_start: 0.8229 (mmpt) cc_final: 0.7918 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1886
  time to fit residues: 14.7006
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  : 0.797 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0010
   chunk 49 optimal weight:    0.4980
   chunk 31 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 130 ASN
** 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 = 0.4050 r_free = 0.4050 target = 0.094710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.070585 restraints weight = 47722.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.071261 restraints weight = 32909.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.071877 restraints weight = 25732.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6794  Z= 0.117
  Angle     :  0.690  10.862   9226  Z= 0.348
  Chirality :  0.045   0.285   1024
  Planarity :  0.005   0.130   1188
  Dihedral  :  6.272  56.615    944
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.86 %
    Favored  : 92.02 %
  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 : 0.36 %

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:  2.14 (0.42), residues: 146
  sheet: -0.83 (0.29), residues: 310
  loop : -2.32 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 128 
 HIS   0.003   0.001   HIS B 285 
 PHE   0.052   0.002   PHE H 185 
 TYR   0.011   0.001   TYR H 125 
 ARG   0.009   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03082 (  281)
  hydrogen bonds       : angle       5.47758 (  774)
  SS BOND              : bond        0.00522 (    6)
  SS BOND              : angle       2.17424 (   12)
  covalent geometry    : bond        0.00249 ( 6788)
  covalent geometry    : angle       0.68571 ( 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
  60 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.731 
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: 0.8749 (mm-30) cc_final: 0.8521 (tt0)
REVERT: A   27 LEU cc_start: 0.8962 (tt) cc_final: 0.8725 (tt)
REVERT: B  298 LEU cc_start: 0.9009 (tp) cc_final: 0.8327 (tp)
REVERT: K   29 ILE cc_start: 0.9252 (mm) cc_final: 0.9034 (mm)
REVERT: K   76 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7963 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2254
  time to fit residues: 17.6927
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  : 0.719 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0470
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    1.8084

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.091640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.067714 restraints weight = 49299.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.068653 restraints weight = 34504.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.069268 restraints weight = 27503.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6794  Z= 0.179
  Angle     :  0.726  10.517   9226  Z= 0.370
  Chirality :  0.046   0.281   1024
  Planarity :  0.006   0.134   1188
  Dihedral  :  6.646  60.048    944
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 21.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.27 %
    Favored  : 90.61 %
  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: -1.60 (0.28), residues: 852
  helix:  1.70 (0.41), residues: 152
  sheet: -0.86 (0.28), residues: 315
  loop : -2.42 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP L  60 
 HIS   0.005   0.002   HIS L 224 
 PHE   0.041   0.002   PHE H 185 
 TYR   0.014   0.002   TYR B 306 
 ARG   0.004   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03392 (  281)
  hydrogen bonds       : angle       5.71721 (  774)
  SS BOND              : bond        0.00528 (    6)
  SS BOND              : angle       1.95419 (   12)
  covalent geometry    : bond        0.00388 ( 6788)
  covalent geometry    : angle       0.72295 ( 9214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2819.66 seconds
wall clock time: 50 minutes 16.39 seconds (3016.39 seconds total)