Starting phenix.real_space_refine
on Wed Jun 11 08:45:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8znj_60273/06_2025/8znj_60273.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8znj_60273/06_2025/8znj_60273.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8znj_60273/06_2025/8znj_60273.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8znj_60273/06_2025/8znj_60273.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8znj_60273/06_2025/8znj_60273.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8znj_60273/06_2025/8znj_60273.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.085
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: 7
    Type Number    sf(0)   Gaussians
     P      43      5.49       5
     Mg      1      5.21       5
     S      14      5.16       5
     C    4023      2.51       5
     N    1112      2.21       5
     O    1316      1.98       5
     H    6190      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12699
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 7310
          Classifications: {'peptide': 444}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 422}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 4038
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 3, 'TRANS': 233}
    Chain: "D"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 663
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 2, 'rna3p': 18}
    Chain: "E"
      Number of atoms: 687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 687
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.91, per 1000 atoms: 0.62
  Number of scatterers: 12699
  At special positions: 0
  Unit cell: (75.97, 77.04, 110.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      14     16.00
     P      43     15.00
     Mg      1     11.99
     O    1316      8.00
     N    1112      7.00
     C    4023      6.00
     H    6190      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  21 " - pdb=" SG  CYS B  85 " distance=2.03

  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: 3.81
  Conformation dependent library (CDL) restraints added in 994.5 milliseconds
  

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1306

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      35.2% alpha, 18.9% beta
      20 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 8.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 27
      No H-bonds generated for 'chain 'A' and resid 25 through 27'
    Processing helix  chain 'A' and resid 28 through 33
    Processing helix  chain 'A' and resid 50 through 62
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 107 through 117
      removed outlier: 3.661A  pdb=" N   SER A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 145
      removed outlier: 4.125A  pdb=" N   GLU A 136 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ASP A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   LYS A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 172 through 184
    Processing helix  chain 'A' and resid 194 through 201
      removed outlier: 4.192A  pdb=" N   ASP A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   SER A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 279
    Processing helix  chain 'A' and resid 295 through 306
    Processing helix  chain 'A' and resid 402 through 416
      removed outlier: 3.529A  pdb=" N   ALA A 416 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 441
    Processing helix  chain 'A' and resid 442 through 444
      No H-bonds generated for 'chain 'A' and resid 442 through 444'
    Processing helix  chain 'A' and resid 454 through 459
    Processing helix  chain 'B' and resid 26 through 38
      removed outlier: 3.809A  pdb=" N   LYS B  32 " --> pdb=" O   LYS B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 74
      removed outlier: 3.510A  pdb=" N   TYR B  74 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 114
      removed outlier: 3.691A  pdb=" N   PHE B  97 " --> pdb=" O   ASN B  93 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU B 114 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 194
      removed outlier: 4.015A  pdb=" N   ARG B 186 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 213
      removed outlier: 3.655A  pdb=" N   ILE B 211 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.858A  pdb=" N   THR A 339 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   LEU A 356 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   SER A 397 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A 286 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   ILE A 315 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ILE A 288 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS A 290 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   MET A 208 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   PHE A 289 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   MET A 210 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A 213 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
    Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41
      removed outlier: 6.248A  pdb=" N   ILE A  40 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100
    Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 370
      removed outlier: 3.738A  pdb=" N   LYS A 370 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 128
      removed outlier: 4.125A  pdb=" N   VAL B 135 " --> pdb=" O   PHE B 155 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL B 151 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ARG B 141 " --> pdb=" O   ILE B 149 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ILE B 149 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ASP B 143 " --> pdb=" O   TYR B 147 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR B 147 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47
      removed outlier: 6.727A  pdb=" N   THR B  55 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 10.134A  pdb=" N   ILE B  18 " --> pdb=" O   THR B  55 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    615 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      49 hydrogen bonds
      98 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 5.62

  Time building geometry restraints manager: 4.57 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6188
        1.03 -     1.23: 27
        1.23 -     1.42: 2858
        1.42 -     1.62: 3815
        1.62 -     1.81: 24
  Bond restraints: 12912
  Sorted by residual:
  bond pdb=" N   VAL B   2 "
       pdb=" CA  VAL B   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.58e+00
  bond pdb=" N   VAL B   2 "
       pdb=" H   VAL B   2 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" C3'  DT E   3 "
       pdb=" O3'  DT E   3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.74e+00
  bond pdb=" CB  ARG A 166 "
       pdb=" CG  ARG A 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.39e+00
  bond pdb=" N   GLY A  49 "
       pdb=" CA  GLY A  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.448  0.010 9.20e-03 1.18e+04 1.17e+00
  ... (remaining 12907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 22443
        1.31 -     2.63: 835
        2.63 -     3.94: 99
        3.94 -     5.26: 8
        5.26 -     6.57: 4
  Bond angle restraints: 23389
  Sorted by residual:
  angle pdb=" N   ARG A 166 "
        pdb=" CA  ARG A 166 "
        pdb=" CB  ARG A 166 "
      ideal   model   delta    sigma   weight residual
     114.17  110.12    4.05 1.14e+00 7.69e-01 1.26e+01
  angle pdb=" CA  ARG A 166 "
        pdb=" CB  ARG A 166 "
        pdb=" CG  ARG A 166 "
      ideal   model   delta    sigma   weight residual
     114.10  120.21   -6.11 2.00e+00 2.50e-01 9.34e+00
  angle pdb=" C   GLY A 327 "
        pdb=" N   ASN A 328 "
        pdb=" CA  ASN A 328 "
      ideal   model   delta    sigma   weight residual
     121.54  127.02   -5.48 1.91e+00 2.74e-01 8.22e+00
  angle pdb=" CB  ARG A 166 "
        pdb=" CG  ARG A 166 "
        pdb=" CD  ARG A 166 "
      ideal   model   delta    sigma   weight residual
     111.30  117.87   -6.57 2.30e+00 1.89e-01 8.17e+00
  angle pdb=" C   LEU A 232 "
        pdb=" N   ASN A 233 "
        pdb=" CA  ASN A 233 "
      ideal   model   delta    sigma   weight residual
     121.54  126.18   -4.64 1.91e+00 2.74e-01 5.90e+00
  ... (remaining 23384 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.94: 5453
       25.94 -    51.88: 411
       51.88 -    77.81: 86
       77.81 -   103.75: 8
      103.75 -   129.69: 2
  Dihedral angle restraints: 5960
    sinusoidal: 3574
      harmonic: 2386
  Sorted by residual:
  dihedral pdb=" CA  ALA A 416 "
           pdb=" C   ALA A 416 "
           pdb=" N   ASP A 417 "
           pdb=" CA  ASP A 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.06   26.94     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  ARG A 216 "
           pdb=" C   ARG A 216 "
           pdb=" N   THR A 217 "
           pdb=" CA  THR A 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.48  -24.52     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CB  CYS B  21 "
           pdb=" SG  CYS B  21 "
           pdb=" SG  CYS B  85 "
           pdb=" CB  CYS B  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.28   40.72     1      1.00e+01 1.00e-02 2.32e+01
  ... (remaining 5957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 674
       0.031 -    0.063: 221
       0.063 -    0.094: 87
       0.094 -    0.125: 66
       0.125 -    0.157: 8
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  ILE A 341 "
            pdb=" N   ILE A 341 "
            pdb=" C   ILE A 341 "
            pdb=" CB  ILE A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.14e-01
  chirality pdb=" CA  ILE B  89 "
            pdb=" N   ILE B  89 "
            pdb=" C   ILE B  89 "
            pdb=" CB  ILE B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  ILE B  51 "
            pdb=" N   ILE B  51 "
            pdb=" C   ILE B  51 "
            pdb=" CB  ILE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1699
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "   -0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO A  95 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 166 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   ARG A 166 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ARG A 166 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LYS A 167 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D   7 "    0.021 2.00e-02 2.50e+03   9.86e-03 2.67e+00
        pdb=" N1    C D   7 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2    C D   7 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C D   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    C D   7 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C D   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C D   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" H5    C D   7 "    0.004 2.00e-02 2.50e+03
        pdb=" H6    C D   7 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1696 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 885
        2.20 -     2.80: 26200
        2.80 -     3.40: 34765
        3.40 -     4.00: 48829
        4.00 -     4.60: 73458
  Nonbonded interactions: 184137
  Sorted by model distance:
  nonbonded pdb=" HZ1 LYS A 183 "
            pdb="MG    MG A 501 "
     model   vdw
     1.601 1.700
  nonbonded pdb="HH12 ARG A 216 "
            pdb=" H22   G D  11 "
     model   vdw
     1.804 2.100
  nonbonded pdb=" OP2   U D   1 "
            pdb="MG    MG A 501 "
     model   vdw
     1.861 2.050
  nonbonded pdb=" H   GLY B  44 "
            pdb="HD21 ASN B 103 "
     model   vdw
     1.864 2.100
  nonbonded pdb=" O   ASN A 165 "
            pdb="HD21 ASN A 165 "
     model   vdw
     1.869 2.450
  ... (remaining 184132 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  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:             0.200
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     42.620
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  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:15.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
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   0.040   6723  Z= 0.138
  Angle     :  0.594   6.572   9266  Z= 0.333
  Chirality :  0.044   0.157   1056
  Planarity :  0.005   0.056   1015
  Dihedral  : 19.149 129.689   2745
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 24.64 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.32), residues: 673
  helix:  0.78 (0.38), residues: 212
  sheet: -1.63 (0.42), residues: 136
  loop : -2.29 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A  24 
 PHE   0.022   0.001   PHE A 109 
 TYR   0.010   0.001   TYR B 175 
 ARG   0.007   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11039 (  272)
  hydrogen bonds       : angle       6.41859 (  713)
  SS BOND              : bond        0.00082 (    1)
  SS BOND              : angle       0.81177 (    2)
  covalent geometry    : bond        0.00297 ( 6722)
  covalent geometry    : angle       0.59353 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.920 
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   70 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7938 (p)
REVERT: A  210 MET cc_start: 0.8381 (ttm) cc_final: 0.8066 (ttp)
REVERT: B  130 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7559 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 92
  average time/residue: 2.0185
  time to fit residues: 197.9339
Evaluate side-chains
  90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   20 ASN
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  11 ASN
A 165 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.184591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.157112 restraints weight = 20744.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.91
r_work: 0.3847 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.0599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6723  Z= 0.167
  Angle     :  0.575   5.345   9266  Z= 0.320
  Chirality :  0.045   0.150   1056
  Planarity :  0.004   0.047   1015
  Dihedral  : 17.873 129.476   1321
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.70 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 24.17 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.33), residues: 673
  helix:  0.94 (0.38), residues: 212
  sheet: -1.54 (0.42), residues: 135
  loop : -2.18 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.015   0.001   PHE A 109 
 TYR   0.011   0.001   TYR B 175 
 ARG   0.004   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  272)
  hydrogen bonds       : angle       4.98112 (  713)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.51319 (    2)
  covalent geometry    : bond        0.00377 ( 6722)
  covalent geometry    : angle       0.57535 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 1.019 
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  210 MET cc_start: 0.8410 (ttm) cc_final: 0.8084 (ttp)
REVERT: A  391 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7986 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 99
  average time/residue: 1.9017
  time to fit residues: 201.4989
Evaluate side-chains
  87 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   20 ASN
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  190 ASN
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.184339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156904 restraints weight = 20924.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 1.93
r_work: 0.3842 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.0729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6723  Z= 0.163
  Angle     :  0.569   5.959   9266  Z= 0.316
  Chirality :  0.044   0.151   1056
  Planarity :  0.004   0.044   1015
  Dihedral  : 17.786 129.257   1309
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.70 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 24.48 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.59 (0.33), residues: 673
  helix:  0.78 (0.37), residues: 218
  sheet: -1.54 (0.41), residues: 148
  loop : -2.19 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.009   0.001   PHE A  17 
 TYR   0.010   0.001   TYR A 396 
 ARG   0.004   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  272)
  hydrogen bonds       : angle       4.79990 (  713)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.59044 (    2)
  covalent geometry    : bond        0.00368 ( 6722)
  covalent geometry    : angle       0.56901 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.086 
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  210 MET cc_start: 0.8390 (ttm) cc_final: 0.8075 (ttp)
REVERT: B  130 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7655 (mp0)
  outliers start: 14
  outliers final: 13
  residues processed: 96
  average time/residue: 2.0814
  time to fit residues: 214.9177
Evaluate side-chains
  92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ARG
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   20 ASN
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 ASN
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0770
   overall best weight:    1.3544

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.184191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.157135 restraints weight = 20404.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 1.90
r_work: 0.3859 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3713 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6723  Z= 0.192
  Angle     :  0.587   6.456   9266  Z= 0.326
  Chirality :  0.045   0.153   1056
  Planarity :  0.004   0.041   1015
  Dihedral  : 17.837 129.230   1309
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 24.80 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.32), residues: 673
  helix:  0.68 (0.37), residues: 219
  sheet: -1.61 (0.39), residues: 158
  loop : -2.21 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.016   0.002   PHE A 109 
 TYR   0.010   0.001   TYR A 433 
 ARG   0.005   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  272)
  hydrogen bonds       : angle       4.73579 (  713)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.52696 (    2)
  covalent geometry    : bond        0.00435 ( 6722)
  covalent geometry    : angle       0.58692 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.964 
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  210 MET cc_start: 0.8383 (ttm) cc_final: 0.8064 (ttp)
REVERT: B  130 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7538 (mp0)
  outliers start: 22
  outliers final: 14
  residues processed: 100
  average time/residue: 2.0714
  time to fit residues: 220.8247
Evaluate side-chains
  96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ARG
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   92 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   20 ASN
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0470
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.3284

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.184038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.157496 restraints weight = 20513.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 1.87
r_work: 0.3862 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3713 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6723  Z= 0.187
  Angle     :  0.588   7.096   9266  Z= 0.327
  Chirality :  0.045   0.151   1056
  Planarity :  0.004   0.041   1015
  Dihedral  : 17.842 129.293   1309
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.76 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.32), residues: 673
  helix:  0.65 (0.36), residues: 219
  sheet: -1.63 (0.39), residues: 158
  loop : -2.26 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.010   0.001   PHE A  17 
 TYR   0.010   0.001   TYR A 433 
 ARG   0.005   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  272)
  hydrogen bonds       : angle       4.70048 (  713)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.51861 (    2)
  covalent geometry    : bond        0.00423 ( 6722)
  covalent geometry    : angle       0.58817 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.997 
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: symmetry clash
REVERT: A  210 MET cc_start: 0.8351 (ttm) cc_final: 0.8045 (ttp)
REVERT: B  130 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7501 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 101
  average time/residue: 2.1441
  time to fit residues: 231.5214
Evaluate side-chains
  98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ARG
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   92 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.186149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.158917 restraints weight = 20626.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 1.93
r_work: 0.3876 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6723  Z= 0.136
  Angle     :  0.565   7.375   9266  Z= 0.313
  Chirality :  0.044   0.150   1056
  Planarity :  0.004   0.040   1015
  Dihedral  : 17.780 129.399   1307
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.40 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 25.28 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.33), residues: 673
  helix:  0.87 (0.37), residues: 219
  sheet: -1.51 (0.40), residues: 158
  loop : -2.22 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.019   0.001   PHE A 109 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.005   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  272)
  hydrogen bonds       : angle       4.56829 (  713)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.56250 (    2)
  covalent geometry    : bond        0.00308 ( 6722)
  covalent geometry    : angle       0.56533 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 1.236 
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: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.8343 (ttm) cc_final: 0.8021 (ttp)
REVERT: B  130 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7553 (mp0)
  outliers start: 18
  outliers final: 14
  residues processed: 96
  average time/residue: 1.9826
  time to fit residues: 204.2652
Evaluate side-chains
  94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  190 ASN
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0970
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.186904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.159908 restraints weight = 20349.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 1.92
r_work: 0.3882 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6723  Z= 0.128
  Angle     :  0.567   8.027   9266  Z= 0.313
  Chirality :  0.044   0.149   1056
  Planarity :  0.004   0.040   1015
  Dihedral  : 17.729 128.910   1307
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 25.60 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.33), residues: 673
  helix:  1.13 (0.38), residues: 213
  sheet: -1.43 (0.40), residues: 158
  loop : -2.19 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 274 
 HIS   0.002   0.001   HIS B  31 
 PHE   0.009   0.001   PHE A 137 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.005   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03350 (  272)
  hydrogen bonds       : angle       4.49289 (  713)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.55969 (    2)
  covalent geometry    : bond        0.00291 ( 6722)
  covalent geometry    : angle       0.56712 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 1.884 
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: symmetry clash
   revert: symmetry clash
REVERT: A   70 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7945 (p)
REVERT: A  210 MET cc_start: 0.8348 (ttm) cc_final: 0.8013 (ttp)
REVERT: B  130 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7559 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 99
  average time/residue: 2.4639
  time to fit residues: 263.7519
Evaluate side-chains
  94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 ASN
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.183303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.155939 restraints weight = 20556.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 1.94
r_work: 0.3852 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6723  Z= 0.191
  Angle     :  0.603   7.676   9266  Z= 0.333
  Chirality :  0.045   0.150   1056
  Planarity :  0.004   0.040   1015
  Dihedral  : 17.735 129.198   1307
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.89 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 26.55 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.33), residues: 673
  helix:  0.76 (0.37), residues: 219
  sheet: -1.52 (0.39), residues: 158
  loop : -2.25 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.021   0.002   PHE A 109 
 TYR   0.012   0.001   TYR A  54 
 ARG   0.007   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  272)
  hydrogen bonds       : angle       4.60188 (  713)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.50904 (    2)
  covalent geometry    : bond        0.00434 ( 6722)
  covalent geometry    : angle       0.60289 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 1.009 
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: symmetry clash
REVERT: A   70 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7988 (p)
REVERT: A  210 MET cc_start: 0.8412 (ttm) cc_final: 0.8100 (ttp)
REVERT: B  130 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7556 (mp0)
  outliers start: 17
  outliers final: 12
  residues processed: 99
  average time/residue: 1.9156
  time to fit residues: 203.7327
Evaluate side-chains
  93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 1.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.182064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154773 restraints weight = 20497.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.93
r_work: 0.3833 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3690 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6723  Z= 0.216
  Angle     :  0.624   7.850   9266  Z= 0.344
  Chirality :  0.046   0.151   1056
  Planarity :  0.005   0.044   1015
  Dihedral  : 17.717 129.641   1307
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.85 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 27.03 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.32), residues: 673
  helix:  0.55 (0.36), residues: 219
  sheet: -1.63 (0.39), residues: 158
  loop : -2.28 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.016   0.002   PHE A 137 
 TYR   0.013   0.002   TYR A  54 
 ARG   0.006   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03886 (  272)
  hydrogen bonds       : angle       4.63020 (  713)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       0.55928 (    2)
  covalent geometry    : bond        0.00491 ( 6722)
  covalent geometry    : angle       0.62393 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.928 
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: symmetry clash
REVERT: A   70 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8038 (p)
REVERT: A  210 MET cc_start: 0.8379 (ttm) cc_final: 0.8084 (ttp)
REVERT: B   23 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7733 (mp0)
REVERT: B  130 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7518 (mp0)
  outliers start: 17
  outliers final: 13
  residues processed: 94
  average time/residue: 1.8393
  time to fit residues: 185.6706
Evaluate side-chains
  93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.185487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.158433 restraints weight = 20281.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 1.91
r_work: 0.3869 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3725 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6723  Z= 0.141
  Angle     :  0.591   7.983   9266  Z= 0.326
  Chirality :  0.044   0.149   1056
  Planarity :  0.004   0.046   1015
  Dihedral  : 17.609 129.786   1307
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.50 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.32), residues: 673
  helix:  0.80 (0.37), residues: 219
  sheet: -1.58 (0.39), residues: 158
  loop : -2.27 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 274 
 HIS   0.002   0.001   HIS B  31 
 PHE   0.025   0.001   PHE A 109 
 TYR   0.012   0.001   TYR A  54 
 ARG   0.006   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 (  272)
  hydrogen bonds       : angle       4.52664 (  713)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.58954 (    2)
  covalent geometry    : bond        0.00319 ( 6722)
  covalent geometry    : angle       0.59117 ( 9264)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.928 
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: symmetry clash
REVERT: A   70 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7987 (p)
REVERT: A  210 MET cc_start: 0.8333 (ttm) cc_final: 0.8027 (ttp)
REVERT: B  130 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7539 (mp0)
  outliers start: 15
  outliers final: 11
  residues processed: 93
  average time/residue: 2.0102
  time to fit residues: 203.4667
Evaluate side-chains
  92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  228 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.182390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.155084 restraints weight = 20600.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 1.94
r_work: 0.3835 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3689 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6723  Z= 0.208
  Angle     :  0.619   7.910   9266  Z= 0.342
  Chirality :  0.046   0.150   1056
  Planarity :  0.005   0.045   1015
  Dihedral  : 17.618 129.541   1306
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.50 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.32), residues: 673
  helix:  0.57 (0.36), residues: 219
  sheet: -1.70 (0.38), residues: 158
  loop : -2.28 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A 138 
 PHE   0.015   0.002   PHE A 137 
 TYR   0.021   0.002   TYR B 175 
 ARG   0.006   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  272)
  hydrogen bonds       : angle       4.58769 (  713)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.52327 (    2)
  covalent geometry    : bond        0.00472 ( 6722)
  covalent geometry    : angle       0.61861 ( 9264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9674.51 seconds
wall clock time: 168 minutes 45.08 seconds (10125.08 seconds total)