Starting phenix.real_space_refine
on Wed Aug  5 07:06:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jfs_61438/08_2026/9jfs_61438.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jfs_61438/08_2026/9jfs_61438.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jfs_61438/08_2026/9jfs_61438.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jfs_61438/08_2026/9jfs_61438.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jfs_61438/08_2026/9jfs_61438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jfs_61438/08_2026/9jfs_61438.map"
  }
  resolution = 2.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     P     175      5.49       5
     S      17      5.16       5
     C    4904      2.51       5
     N    1579      2.21       5
     O    2121      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8796
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4285
          Classifications: {'peptide': 529}
          Link IDs: {'PTRANS': 21, 'TRANS': 507}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 2938
          Classifications: {'RNA': 138}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 64, 'rna3p_pyr': 60}
          Link IDs: {'rna2p': 14, 'rna3p': 123}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 546
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "D"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 225
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 802
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99}
  Time building chain proxies: 2.02, per 1000 atoms: 0.23
  Number of scatterers: 8796
  At special positions: 0
  Unit cell: (108.992, 101.504, 123.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      17     16.00
     P     175     15.00
     O    2121      8.00
     N    1579      7.00
     C    4904      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 550 " - pdb=" SG  CYS A 567 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  33 " - pdb=" SG  CYS E  36 " 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: 0.81
  Conformation dependent library (CDL) restraints added in 141.8 milliseconds
  

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1198

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      52.2% alpha, 11.4% beta
      68 base pairs and 107 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 64
      removed outlier: 4.795A  pdb=" N   CYS A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   VAL A  42 " --> pdb=" O   HIS A  38 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   THR A  43 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 79
      removed outlier: 3.779A  pdb=" N   GLN A  70 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   GLN A  71 " --> pdb=" O   PRO A  67 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   LEU A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 96
      removed outlier: 3.610A  pdb=" N   LEU A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 182 through 186
      removed outlier: 3.975A  pdb=" N   PHE A 185 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLU A 186 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 182 through 186'
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 198 through 209
    Processing helix  chain 'A' and resid 217 through 237
      removed outlier: 3.554A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 323 through 332
    Processing helix  chain 'A' and resid 333 through 341
    Processing helix  chain 'A' and resid 345 through 365
    Processing helix  chain 'A' and resid 396 through 428
      removed outlier: 4.311A  pdb=" N   GLU A 400 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ARG A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A 402 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY A 428 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 472
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 4.284A  pdb=" N   ASN A 483 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 519 through 535
    Processing helix  chain 'A' and resid 581 through 593
    Processing helix  chain 'E' and resid 12 through 18
    Processing helix  chain 'E' and resid 33 through 50
      removed outlier: 3.857A  pdb=" N   LYS E  37 " --> pdb=" O   CYS E  33 " (cutoff:3.500A)
      Proline residue:  E  41  - end of helix
      removed outlier: 3.621A  pdb=" N   ASP E  48 " --> pdb=" O   ASP E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 71
      removed outlier: 3.964A  pdb=" N   LYS E  70 " --> pdb=" O   GLY E  66 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR E  71 " --> pdb=" O   THR E  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 66 through 71'
    Processing helix  chain 'E' and resid 96 through 108
    Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 260
      removed outlier: 6.603A  pdb=" N   ALA A 320 " --> pdb=" O   PRO A 301 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   THR A 303 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   TYR A 313 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   THR A 284 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 393
      removed outlier: 3.914A  pdb=" N   VAL A 385 " --> pdb=" O   PHE A 393 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE A 475 " --> pdb=" O   HIS A 539 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7
      removed outlier: 6.494A  pdb=" N   ILE E   6 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ASN E  60 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   LEU E  25 " --> pdb=" O   ALA E  57 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   LEU E  59 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ASP E  27 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR E  78 " --> pdb=" O   PHE E  28 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU E  79 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR E  90 " --> pdb=" O   LEU E  79 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LEU E  81 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU E  86 " --> pdb=" O   LYS E  83 " (cutoff:3.500A)

    266 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      170 hydrogen bonds
      332 hydrogen bond angles
      0 basepair planarities
      68 basepair parallelities
      107 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2142
        1.33 -     1.46: 2831
        1.46 -     1.58: 3998
        1.58 -     1.70: 344
        1.70 -     1.82: 22
  Bond restraints: 9337
  Sorted by residual:
  bond pdb=" C1'  DT D  10 "
       pdb=" N1   DT D  10 "
    ideal  model  delta    sigma   weight residual
    1.468  1.512 -0.044 1.40e-02 5.10e+03 9.90e+00
  bond pdb=" N1    C B 177 "
       pdb=" C6    C B 177 "
    ideal  model  delta    sigma   weight residual
    1.367  1.352  0.015 6.00e-03 2.78e+04 6.65e+00
  bond pdb=" C4'  DA C  12 "
       pdb=" C3'  DA C  12 "
    ideal  model  delta    sigma   weight residual
    1.529  1.503  0.026 1.00e-02 1.00e+04 6.59e+00
  bond pdb=" C1'  DT C  24 "
       pdb=" N1   DT C  24 "
    ideal  model  delta    sigma   weight residual
    1.468  1.504 -0.036 1.40e-02 5.10e+03 6.55e+00
  bond pdb=" C4    C B 180 "
       pdb=" C5    C B 180 "
    ideal  model  delta    sigma   weight residual
    1.425  1.405  0.020 8.00e-03 1.56e+04 6.37e+00
  ... (remaining 9332 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 12138
        1.02 -     2.04: 890
        2.04 -     3.06: 354
        3.06 -     4.07: 52
        4.07 -     5.09: 4
  Bond angle restraints: 13438
  Sorted by residual:
  angle pdb=" N3   DT C  18 "
        pdb=" C4   DT C  18 "
        pdb=" O4   DT C  18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.44   -2.54 6.00e-01 2.78e+00 1.79e+01
  angle pdb=" N3   DT D   6 "
        pdb=" C4   DT D   6 "
        pdb=" O4   DT D   6 "
      ideal   model   delta    sigma   weight residual
     119.90  122.33   -2.43 6.00e-01 2.78e+00 1.64e+01
  angle pdb=" N3   DT D  10 "
        pdb=" C4   DT D  10 "
        pdb=" O4   DT D  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.30   -2.40 6.00e-01 2.78e+00 1.60e+01
  angle pdb=" O5'   C B  84 "
        pdb=" C5'   C B  84 "
        pdb=" C4'   C B  84 "
      ideal   model   delta    sigma   weight residual
     109.40  112.57   -3.17 8.00e-01 1.56e+00 1.57e+01
  angle pdb=" O5'   U B  10 "
        pdb=" C5'   U B  10 "
        pdb=" C4'   U B  10 "
      ideal   model   delta    sigma   weight residual
     109.40  112.57   -3.17 8.00e-01 1.56e+00 1.57e+01
  ... (remaining 13433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.41: 5207
       31.41 -    62.82: 425
       62.82 -    94.23: 79
       94.23 -   125.63: 1
      125.63 -   157.04: 2
  Dihedral angle restraints: 5714
    sinusoidal: 3871
      harmonic: 1843
  Sorted by residual:
  dihedral pdb=" C4'   A B 105 "
           pdb=" C3'   A B 105 "
           pdb=" O3'   A B 105 "
           pdb=" P     U B 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   47.04 -157.04     1      3.50e+01 8.16e-04 1.51e+01
  dihedral pdb=" C4'   U B 181 "
           pdb=" C3'   U B 181 "
           pdb=" O3'   U B 181 "
           pdb=" P     U B 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.72  144.28     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" O4'   U B 174 "
           pdb=" C1'   U B 174 "
           pdb=" N1    U B 174 "
           pdb=" C2    U B 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -74.00  -54.00     1      1.70e+01 3.46e-03 1.37e+01
  ... (remaining 5711 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1147
       0.043 -    0.086: 238
       0.086 -    0.129: 195
       0.129 -    0.173: 27
       0.173 -    0.216: 6
  Chirality restraints: 1613
  Sorted by residual:
  chirality pdb=" C3'  DA C  15 "
            pdb=" C4'  DA C  15 "
            pdb=" O3'  DA C  15 "
            pdb=" C2'  DA C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.51   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C3'  DC C  20 "
            pdb=" C4'  DC C  20 "
            pdb=" O3'  DC C  20 "
            pdb=" C2'  DC C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.53   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C1'   G B 175 "
            pdb=" O4'   G B 175 "
            pdb=" C2'   G B 175 "
            pdb=" N9    G B 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.28    0.19 2.00e-01 2.50e+01 9.23e-01
  ... (remaining 1610 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 178 "   -0.032 2.00e-02 2.50e+03   1.59e-02 5.71e+00
        pdb=" N1    C B 178 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    C B 178 "    0.003 2.00e-02 2.50e+03
        pdb=" O2    C B 178 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C B 178 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C B 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4    C B 178 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5    C B 178 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    C B 178 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 175 "   -0.029 2.00e-02 2.50e+03   1.29e-02 4.98e+00
        pdb=" N9    G B 175 "    0.032 2.00e-02 2.50e+03
        pdb=" C8    G B 175 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G B 175 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G B 175 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B 175 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G B 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G B 175 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B 175 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G B 175 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B 175 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   8 "   -0.027 2.00e-02 2.50e+03   1.48e-02 4.95e+00
        pdb=" N1    U B   8 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    U B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    U B   8 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    U B   8 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    U B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4    U B   8 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    U B   8 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U B   8 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 35
        2.55 -     3.14: 6494
        3.14 -     3.72: 14522
        3.72 -     4.31: 21297
        4.31 -     4.90: 30731
  Nonbonded interactions: 73079
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 414 "
            pdb=" O2'   U B 185 "
     model   vdw
     1.960 3.040
  nonbonded pdb=" O2'   U B 181 "
            pdb=" O5'   U B 182 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OE1 GLU A 417 "
            pdb=" NH2 ARG A 433 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" N   ASP E  10 "
            pdb=" OD1 ASN E  64 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   GLY A 201 "
            pdb=" OG1 THR A 204 "
     model   vdw
     2.212 3.040
  ... (remaining 73074 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:             4.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
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      :  0.005   0.044   9339  Z= 0.447
  Angle     :  0.674   5.092  13442  Z= 0.579
  Chirality :  0.051   0.216   1613
  Planarity :  0.004   0.032   1071
  Dihedral  : 19.720 157.041   4510
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  2.84 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.34), residues: 626
  helix:  2.55 (0.31), residues: 300
  sheet:  0.32 (0.55), residues: 73
  loop : -0.77 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.007   0.001   TYR A 314 
 PHE   0.013   0.002   PHE E  82 
 TRP   0.011   0.002   TRP A  47 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00517 /  0.45 ( 9337)
  covalent geometry    : angle       0.67359 /  0.58 (13438)
  SS BOND              : bond        0.00388 /  0.20 (    2)
  SS BOND              : angle       0.83418 /  0.43 (    4)
  hydrogen bonds       : bond        0.10661 /  6.75 (  436)
  hydrogen bonds       : angle       4.15313 /  3.00 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  359 GLU cc_start: 0.7606 (tp30) cc_final: 0.7284 (tp30)
REVERT: A  372 ASP cc_start: 0.7612 (t0) cc_final: 0.7208 (t0)
REVERT: A  382 GLN cc_start: 0.7601 (tt0) cc_final: 0.7390 (tt0)
REVERT: E    8 LEU cc_start: 0.5697 (mp) cc_final: 0.5481 (mp)
  outliers start: 3
  outliers final: 1
  residues processed: 99
  average time/residue: 0.6273
  time to fit residues: 65.3427
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 215 GLN
A 219 HIS
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 512 ASN
A 569 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.143381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.113195 restraints weight = 12925.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.42
r_work: 0.3331 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.079   9339  Z= 0.379
  Angle     :  0.670   7.642  13442  Z= 0.373
  Chirality :  0.052   0.496   1613
  Planarity :  0.005   0.038   1071
  Dihedral  : 22.220 169.129   3210
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  7.80 %
    Favored  : 90.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.33), residues: 626
  helix:  2.20 (0.30), residues: 302
  sheet:  0.32 (0.57), residues: 72
  loop : -0.79 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 206 
 TYR   0.011   0.002   TYR A  45 
 PHE   0.020   0.003   PHE E  82 
 TRP   0.024   0.003   TRP A 424 
 HIS   0.009   0.003   HIS A 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00800 /  0.38 ( 9337)
  covalent geometry    : angle       0.67025 /  0.37 (13438)
  SS BOND              : bond        0.00373 /  0.20 (    2)
  SS BOND              : angle       1.19093 /  0.58 (    4)
  hydrogen bonds       : bond        0.08515 /  5.74 (  436)
  hydrogen bonds       : angle       3.65966 /  2.67 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  359 GLU cc_start: 0.7743 (tp30) cc_final: 0.7455 (tp30)
REVERT: A  372 ASP cc_start: 0.7610 (t0) cc_final: 0.7236 (t0)
REVERT: A  382 GLN cc_start: 0.7792 (tt0) cc_final: 0.7550 (tt0)
REVERT: A  421 ASP cc_start: 0.7915 (m-30) cc_final: 0.7656 (m-30)
REVERT: A  433 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8267 (ttm170)
REVERT: A  478 GLU cc_start: 0.6764 (tp30) cc_final: 0.6549 (tp30)
REVERT: E    8 LEU cc_start: 0.6039 (mp) cc_final: 0.5767 (mp)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 0.6297
  time to fit residues: 67.9196
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain E residue   33 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0970
   chunk 14 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.146839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.116593 restraints weight = 12963.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.45
r_work: 0.3383 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9339  Z= 0.150
  Angle     :  0.491   6.333  13442  Z= 0.293
  Chirality :  0.038   0.418   1613
  Planarity :  0.004   0.036   1071
  Dihedral  : 22.230 166.691   3210
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  9.40 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.34), residues: 626
  helix:  2.67 (0.30), residues: 303
  sheet:  0.47 (0.58), residues: 72
  loop : -0.56 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.013   0.001   TYR A  45 
 PHE   0.015   0.002   PHE E  82 
 TRP   0.017   0.002   TRP A  47 
 HIS   0.004   0.001   HIS A 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.15 ( 9337)
  covalent geometry    : angle       0.49117 /  0.29 (13438)
  SS BOND              : bond        0.00301 /  0.15 (    2)
  SS BOND              : angle       0.84125 /  0.42 (    4)
  hydrogen bonds       : bond        0.06051 /  4.06 (  436)
  hydrogen bonds       : angle       3.31472 /  2.41 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8223 (t0) cc_final: 0.7980 (t70)
REVERT: A  359 GLU cc_start: 0.7768 (tp30) cc_final: 0.7424 (tp30)
REVERT: A  372 ASP cc_start: 0.7624 (t0) cc_final: 0.7256 (t0)
REVERT: A  382 GLN cc_start: 0.7777 (tt0) cc_final: 0.7519 (tt0)
REVERT: E    8 LEU cc_start: 0.5888 (mp) cc_final: 0.5649 (mp)
  outliers start: 12
  outliers final: 5
  residues processed: 106
  average time/residue: 0.5571
  time to fit residues: 62.2607
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0870
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 512 ASN
** E  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.146368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.116192 restraints weight = 13058.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.44
r_work: 0.3375 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9339  Z= 0.173
  Angle     :  0.497   6.573  13442  Z= 0.292
  Chirality :  0.039   0.438   1613
  Planarity :  0.004   0.038   1071
  Dihedral  : 22.212 167.521   3210
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.46 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.34), residues: 626
  helix:  2.77 (0.29), residues: 303
  sheet:  0.46 (0.58), residues: 72
  loop : -0.61 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.019   0.001   TYR A  45 
 PHE   0.013   0.002   PHE A 228 
 TRP   0.015   0.002   TRP A  47 
 HIS   0.005   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.17 ( 9337)
  covalent geometry    : angle       0.49703 /  0.29 (13438)
  SS BOND              : bond        0.00258 /  0.13 (    2)
  SS BOND              : angle       0.74767 /  0.37 (    4)
  hydrogen bonds       : bond        0.06145 /  4.12 (  436)
  hydrogen bonds       : angle       3.24050 /  2.36 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8245 (t0) cc_final: 0.8016 (t70)
REVERT: A  359 GLU cc_start: 0.7788 (tp30) cc_final: 0.7457 (tp30)
REVERT: A  372 ASP cc_start: 0.7619 (t0) cc_final: 0.7255 (t0)
REVERT: A  382 GLN cc_start: 0.7788 (tt0) cc_final: 0.7528 (tt0)
REVERT: A  414 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (m-30)
REVERT: E    8 LEU cc_start: 0.5881 (mp) cc_final: 0.5661 (mp)
  outliers start: 13
  outliers final: 6
  residues processed: 105
  average time/residue: 0.5651
  time to fit residues: 62.7254
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    0.2980
   chunk 42 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0770
   chunk 21 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** 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 = 0.3910 r_free = 0.3910 target = 0.148130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117988 restraints weight = 12970.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.44
r_work: 0.3401 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9339  Z= 0.130
  Angle     :  0.456   6.304  13442  Z= 0.273
  Chirality :  0.037   0.410   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.218 166.240   3210
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.46 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.34), residues: 626
  helix:  2.97 (0.30), residues: 303
  sheet:  0.53 (0.56), residues: 79
  loop : -0.52 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.021   0.001   TYR A  45 
 PHE   0.011   0.001   PHE E  82 
 TRP   0.014   0.002   TRP A  47 
 HIS   0.003   0.001   HIS A 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.13 ( 9337)
  covalent geometry    : angle       0.45625 /  0.27 (13438)
  SS BOND              : bond        0.00291 /  0.14 (    2)
  SS BOND              : angle       0.78603 /  0.39 (    4)
  hydrogen bonds       : bond        0.05444 /  3.65 (  436)
  hydrogen bonds       : angle       3.14626 /  2.29 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8207 (t0) cc_final: 0.7986 (t70)
REVERT: A  359 GLU cc_start: 0.7739 (tp30) cc_final: 0.7426 (tp30)
REVERT: A  372 ASP cc_start: 0.7603 (t0) cc_final: 0.7237 (t0)
REVERT: A  382 GLN cc_start: 0.7788 (tt0) cc_final: 0.7525 (tt0)
REVERT: A  414 ASP cc_start: 0.8144 (m-30) cc_final: 0.7799 (m-30)
REVERT: A  417 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: E    8 LEU cc_start: 0.5826 (mp) cc_final: 0.5604 (mp)
  outliers start: 13
  outliers final: 7
  residues processed: 109
  average time/residue: 0.5313
  time to fit residues: 61.5391
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0170
   chunk 27 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** 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 = 0.3905 r_free = 0.3905 target = 0.147677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.117723 restraints weight = 13044.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.43
r_work: 0.3397 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9339  Z= 0.138
  Angle     :  0.457   6.405  13442  Z= 0.271
  Chirality :  0.037   0.420   1613
  Planarity :  0.004   0.036   1071
  Dihedral  : 22.204 166.976   3210
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.35 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.34), residues: 626
  helix:  3.05 (0.30), residues: 303
  sheet:  0.61 (0.59), residues: 72
  loop : -0.49 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.019   0.001   TYR A  45 
 PHE   0.011   0.002   PHE A 228 
 TRP   0.013   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.14 ( 9337)
  covalent geometry    : angle       0.45717 /  0.27 (13438)
  SS BOND              : bond        0.00261 /  0.13 (    2)
  SS BOND              : angle       0.76082 /  0.38 (    4)
  hydrogen bonds       : bond        0.05479 /  3.66 (  436)
  hydrogen bonds       : angle       3.09274 /  2.25 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8198 (t0) cc_final: 0.7983 (t70)
REVERT: A  359 GLU cc_start: 0.7760 (tp30) cc_final: 0.7462 (tp30)
REVERT: A  372 ASP cc_start: 0.7608 (t0) cc_final: 0.7269 (t0)
REVERT: A  382 GLN cc_start: 0.7786 (tt0) cc_final: 0.7521 (tt0)
REVERT: A  414 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7801 (m-30)
REVERT: A  417 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7380 (mm-30)
REVERT: E    8 LEU cc_start: 0.5835 (mp) cc_final: 0.5617 (mp)
  outliers start: 14
  outliers final: 9
  residues processed: 103
  average time/residue: 0.5494
  time to fit residues: 59.7412
Evaluate side-chains
  104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    2.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.142150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112018 restraints weight = 13023.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.46
r_work: 0.3318 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.093   9339  Z= 0.484
  Angle     :  0.735   8.186  13442  Z= 0.401
  Chirality :  0.059   0.563   1613
  Planarity :  0.006   0.039   1071
  Dihedral  : 22.348 175.602   3210
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.70 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.33), residues: 626
  helix:  2.12 (0.29), residues: 304
  sheet:  0.06 (0.57), residues: 73
  loop : -0.85 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 534 
 TYR   0.024   0.003   TYR A  45 
 PHE   0.020   0.003   PHE A 235 
 TRP   0.030   0.004   TRP A 424 
 HIS   0.009   0.003   HIS A 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01016 /  0.48 ( 9337)
  covalent geometry    : angle       0.73507 /  0.40 (13438)
  SS BOND              : bond        0.00351 /  0.18 (    2)
  SS BOND              : angle       0.96593 /  0.48 (    4)
  hydrogen bonds       : bond        0.09304 /  6.32 (  436)
  hydrogen bonds       : angle       3.56666 /  2.59 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8288 (t0) cc_final: 0.8053 (t70)
REVERT: A  359 GLU cc_start: 0.7755 (tp30) cc_final: 0.7451 (tp30)
REVERT: A  372 ASP cc_start: 0.7640 (t0) cc_final: 0.7381 (t0)
REVERT: A  382 GLN cc_start: 0.7832 (tt0) cc_final: 0.7561 (tt0)
REVERT: A  414 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7852 (m-30)
REVERT: A  417 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7394 (mm-30)
REVERT: A  478 GLU cc_start: 0.6766 (tp30) cc_final: 0.6516 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 105
  average time/residue: 0.5921
  time to fit residues: 65.8041
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   38 MET
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0670
   chunk 73 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.146463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116316 restraints weight = 12988.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.44
r_work: 0.3383 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9339  Z= 0.144
  Angle     :  0.496   6.276  13442  Z= 0.293
  Chirality :  0.038   0.427   1613
  Planarity :  0.004   0.041   1071
  Dihedral  : 22.345 167.812   3210
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.01 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.34), residues: 626
  helix:  2.78 (0.30), residues: 303
  sheet:  0.32 (0.57), residues: 73
  loop : -0.64 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 534 
 TYR   0.020   0.001   TYR A  45 
 PHE   0.015   0.002   PHE E  82 
 TRP   0.020   0.002   TRP A 424 
 HIS   0.003   0.001   HIS A 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 ( 9337)
  covalent geometry    : angle       0.49584 /  0.29 (13438)
  SS BOND              : bond        0.00293 /  0.15 (    2)
  SS BOND              : angle       0.80133 /  0.41 (    4)
  hydrogen bonds       : bond        0.05900 /  4.00 (  436)
  hydrogen bonds       : angle       3.20003 /  2.32 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8240 (t0) cc_final: 0.8034 (t70)
REVERT: A  359 GLU cc_start: 0.7762 (tp30) cc_final: 0.7447 (tp30)
REVERT: A  372 ASP cc_start: 0.7576 (t0) cc_final: 0.7228 (t0)
REVERT: A  382 GLN cc_start: 0.7775 (tt0) cc_final: 0.7524 (tt0)
REVERT: A  414 ASP cc_start: 0.8118 (m-30) cc_final: 0.7753 (m-30)
REVERT: E    8 LEU cc_start: 0.6116 (mp) cc_final: 0.5852 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 101
  average time/residue: 0.5732
  time to fit residues: 61.3029
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0980
   chunk 69 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.146195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116193 restraints weight = 12915.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.42
r_work: 0.3382 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9339  Z= 0.162
  Angle     :  0.490   6.473  13442  Z= 0.287
  Chirality :  0.039   0.434   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.275 167.703   3210
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.83 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.34), residues: 626
  helix:  2.83 (0.30), residues: 303
  sheet:  0.41 (0.57), residues: 72
  loop : -0.57 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 534 
 TYR   0.008   0.001   TYR A 314 
 PHE   0.013   0.002   PHE E  82 
 TRP   0.020   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.16 ( 9337)
  covalent geometry    : angle       0.48948 /  0.29 (13438)
  SS BOND              : bond        0.00252 /  0.13 (    2)
  SS BOND              : angle       0.75387 /  0.38 (    4)
  hydrogen bonds       : bond        0.05924 /  3.98 (  436)
  hydrogen bonds       : angle       3.16056 /  2.28 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8249 (t0) cc_final: 0.8026 (t70)
REVERT: A  359 GLU cc_start: 0.7745 (tp30) cc_final: 0.7428 (tp30)
REVERT: A  372 ASP cc_start: 0.7578 (t0) cc_final: 0.7231 (t0)
REVERT: A  382 GLN cc_start: 0.7813 (tt0) cc_final: 0.7544 (tt0)
REVERT: A  414 ASP cc_start: 0.8130 (m-30) cc_final: 0.7751 (m-30)
REVERT: E    8 LEU cc_start: 0.6096 (mp) cc_final: 0.5792 (mp)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.5361
  time to fit residues: 57.5482
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0870
   chunk 28 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** 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 = 0.3895 r_free = 0.3895 target = 0.146767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.116736 restraints weight = 12964.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.42
r_work: 0.3389 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9339  Z= 0.149
  Angle     :  0.478   6.419  13442  Z= 0.281
  Chirality :  0.038   0.426   1613
  Planarity :  0.004   0.036   1071
  Dihedral  : 22.264 167.358   3210
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.01 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.34), residues: 626
  helix:  2.91 (0.30), residues: 303
  sheet:  0.43 (0.57), residues: 72
  loop : -0.51 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 534 
 TYR   0.011   0.001   TYR A 314 
 PHE   0.012   0.002   PHE E  82 
 TRP   0.019   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 ( 9337)
  covalent geometry    : angle       0.47773 /  0.28 (13438)
  SS BOND              : bond        0.00275 /  0.14 (    2)
  SS BOND              : angle       0.76646 /  0.39 (    4)
  hydrogen bonds       : bond        0.05648 /  3.79 (  436)
  hydrogen bonds       : angle       3.11340 /  2.24 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  269 ASP cc_start: 0.8239 (t0) cc_final: 0.8023 (t70)
REVERT: A  359 GLU cc_start: 0.7755 (tp30) cc_final: 0.7447 (tp30)
REVERT: A  372 ASP cc_start: 0.7601 (t0) cc_final: 0.7349 (t0)
REVERT: A  382 GLN cc_start: 0.7805 (tt0) cc_final: 0.7535 (tt0)
REVERT: A  414 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7748 (m-30)
REVERT: E    8 LEU cc_start: 0.6064 (mp) cc_final: 0.5754 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 99
  average time/residue: 0.5216
  time to fit residues: 54.5669
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0470
   chunk 49 optimal weight:    0.0170
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.4716

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.147486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.117595 restraints weight = 12873.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.42
r_work: 0.3398 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9339  Z= 0.131
  Angle     :  0.464   6.340  13442  Z= 0.275
  Chirality :  0.037   0.418   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.254 166.950   3210
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.18 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.34), residues: 626
  helix:  3.02 (0.30), residues: 303
  sheet:  0.41 (0.55), residues: 79
  loop : -0.47 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 534 
 TYR   0.011   0.001   TYR A 304 
 PHE   0.012   0.002   PHE E  82 
 TRP   0.019   0.002   TRP A 424 
 HIS   0.003   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.13 ( 9337)
  covalent geometry    : angle       0.46421 /  0.27 (13438)
  SS BOND              : bond        0.00270 /  0.14 (    2)
  SS BOND              : angle       0.72831 /  0.38 (    4)
  hydrogen bonds       : bond        0.05410 /  3.62 (  436)
  hydrogen bonds       : angle       3.07605 /  2.21 ( 1085)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3302.05 seconds
wall clock time: 56 minutes 49.53 seconds (3409.53 seconds total)