Starting phenix.real_space_refine
on Fri Jun 13 22:10:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ces_45517/06_2025/9ces_45517_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ces_45517/06_2025/9ces_45517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ces_45517/06_2025/9ces_45517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ces_45517/06_2025/9ces_45517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ces_45517/06_2025/9ces_45517_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ces_45517/06_2025/9ces_45517_neut.cif"
  }
  resolution = 3.28
  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=   0.002 sd=   0.036
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: 6
    Type Number    sf(0)   Gaussians
     P     181      5.49       5
     S      38      5.16       5
     C    4897      2.51       5
     N    1619      2.21       5
     O    2103      1.98       5
     H    7001      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 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: 15839
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "N"
      Number of atoms: 475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 475
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "P"
      Number of atoms: 10029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 10029
          Classifications: {'peptide': 612}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 591}
          Chain breaks: 3
    Chain: "T"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 761
          Classifications: {'DNA': 24}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 23}
    Chain: "W"
      Number of atoms: 4574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 4574
          Classifications: {'RNA': 142}
          Modifications used: {'3*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 69, 'rna3p_pyr': 50}
          Link IDs: {'rna2p': 23, 'rna3p': 118}
  Time building chain proxies: 8.77, per 1000 atoms: 0.55
  Number of scatterers: 15839
  At special positions: 0
  Unit cell: (81.549, 111.384, 166.413, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      38     16.00
     P     181     15.00
     O    2103      8.00
     N    1619      7.00
     C    4897      6.00
     H    7001      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 4.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 3 sheets defined
      57.0% alpha, 8.8% beta
      54 base pairs and 93 stacking pairs defined.
    Time for finding SS restraints: 7.99
  Creating SS restraints...
    Processing helix  chain 'P' and resid 16 through 53
    Processing helix  chain 'P' and resid 65 through 77
    Processing helix  chain 'P' and resid 88 through 110
    Processing helix  chain 'P' and resid 114 through 119
    Processing helix  chain 'P' and resid 124 through 162
      removed outlier: 3.862A  pdb=" N   ALA P 129 " --> pdb=" O   SER P 125 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   TYR P 130 " --> pdb=" O   HIS P 126 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER P 131 " --> pdb=" O   VAL P 127 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS P 146 " --> pdb=" O   ASN P 142 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER P 148 " --> pdb=" O   GLU P 144 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LYS P 149 " --> pdb=" O   ALA P 145 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR P 150 " --> pdb=" O   HIS P 146 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 165 through 182
    Processing helix  chain 'P' and resid 217 through 222
      removed outlier: 3.943A  pdb=" N   ASP P 221 " --> pdb=" O   PRO P 217 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU P 222 " --> pdb=" O   ARG P 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 217 through 222'
    Processing helix  chain 'P' and resid 225 through 228
    Processing helix  chain 'P' and resid 229 through 243
    Processing helix  chain 'P' and resid 273 through 281
    Processing helix  chain 'P' and resid 282 through 298
      removed outlier: 4.355A  pdb=" N   ASP P 288 " --> pdb=" O   ASP P 284 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 312 through 318
    Processing helix  chain 'P' and resid 323 through 339
      removed outlier: 3.621A  pdb=" N   ALA P 327 " --> pdb=" O   SER P 323 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 346 through 351
      removed outlier: 3.671A  pdb=" N   LEU P 350 " --> pdb=" O   GLN P 346 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 385 through 387
      No H-bonds generated for 'chain 'P' and resid 385 through 387'
    Processing helix  chain 'P' and resid 416 through 421
    Processing helix  chain 'P' and resid 447 through 454
    Processing helix  chain 'P' and resid 455 through 470
    Processing helix  chain 'P' and resid 472 through 479
    Processing helix  chain 'P' and resid 480 through 483
    Processing helix  chain 'P' and resid 489 through 512
      removed outlier: 3.729A  pdb=" N   TYR P 496 " --> pdb=" O   MET P 492 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG P 502 " --> pdb=" O   CYS P 498 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET P 503 " --> pdb=" O   SER P 499 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   HIS P 505 " --> pdb=" O   LYS P 501 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   MET P 506 " --> pdb=" O   ARG P 502 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 513 through 543
      removed outlier: 4.155A  pdb=" N   ARG P 517 " --> pdb=" O   HIS P 513 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TYR P 524 " --> pdb=" O   LYS P 520 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS P 528 " --> pdb=" O   TYR P 524 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER P 529 " --> pdb=" O   ASN P 525 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 556 through 564
    Processing helix  chain 'P' and resid 569 through 571
      No H-bonds generated for 'chain 'P' and resid 569 through 571'
    Processing helix  chain 'P' and resid 600 through 604
    Processing helix  chain 'P' and resid 657 through 670
    Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 10
      removed outlier: 6.995A  pdb=" N   SER P 376 " --> pdb=" O   VAL P 371 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   VAL P 371 " --> pdb=" O   SER P 376 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   SER P 378 " --> pdb=" O   ALA P 369 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ALA P 369 " --> pdb=" O   SER P 378 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   GLN P 380 " --> pdb=" O   ASP P 367 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 442 through 446
      removed outlier: 6.298A  pdb=" N   LYS P 422 " --> pdb=" O   ILE P 574 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   GLY P 576 " --> pdb=" O   LYS P 422 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU P 424 " --> pdb=" O   GLY P 576 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   GLY P 578 " --> pdb=" O   LEU P 424 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   CYS P 426 " --> pdb=" O   GLY P 578 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 629 through 631

    258 hydrogen bonds defined for protein.
    762 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      138 hydrogen bonds
      268 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      93 stacking parallelities
  Total time for adding SS restraints: 6.40

  Time building geometry restraints manager: 5.08 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 6984
        1.11 -     1.29: 958
        1.29 -     1.47: 4240
        1.47 -     1.64: 4163
        1.64 -     1.82: 59
  Bond restraints: 16404
  Sorted by residual:
  bond pdb=" C2    A W 137 "
       pdb=" H2    A W 137 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C5    U W  41 "
       pdb=" H5    U W  41 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C8    A W 141 "
       pdb=" H8    A W 141 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C5    U W  20 "
       pdb=" H5    U W  20 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   ASN P 114 "
       pdb=" H   ASN P 114 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 16399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 25375
        2.71 -     5.41: 3355
        5.41 -     8.12: 707
        8.12 -    10.82: 37
       10.82 -    13.53: 19
  Bond angle restraints: 29493
  Sorted by residual:
  angle pdb=" C4'   C W  81 "
        pdb=" O4'   C W  81 "
        pdb=" C1'   C W  81 "
      ideal   model   delta    sigma   weight residual
     109.70   99.16   10.54 1.00e+00 1.00e+00 1.11e+02
  angle pdb=" C4'   G W  79 "
        pdb=" O4'   G W  79 "
        pdb=" C1'   G W  79 "
      ideal   model   delta    sigma   weight residual
     109.70  100.22    9.48 1.00e+00 1.00e+00 8.99e+01
  angle pdb=" O4'   C W  81 "
        pdb=" C1'   C W  81 "
        pdb=" C2'   C W  81 "
      ideal   model   delta    sigma   weight residual
     105.80   96.55    9.25 1.00e+00 1.00e+00 8.55e+01
  angle pdb=" O3'   A W  82 "
        pdb=" C3'   A W  82 "
        pdb=" C2'   A W  82 "
      ideal   model   delta    sigma   weight residual
     109.50  123.03  -13.53 1.50e+00 4.44e-01 8.13e+01
  angle pdb=" C4'   U W  41 "
        pdb=" C3'   U W  41 "
        pdb=" C2'   U W  41 "
      ideal   model   delta    sigma   weight residual
     102.60   94.59    8.01 1.00e+00 1.00e+00 6.41e+01
  ... (remaining 29488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.55: 6851
       33.55 -    67.10: 711
       67.10 -   100.65: 92
      100.65 -   134.19: 9
      134.19 -   167.74: 3
  Dihedral angle restraints: 7666
    sinusoidal: 5519
      harmonic: 2147
  Sorted by residual:
  dihedral pdb=" O4'   A W  53 "
           pdb=" C2'   A W  53 "
           pdb=" C1'   A W  53 "
           pdb=" C3'   A W  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -28.09   53.09     1      8.00e+00 1.56e-02 5.99e+01
  dihedral pdb=" C5'   G W  79 "
           pdb=" C4'   G W  79 "
           pdb=" C3'   G W  79 "
           pdb=" O3'   G W  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   94.16   52.84     1      8.00e+00 1.56e-02 5.94e+01
  dihedral pdb=" C3'   G W  45 "
           pdb=" C4'   G W  45 "
           pdb=" O4'   G W  45 "
           pdb=" C1'   G W  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00  -32.55   52.55     1      8.00e+00 1.56e-02 5.88e+01
  ... (remaining 7663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1216
       0.105 -    0.210: 328
       0.210 -    0.315: 37
       0.315 -    0.420: 14
       0.420 -    0.525: 2
  Chirality restraints: 1597
  Sorted by residual:
  chirality pdb=" C4'   C W  81 "
            pdb=" C5'   C W  81 "
            pdb=" O4'   C W  81 "
            pdb=" C3'   C W  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.98   -0.53 2.00e-01 2.50e+01 6.90e+00
  chirality pdb=" C4'   A W  43 "
            pdb=" C5'   A W  43 "
            pdb=" O4'   A W  43 "
            pdb=" C3'   A W  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.06   -0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" C4'   U W  41 "
            pdb=" C5'   U W  41 "
            pdb=" O4'   U W  41 "
            pdb=" C3'   U W  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.09   -0.40 2.00e-01 2.50e+01 4.07e+00
  ... (remaining 1594 not shown)

  Planarity restraints: 1785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W 110 "   -0.461 2.00e-02 2.50e+03   1.75e-01 1.07e+03
        pdb=" N9    G W 110 "    0.001 2.00e-02 2.50e+03
        pdb=" C8    G W 110 "    0.149 2.00e-02 2.50e+03
        pdb=" N7    G W 110 "    0.133 2.00e-02 2.50e+03
        pdb=" C5    G W 110 "    0.013 2.00e-02 2.50e+03
        pdb=" C6    G W 110 "   -0.112 2.00e-02 2.50e+03
        pdb=" O6    G W 110 "   -0.224 2.00e-02 2.50e+03
        pdb=" N1    G W 110 "   -0.057 2.00e-02 2.50e+03
        pdb=" C2    G W 110 "    0.047 2.00e-02 2.50e+03
        pdb=" N2    G W 110 "    0.246 2.00e-02 2.50e+03
        pdb=" N3    G W 110 "    0.056 2.00e-02 2.50e+03
        pdb=" C4    G W 110 "    0.041 2.00e-02 2.50e+03
        pdb=" H8    G W 110 "    0.204 2.00e-02 2.50e+03
        pdb=" H1    G W 110 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W  71 "   -0.457 2.00e-02 2.50e+03   1.74e-01 1.06e+03
        pdb=" N9    G W  71 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    G W  71 "    0.156 2.00e-02 2.50e+03
        pdb=" N7    G W  71 "    0.049 2.00e-02 2.50e+03
        pdb=" C5    G W  71 "   -0.021 2.00e-02 2.50e+03
        pdb=" C6    G W  71 "   -0.109 2.00e-02 2.50e+03
        pdb=" O6    G W  71 "   -0.237 2.00e-02 2.50e+03
        pdb=" N1    G W  71 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2    G W  71 "    0.045 2.00e-02 2.50e+03
        pdb=" N2    G W  71 "    0.198 2.00e-02 2.50e+03
        pdb=" N3    G W  71 "    0.043 2.00e-02 2.50e+03
        pdb=" C4    G W  71 "    0.032 2.00e-02 2.50e+03
        pdb=" H8    G W  71 "    0.268 2.00e-02 2.50e+03
        pdb=" H1    G W  71 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C W  81 "    0.377 2.00e-02 2.50e+03   1.85e-01 9.43e+02
        pdb=" N1    C W  81 "    0.058 2.00e-02 2.50e+03
        pdb=" C2    C W  81 "   -0.054 2.00e-02 2.50e+03
        pdb=" O2    C W  81 "   -0.357 2.00e-02 2.50e+03
        pdb=" N3    C W  81 "    0.043 2.00e-02 2.50e+03
        pdb=" C4    C W  81 "    0.104 2.00e-02 2.50e+03
        pdb=" N4    C W  81 "    0.206 2.00e-02 2.50e+03
        pdb=" C5    C W  81 "   -0.052 2.00e-02 2.50e+03
        pdb=" C6    C W  81 "   -0.039 2.00e-02 2.50e+03
        pdb=" H5    C W  81 "   -0.164 2.00e-02 2.50e+03
        pdb=" H6    C W  81 "   -0.122 2.00e-02 2.50e+03
  ... (remaining 1782 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 770
        2.11 -     2.73: 20927
        2.73 -     3.35: 44014
        3.35 -     3.98: 58796
        3.98 -     4.60: 84987
  Nonbonded interactions: 209494
  Sorted by model distance:
  nonbonded pdb="HO2'   C W  78 "
            pdb=" H4'   G W  79 "
     model   vdw
     1.487 2.270
  nonbonded pdb="HO2'   G W  42 "
            pdb=" H4'   A W  43 "
     model   vdw
     1.507 2.270
  nonbonded pdb="HO2'   C W  81 "
            pdb=" OP1   A W  82 "
     model   vdw
     1.561 2.450
  nonbonded pdb="HO2'   A W 123 "
            pdb=" OP2   A W 124 "
     model   vdw
     1.563 2.450
  nonbonded pdb="HO2'   A W  82 "
            pdb=" OP2   U W  83 "
     model   vdw
     1.565 2.450
  ... (remaining 209489 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:             3.410
  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:             0.230
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     43.050
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4396
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      :  0.013   0.057   9403  Z= 0.791
  Angle     :  1.955  13.527  13534  Z= 1.297
  Chirality :  0.096   0.525   1597
  Planarity :  0.034   0.180   1055
  Dihedral  : 23.225 167.742   4512
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  2.00 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.87 (0.32), residues: 604
  helix: -0.39 (0.27), residues: 316
  sheet: -1.56 (0.62), residues: 40
  loop : -0.41 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.116   0.021   TRP P 654 
 HIS   0.012   0.003   HIS P 641 
 PHE   0.054   0.012   PHE P 519 
 TYR   0.074   0.019   TYR P 445 
 ARG   0.015   0.001   ARG P 668 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14811 (  396)
  hydrogen bonds       : angle       7.94823 ( 1030)
  covalent geometry    : bond        0.01345 ( 9403)
  covalent geometry    : angle       1.95536 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.940 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  256 ASN cc_start: 0.5854 (t0) cc_final: 0.5475 (t0)
REVERT: P  272 ASP cc_start: 0.7284 (p0) cc_final: 0.7032 (p0)
REVERT: P  492 MET cc_start: 0.6846 (mmm) cc_final: 0.6321 (tpt)
  outliers start: 5
  outliers final: 2
  residues processed: 134
  average time/residue: 0.7646
  time to fit residues: 124.1584
Evaluate side-chains
  75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  567 VAL
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.232299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.188687 restraints weight = 33282.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.4382 rms_B_bonded: 2.80
r_work: 0.3952 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9403  Z= 0.200
  Angle     :  0.830  10.920  13534  Z= 0.454
  Chirality :  0.047   0.290   1597
  Planarity :  0.005   0.044   1055
  Dihedral  : 25.153 167.072   3246
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.09 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.60 (0.34), residues: 604
  helix:  1.18 (0.29), residues: 318
  sheet: -1.77 (0.59), residues: 53
  loop :  0.02 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P 655 
 HIS   0.005   0.001   HIS P  68 
 PHE   0.017   0.002   PHE P  67 
 TYR   0.011   0.001   TYR P  45 
 ARG   0.004   0.001   ARG P 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06876 (  396)
  hydrogen bonds       : angle       4.58760 ( 1030)
  covalent geometry    : bond        0.00403 ( 9403)
  covalent geometry    : angle       0.82979 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  140 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7933 (pttt)
REVERT: P  484 GLN cc_start: 0.5254 (tp-100) cc_final: 0.4886 (pt0)
REVERT: P  492 MET cc_start: 0.7270 (mmm) cc_final: 0.6935 (tpt)
  outliers start: 9
  outliers final: 5
  residues processed: 88
  average time/residue: 0.4637
  time to fit residues: 54.5017
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  489 HIS
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.226860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.170756 restraints weight = 32100.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.4187 rms_B_bonded: 1.87
r_work: 0.3952 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.5059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9403  Z= 0.258
  Angle     :  0.782   7.648  13534  Z= 0.433
  Chirality :  0.045   0.221   1597
  Planarity :  0.007   0.069   1055
  Dihedral  : 25.094 176.284   3245
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 10.00 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.07 (0.34), residues: 604
  helix:  0.76 (0.28), residues: 317
  sheet: -1.91 (0.66), residues: 51
  loop : -0.32 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP P 364 
 HIS   0.005   0.001   HIS P 146 
 PHE   0.023   0.003   PHE P 260 
 TYR   0.019   0.002   TYR P 445 
 ARG   0.008   0.001   ARG P  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07538 (  396)
  hydrogen bonds       : angle       4.71043 ( 1030)
  covalent geometry    : bond        0.00544 ( 9403)
  covalent geometry    : angle       0.78208 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6849 (mtt90)
REVERT: P  560 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7573 (mtm180)
  outliers start: 18
  outliers final: 10
  residues processed: 77
  average time/residue: 0.6643
  time to fit residues: 63.7454
Evaluate side-chains
  69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 568 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.230386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.187963 restraints weight = 33309.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 3.03
r_work: 0.3894 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9403  Z= 0.158
  Angle     :  0.630   6.761  13534  Z= 0.346
  Chirality :  0.038   0.191   1597
  Planarity :  0.005   0.043   1055
  Dihedral  : 24.823 175.230   3245
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.45 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.80 (0.35), residues: 604
  helix:  1.51 (0.29), residues: 316
  sheet: -1.63 (0.61), residues: 58
  loop : -0.13 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P 577 
 HIS   0.005   0.001   HIS P  68 
 PHE   0.013   0.001   PHE P  67 
 TYR   0.009   0.001   TYR P  45 
 ARG   0.006   0.000   ARG P  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05814 (  396)
  hydrogen bonds       : angle       4.11166 ( 1030)
  covalent geometry    : bond        0.00318 ( 9403)
  covalent geometry    : angle       0.63021 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  484 GLN cc_start: 0.5791 (pm20) cc_final: 0.4351 (pt0)
REVERT: P  492 MET cc_start: 0.7401 (mmm) cc_final: 0.7183 (mmp)
REVERT: P  560 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7652 (mtm180)
  outliers start: 10
  outliers final: 10
  residues processed: 73
  average time/residue: 0.4992
  time to fit residues: 49.3546
Evaluate side-chains
  71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  522 LEU
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 71 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
P 635 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.227626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.181751 restraints weight = 33718.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4307 rms_B_bonded: 3.17
r_work: 0.3856 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.5972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9403  Z= 0.202
  Angle     :  0.663   6.080  13534  Z= 0.365
  Chirality :  0.039   0.186   1597
  Planarity :  0.006   0.050   1055
  Dihedral  : 24.868 178.548   3245
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.82 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.51 (0.35), residues: 604
  helix:  1.29 (0.29), residues: 316
  sheet: -1.71 (0.64), residues: 56
  loop : -0.33 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 335 
 HIS   0.008   0.001   HIS P  68 
 PHE   0.018   0.002   PHE P 260 
 TYR   0.017   0.002   TYR P  44 
 ARG   0.005   0.000   ARG P 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06476 (  396)
  hydrogen bonds       : angle       4.26091 ( 1030)
  covalent geometry    : bond        0.00427 ( 9403)
  covalent geometry    : angle       0.66300 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7415 (mtt90)
REVERT: P  492 MET cc_start: 0.7515 (mmm) cc_final: 0.7177 (mmp)
REVERT: P  560 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7720 (mtm180)
  outliers start: 14
  outliers final: 12
  residues processed: 80
  average time/residue: 0.6410
  time to fit residues: 68.2851
Evaluate side-chains
  76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    4 ILE
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  263 SER
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.229051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.184211 restraints weight = 33687.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 3.19
r_work: 0.3875 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.6318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9403  Z= 0.178
  Angle     :  0.622   6.395  13534  Z= 0.340
  Chirality :  0.037   0.177   1597
  Planarity :  0.005   0.045   1055
  Dihedral  : 24.770 178.048   3245
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.91 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.73 (0.35), residues: 604
  helix:  1.49 (0.29), residues: 317
  sheet: -1.74 (0.67), residues: 53
  loop : -0.27 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P 577 
 HIS   0.008   0.001   HIS P  68 
 PHE   0.014   0.002   PHE P 260 
 TYR   0.017   0.002   TYR P 475 
 ARG   0.006   0.000   ARG P 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05894 (  396)
  hydrogen bonds       : angle       4.07232 ( 1030)
  covalent geometry    : bond        0.00371 ( 9403)
  covalent geometry    : angle       0.62166 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7213 (mtt90)
REVERT: P  492 MET cc_start: 0.7558 (mmm) cc_final: 0.7346 (mmp)
REVERT: P  560 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7834 (mtm180)
  outliers start: 11
  outliers final: 9
  residues processed: 69
  average time/residue: 0.5090
  time to fit residues: 46.0891
Evaluate side-chains
  68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  522 LEU
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 73 optimal weight:   40.0000
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.226201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.184212 restraints weight = 33629.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.4338 rms_B_bonded: 3.18
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.6587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9403  Z= 0.225
  Angle     :  0.673   6.456  13534  Z= 0.367
  Chirality :  0.039   0.183   1597
  Planarity :  0.006   0.051   1055
  Dihedral  : 24.868 178.648   3245
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.18 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.40 (0.35), residues: 604
  helix:  1.19 (0.29), residues: 317
  sheet: -1.82 (0.68), residues: 51
  loop : -0.41 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P 577 
 HIS   0.005   0.001   HIS P  68 
 PHE   0.019   0.002   PHE P 260 
 TYR   0.017   0.002   TYR P 105 
 ARG   0.004   0.001   ARG P 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06635 (  396)
  hydrogen bonds       : angle       4.31282 ( 1030)
  covalent geometry    : bond        0.00482 ( 9403)
  covalent geometry    : angle       0.67295 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6984 (mpt180)
REVERT: P  492 MET cc_start: 0.6907 (mmm) cc_final: 0.6658 (mmp)
  outliers start: 14
  outliers final: 11
  residues processed: 76
  average time/residue: 0.4922
  time to fit residues: 50.0517
Evaluate side-chains
  74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    4 ILE
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  263 SER
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  334 MET
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  638 MET
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0030
   chunk 9 optimal weight:    0.0980
   chunk 64 optimal weight:    8.9990
   chunk 74 optimal weight:   30.0000
   chunk 20 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0970
   chunk 16 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.3988

-------------------------------------------------------------------------------
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 = 0.4850 r_free = 0.4850 target = 0.233903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.194604 restraints weight = 34020.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.4438 rms_B_bonded: 2.80
r_work: 0.3975 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.6864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9403  Z= 0.128
  Angle     :  0.588   6.986  13534  Z= 0.319
  Chirality :  0.035   0.160   1597
  Planarity :  0.004   0.044   1055
  Dihedral  : 24.614 179.666   3245
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.09 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.07 (0.35), residues: 604
  helix:  1.79 (0.29), residues: 317
  sheet: -1.73 (0.67), residues: 53
  loop : -0.10 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 655 
 HIS   0.006   0.001   HIS P  68 
 PHE   0.012   0.001   PHE P  67 
 TYR   0.010   0.001   TYR P  45 
 ARG   0.002   0.000   ARG P 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05116 (  396)
  hydrogen bonds       : angle       3.88075 ( 1030)
  covalent geometry    : bond        0.00259 ( 9403)
  covalent geometry    : angle       0.58819 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7299 (mpt180)
  outliers start: 8
  outliers final: 7
  residues processed: 70
  average time/residue: 0.5596
  time to fit residues: 51.7810
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  489 HIS
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 74 optimal weight:   30.0000
   chunk 70 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 647 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.228071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.183576 restraints weight = 33737.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.4329 rms_B_bonded: 2.95
r_work: 0.3876 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.6994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9403  Z= 0.229
  Angle     :  0.658   6.406  13534  Z= 0.358
  Chirality :  0.038   0.166   1597
  Planarity :  0.005   0.047   1055
  Dihedral  : 24.753 179.479   3245
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.36 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.60 (0.35), residues: 604
  helix:  1.37 (0.29), residues: 317
  sheet: -1.69 (0.70), residues: 51
  loop : -0.34 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP P 577 
 HIS   0.004   0.001   HIS P  68 
 PHE   0.022   0.002   PHE P  49 
 TYR   0.016   0.002   TYR P 105 
 ARG   0.003   0.000   ARG P 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06476 (  396)
  hydrogen bonds       : angle       4.24963 ( 1030)
  covalent geometry    : bond        0.00491 ( 9403)
  covalent geometry    : angle       0.65795 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.930 
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: P    5 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7456 (mtt90)
REVERT: P  492 MET cc_start: 0.7474 (mmm) cc_final: 0.7189 (mmp)
  outliers start: 13
  outliers final: 11
  residues processed: 72
  average time/residue: 0.5466
  time to fit residues: 51.7414
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  334 MET
Chi-restraints excluded: chain P residue  386 MET
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  489 HIS
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  559 MET
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4826 r_free = 0.4826 target = 0.231483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.192054 restraints weight = 33930.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.4418 rms_B_bonded: 2.97
r_work: 0.3918 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.7148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9403  Z= 0.138
  Angle     :  0.586   6.233  13534  Z= 0.319
  Chirality :  0.035   0.160   1597
  Planarity :  0.004   0.045   1055
  Dihedral  : 24.624 179.825   3245
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.73 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.04 (0.36), residues: 604
  helix:  1.78 (0.30), residues: 317
  sheet: -1.78 (0.67), residues: 53
  loop : -0.13 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 335 
 HIS   0.006   0.001   HIS P  68 
 PHE   0.019   0.001   PHE P  49 
 TYR   0.010   0.001   TYR P  45 
 ARG   0.002   0.000   ARG P 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05287 (  396)
  hydrogen bonds       : angle       3.92147 ( 1030)
  covalent geometry    : bond        0.00281 ( 9403)
  covalent geometry    : angle       0.58578 (13534)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7430 (mpt180)
REVERT: P  492 MET cc_start: 0.7409 (mmm) cc_final: 0.7179 (mmp)
REVERT: P  559 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6892 (mtt)
  outliers start: 11
  outliers final: 9
  residues processed: 70
  average time/residue: 0.5854
  time to fit residues: 52.8501
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  334 MET
Chi-restraints excluded: chain P residue  432 ASP
Chi-restraints excluded: chain P residue  489 HIS
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  559 MET
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
P 118 ASN
P 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.229428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.185348 restraints weight = 33708.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.4343 rms_B_bonded: 2.93
r_work: 0.3899 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.7296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9403  Z= 0.177
  Angle     :  0.613   6.207  13534  Z= 0.334
  Chirality :  0.036   0.161   1597
  Planarity :  0.005   0.046   1055
  Dihedral  : 24.694 179.569   3245
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.91 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.86 (0.35), residues: 604
  helix:  1.61 (0.29), residues: 317
  sheet: -1.80 (0.68), residues: 53
  loop : -0.19 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP P 577 
 HIS   0.004   0.001   HIS P  68 
 PHE   0.021   0.002   PHE P  49 
 TYR   0.013   0.002   TYR P 105 
 ARG   0.002   0.000   ARG P 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05855 (  396)
  hydrogen bonds       : angle       4.06671 ( 1030)
  covalent geometry    : bond        0.00375 ( 9403)
  covalent geometry    : angle       0.61271 (13534)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9281.14 seconds
wall clock time: 160 minutes 3.31 seconds (9603.31 seconds total)