Starting phenix.real_space_refine
on Tue Mar  3 16:08:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8in8_35592/03_2026/8in8_35592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8in8_35592/03_2026/8in8_35592.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_2026/8in8_35592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_2026/8in8_35592.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_2026/8in8_35592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8in8_35592/03_2026/8in8_35592.map"
  }
  resolution = 3.0
  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=   0.001 sd=   0.072
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      47      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    4098      2.51       5
     N    1140      2.21       5
     O    1355      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6663
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 2009
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 3685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3685
          Classifications: {'peptide': 470}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 28, 'TRANS': 441}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "I"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 506
          Classifications: {'RNA': 24}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 13}
          Link IDs: {'rna2p': 2, 'rna3p': 21}
    Chain: "J"
      Number of atoms: 462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 462
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.80, per 1000 atoms: 0.27
  Number of scatterers: 6663
  At special positions: 0
  Unit cell: (71.6214, 87.0336, 107.885, 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      22     16.00
     P      47     15.00
     Mg      1     11.99
     O    1355      8.00
     N    1140      7.00
     C    4098      6.00
    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: 0.95
  Conformation dependent library (CDL) restraints added in 229.1 milliseconds
  

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      36.0% alpha, 20.7% beta
      17 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'B' and resid 356 through 367
    Processing helix  chain 'B' and resid 383 through 391
      removed outlier: 3.604A  pdb=" N   ILE B 387 " --> pdb=" O   GLY B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 414
    Processing helix  chain 'B' and resid 414 through 430
      removed outlier: 3.694A  pdb=" N   LYS B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 458
      No H-bonds generated for 'chain 'B' and resid 456 through 458'
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.616A  pdb=" N   ALA B 464 " --> pdb=" O   ASP B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 519
      removed outlier: 3.688A  pdb=" N   ARG B 516 " --> pdb=" O   PRO B 513 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   GLU B 518 " --> pdb=" O   ASP B 515 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU B 519 " --> pdb=" O   ARG B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 529
    Processing helix  chain 'B' and resid 532 through 549
    Processing helix  chain 'C' and resid 29 through 37
    Processing helix  chain 'C' and resid 39 through 43
    Processing helix  chain 'C' and resid 60 through 73
      removed outlier: 3.693A  pdb=" N   LEU C  64 " --> pdb=" O   HIS C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 95
    Processing helix  chain 'C' and resid 111 through 120
      removed outlier: 4.191A  pdb=" N   GLY C 115 " --> pdb=" O   ASP C 111 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 134
    Processing helix  chain 'C' and resid 135 through 137
      No H-bonds generated for 'chain 'C' and resid 135 through 137'
    Processing helix  chain 'C' and resid 151 through 157
      removed outlier: 4.931A  pdb=" N   LYS C 156 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 174
    Processing helix  chain 'C' and resid 184 through 190
      removed outlier: 3.736A  pdb=" N   LEU C 188 " --> pdb=" O   ASN C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 208
      removed outlier: 4.008A  pdb=" N   VAL C 196 " --> pdb=" O   CYS C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 295
      removed outlier: 3.542A  pdb=" N   LYS C 286 " --> pdb=" O   SER C 282 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER C 287 " --> pdb=" O   VAL C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 322
    Processing helix  chain 'C' and resid 418 through 430
      removed outlier: 3.872A  pdb=" N   LYS C 430 " --> pdb=" O   LEU C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 459
    Processing helix  chain 'C' and resid 470 through 473
      removed outlier: 3.997A  pdb=" N   MET C 473 " --> pdb=" O   ARG C 470 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 470 through 473'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 579 through 581
      removed outlier: 3.812A  pdb=" N   ALA C 355 " --> pdb=" O   ASP C 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 335 through 337
      removed outlier: 4.098A  pdb=" N   HIS B 444 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 337
    Processing sheet with id=AA4, first strand: chain 'B' and resid 371 through 373
      removed outlier: 3.819A  pdb=" N   VAL B 378 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 561
    Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13
    Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27
    Processing sheet with id=AA8, first strand: chain 'C' and resid 106 through 108
      removed outlier: 3.939A  pdb=" N   CYS C 107 " --> pdb=" O   TYR C  54 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA C  56 " --> pdb=" O   CYS C 107 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ALA C  53 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   TYR C 149 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   LEU C  55 " --> pdb=" O   TYR C 149 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 160
      removed outlier: 3.550A  pdb=" N   TYR C 160 " --> pdb=" O   PHE C 163 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 307
      removed outlier: 4.151A  pdb=" N   TYR C 224 " --> pdb=" O   PHE C 248 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR C 467 " --> pdb=" O   ALA C 259 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 303
    Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382

    255 hydrogen bonds defined for protein.
    690 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      40 hydrogen bonds
      78 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 1.18 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: 1657
        1.33 -     1.45: 1554
        1.45 -     1.57: 3578
        1.57 -     1.69: 92
        1.69 -     1.81: 32
  Bond restraints: 6913
  Sorted by residual:
  bond pdb=" C3'  DA J   1 "
       pdb=" O3'  DA J   1 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" CB  ARG C 138 "
       pdb=" CG  ARG C 138 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.61e+00
  bond pdb=" C3'  DC J  -1 "
       pdb=" O3'  DC J  -1 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.25e+00
  bond pdb=" CG  LEU B 426 "
       pdb=" CD1 LEU B 426 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.11e+00
  bond pdb=" CG  PRO C 273 "
       pdb=" CD  PRO C 273 "
    ideal  model  delta    sigma   weight residual
    1.503  1.468  0.035 3.40e-02 8.65e+02 1.05e+00
  ... (remaining 6908 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 9482
        2.52 -     5.04: 92
        5.04 -     7.55: 10
        7.55 -    10.07: 1
       10.07 -    12.59: 1
  Bond angle restraints: 9586
  Sorted by residual:
  angle pdb=" CA  GLU B 508 "
        pdb=" CB  GLU B 508 "
        pdb=" CG  GLU B 508 "
      ideal   model   delta    sigma   weight residual
     114.10  121.58   -7.48 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" CA  LEU C  98 "
        pdb=" CB  LEU C  98 "
        pdb=" CG  LEU C  98 "
      ideal   model   delta    sigma   weight residual
     116.30  128.89  -12.59 3.50e+00 8.16e-02 1.29e+01
  angle pdb=" CB  MET C 299 "
        pdb=" CG  MET C 299 "
        pdb=" SD  MET C 299 "
      ideal   model   delta    sigma   weight residual
     112.70  121.32   -8.62 3.00e+00 1.11e-01 8.25e+00
  angle pdb=" CA  ARG C 138 "
        pdb=" CB  ARG C 138 "
        pdb=" CG  ARG C 138 "
      ideal   model   delta    sigma   weight residual
     114.10  119.46   -5.36 2.00e+00 2.50e-01 7.17e+00
  angle pdb=" CA  PRO C 273 "
        pdb=" N   PRO C 273 "
        pdb=" CD  PRO C 273 "
      ideal   model   delta    sigma   weight residual
     112.00  108.37    3.63 1.40e+00 5.10e-01 6.73e+00
  ... (remaining 9581 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.12: 3813
       35.12 -    70.25: 289
       70.25 -   105.37: 15
      105.37 -   140.50: 1
      140.50 -   175.62: 3
  Dihedral angle restraints: 4121
    sinusoidal: 2018
      harmonic: 2103
  Sorted by residual:
  dihedral pdb=" CA  PHE B 328 "
           pdb=" C   PHE B 328 "
           pdb=" N   PRO B 329 "
           pdb=" CA  PRO B 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.35   26.65     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  VAL C 463 "
           pdb=" C   VAL C 463 "
           pdb=" N   ASN C 464 "
           pdb=" CA  ASN C 464 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.78  -24.22     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  ILE C  14 "
           pdb=" C   ILE C  14 "
           pdb=" N   PRO C  15 "
           pdb=" CA  PRO C  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.56  -22.44     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 4118 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 684
       0.029 -    0.059: 269
       0.059 -    0.088: 71
       0.088 -    0.117: 45
       0.117 -    0.147: 17
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" C1'   G I   7 "
            pdb=" O4'   G I   7 "
            pdb=" C2'   G I   7 "
            pdb=" N9    G I   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" CA  ILE C 407 "
            pdb=" N   ILE C 407 "
            pdb=" C   ILE C 407 "
            pdb=" CB  ILE C 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CB  ILE C 305 "
            pdb=" CA  ILE C 305 "
            pdb=" CG1 ILE C 305 "
            pdb=" CG2 ILE C 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1083 not shown)

  Planarity restraints: 1063
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 272 "    0.058 5.00e-02 4.00e+02   8.58e-02 1.18e+01
        pdb=" N   PRO C 273 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO C 273 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO C 273 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  56 "    0.038 5.00e-02 4.00e+02   5.79e-02 5.37e+00
        pdb=" N   PRO C  57 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C  57 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  57 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U I   5 "    0.025 2.00e-02 2.50e+03   1.25e-02 3.53e+00
        pdb=" N1    U I   5 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2    U I   5 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    U I   5 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    U I   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U I   5 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U I   5 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    U I   5 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U I   5 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1060 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 43
        2.54 -     3.13: 4720
        3.13 -     3.72: 10334
        3.72 -     4.31: 14501
        4.31 -     4.90: 23667
  Nonbonded interactions: 53265
  Sorted by model distance:
  nonbonded pdb=" OP1   A I   1 "
            pdb="MG    MG I 101 "
     model   vdw
     1.950 2.170
  nonbonded pdb=" OP3   A I   1 "
            pdb="MG    MG I 101 "
     model   vdw
     2.001 2.170
  nonbonded pdb=" O   MET C 473 "
            pdb="MG    MG I 101 "
     model   vdw
     2.015 2.170
  nonbonded pdb=" O   GLN C 281 "
            pdb=" OG  SER C 285 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   LEU C 426 "
            pdb=" OG1 THR C 429 "
     model   vdw
     2.233 3.040
  ... (remaining 53260 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.430
  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:             0.010
  Load rotamer database and sin/cos tables:9.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6913  Z= 0.134
  Angle     :  0.615  12.588   9586  Z= 0.325
  Chirality :  0.040   0.147   1086
  Planarity :  0.005   0.086   1063
  Dihedral  : 21.500 175.621   2769
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.13 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 33.50 %
    Favored  : 62.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.30 (0.32), residues: 718
  helix:  1.49 (0.37), residues: 211
  sheet: -0.16 (0.44), residues: 160
  loop : -1.30 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  62 
 TYR   0.013   0.001   TYR C 469 
 PHE   0.010   0.001   PHE C 158 
 TRP   0.007   0.001   TRP B 502 
 HIS   0.003   0.001   HIS B 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6913)
  covalent geometry    : angle       0.61521 ( 9586)
  hydrogen bonds       : bond        0.14572 (  281)
  hydrogen bonds       : angle       6.32515 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 21
  residues processed: 75
  average time/residue: 0.4348
  time to fit residues: 34.7449
Evaluate side-chains
  74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  260 TYR
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  285 SER
Chi-restraints excluded: chain C residue  358 SER
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  401 THR
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  447 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.162953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.131228 restraints weight = 7879.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.95
r_work: 0.3648 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.0767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6913  Z= 0.133
  Angle     :  0.571   8.151   9586  Z= 0.302
  Chirality :  0.040   0.148   1086
  Planarity :  0.005   0.059   1063
  Dihedral  : 19.487 173.664   1455
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 30.03 %
    Favored  : 64.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.16 (0.32), residues: 718
  helix:  1.53 (0.36), residues: 224
  sheet:  0.05 (0.44), residues: 156
  loop : -1.34 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  62 
 TYR   0.012   0.001   TYR C 341 
 PHE   0.008   0.001   PHE C 158 
 TRP   0.007   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6913)
  covalent geometry    : angle       0.57062 ( 9586)
  hydrogen bonds       : bond        0.03947 (  281)
  hydrogen bonds       : angle       4.75398 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 62
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 13
  residues processed: 87
  average time/residue: 0.4037
  time to fit residues: 37.6434
Evaluate side-chains
  71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  260 TYR
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  407 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 55 optimal weight:    0.3980
   chunk 70 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4150 r_free = 0.4150 target = 0.162904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.131380 restraints weight = 7857.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 1.95
r_work: 0.3664 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6913  Z= 0.126
  Angle     :  0.559   8.747   9586  Z= 0.295
  Chirality :  0.041   0.201   1086
  Planarity :  0.005   0.052   1063
  Dihedral  : 19.436 175.241   1438
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 32.67 %
    Favored  : 63.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.06 (0.32), residues: 718
  helix:  1.66 (0.36), residues: 225
  sheet:  0.11 (0.44), residues: 157
  loop : -1.33 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  62 
 TYR   0.011   0.001   TYR C 341 
 PHE   0.008   0.001   PHE C 158 
 TRP   0.007   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6913)
  covalent geometry    : angle       0.55908 ( 9586)
  hydrogen bonds       : bond        0.03699 (  281)
  hydrogen bonds       : angle       4.50817 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 63
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: B  455 ASP cc_start: 0.7986 (m-30) cc_final: 0.7755 (m-30)
REVERT: B  528 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7107 (ttt-90)
REVERT: C  260 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7016 (p90)
  outliers start: 25
  outliers final: 8
  residues processed: 83
  average time/residue: 0.4508
  time to fit residues: 39.9183
Evaluate side-chains
  69 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  528 ARG
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  260 TYR
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  407 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0050
   chunk 17 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 65 optimal weight:    0.3980
   chunk 8 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0970
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8996

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

Flipped N/Q/H residues before XYZ refinement:
B 558 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.161539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129736 restraints weight = 7992.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.97
r_work: 0.3659 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6913  Z= 0.133
  Angle     :  0.562   7.509   9586  Z= 0.299
  Chirality :  0.041   0.177   1086
  Planarity :  0.005   0.056   1063
  Dihedral  : 19.413 175.082   1437
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 31.68 %
    Favored  : 63.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.05 (0.32), residues: 718
  helix:  1.67 (0.36), residues: 226
  sheet:  0.19 (0.44), residues: 154
  loop : -1.36 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  62 
 TYR   0.013   0.001   TYR C 341 
 PHE   0.007   0.001   PHE C 158 
 TRP   0.006   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6913)
  covalent geometry    : angle       0.56237 ( 9586)
  hydrogen bonds       : bond        0.03673 (  281)
  hydrogen bonds       : angle       4.43249 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: B  455 ASP cc_start: 0.7939 (m-30) cc_final: 0.7649 (m-30)
REVERT: B  528 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7134 (ttt-90)
REVERT: C  260 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6900 (p90)
  outliers start: 28
  outliers final: 9
  residues processed: 85
  average time/residue: 0.4365
  time to fit residues: 39.4795
Evaluate side-chains
  69 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  485 SER
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  528 ARG
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  260 TYR
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.0010
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6986

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.165418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.134631 restraints weight = 7942.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 1.94
r_work: 0.3659 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6913  Z= 0.123
  Angle     :  0.555   6.860   9586  Z= 0.295
  Chirality :  0.040   0.184   1086
  Planarity :  0.005   0.056   1063
  Dihedral  : 19.386 175.457   1437
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 32.51 %
    Favored  : 63.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.12 (0.33), residues: 718
  helix:  1.79 (0.36), residues: 226
  sheet:  0.33 (0.44), residues: 156
  loop : -1.29 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 263 
 TYR   0.010   0.001   TYR C 341 
 PHE   0.006   0.001   PHE C 158 
 TRP   0.006   0.001   TRP B 502 
 HIS   0.002   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6913)
  covalent geometry    : angle       0.55522 ( 9586)
  hydrogen bonds       : bond        0.03437 (  281)
  hydrogen bonds       : angle       4.36120 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: B  455 ASP cc_start: 0.7879 (m-30) cc_final: 0.7521 (m-30)
REVERT: B  528 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7113 (ttt-90)
REVERT: C  119 ASN cc_start: 0.7509 (p0) cc_final: 0.6818 (m110)
REVERT: C  346 ASP cc_start: 0.7792 (m-30) cc_final: 0.7173 (m-30)
  outliers start: 26
  outliers final: 9
  residues processed: 89
  average time/residue: 0.4344
  time to fit residues: 41.2653
Evaluate side-chains
  71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  528 ARG
Chi-restraints excluded: chain B residue  580 SER
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  127 ASP
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  407 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 30 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.163420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.132105 restraints weight = 7962.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 1.95
r_work: 0.3671 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6913  Z= 0.120
  Angle     :  0.570   8.668   9586  Z= 0.301
  Chirality :  0.040   0.173   1086
  Planarity :  0.005   0.058   1063
  Dihedral  : 19.358 175.896   1435
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 33.00 %
    Favored  : 63.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.11 (0.33), residues: 718
  helix:  1.84 (0.36), residues: 220
  sheet:  0.32 (0.44), residues: 159
  loop : -1.29 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 263 
 TYR   0.009   0.001   TYR C 341 
 PHE   0.006   0.001   PHE C 158 
 TRP   0.006   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6913)
  covalent geometry    : angle       0.57043 ( 9586)
  hydrogen bonds       : bond        0.03322 (  281)
  hydrogen bonds       : angle       4.25517 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: B  455 ASP cc_start: 0.7883 (m-30) cc_final: 0.7508 (m-30)
REVERT: B  528 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7128 (ttt-90)
REVERT: C  119 ASN cc_start: 0.7435 (p0) cc_final: 0.6832 (m110)
REVERT: C  346 ASP cc_start: 0.7775 (m-30) cc_final: 0.7145 (m-30)
REVERT: C  352 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6082 (tttt)
  outliers start: 23
  outliers final: 11
  residues processed: 83
  average time/residue: 0.4383
  time to fit residues: 38.9242
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  528 ARG
Chi-restraints excluded: chain B residue  580 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  127 ASP
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  352 LYS
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  473 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 558 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.156444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.124607 restraints weight = 7980.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 1.96
r_work: 0.3596 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6913  Z= 0.221
  Angle     :  0.669   7.989   9586  Z= 0.351
  Chirality :  0.046   0.227   1086
  Planarity :  0.006   0.064   1063
  Dihedral  : 19.556 175.523   1435
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.55 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 32.67 %
    Favored  : 62.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.33 (0.32), residues: 718
  helix:  1.22 (0.35), residues: 224
  sheet:  0.27 (0.44), residues: 156
  loop : -1.49 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 263 
 TYR   0.028   0.002   TYR C 341 
 PHE   0.013   0.002   PHE C 143 
 TRP   0.009   0.002   TRP C 377 
 HIS   0.003   0.001   HIS C  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 6913)
  covalent geometry    : angle       0.66873 ( 9586)
  hydrogen bonds       : bond        0.04752 (  281)
  hydrogen bonds       : angle       4.75864 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: B  418 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6411 (tptp)
REVERT: B  455 ASP cc_start: 0.7936 (m-30) cc_final: 0.7556 (m-30)
REVERT: B  528 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7202 (ttt-90)
REVERT: C  352 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5826 (tttt)
  outliers start: 31
  outliers final: 14
  residues processed: 86
  average time/residue: 0.4307
  time to fit residues: 39.4513
Evaluate side-chains
  75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  418 LYS
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  580 SER
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  127 ASP
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  352 LYS
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  429 THR
Chi-restraints excluded: chain C residue  462 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.161019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.129714 restraints weight = 7917.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.95
r_work: 0.3593 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6913  Z= 0.157
  Angle     :  0.626   7.923   9586  Z= 0.327
  Chirality :  0.043   0.197   1086
  Planarity :  0.005   0.063   1063
  Dihedral  : 19.528 175.519   1435
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 34.16 %
    Favored  : 62.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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: -0.31 (0.32), residues: 718
  helix:  1.29 (0.35), residues: 219
  sheet:  0.28 (0.45), residues: 149
  loop : -1.44 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 263 
 TYR   0.018   0.001   TYR C 341 
 PHE   0.009   0.001   PHE C  90 
 TRP   0.007   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6913)
  covalent geometry    : angle       0.62602 ( 9586)
  hydrogen bonds       : bond        0.03997 (  281)
  hydrogen bonds       : angle       4.57076 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: B  418 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6389 (tptp)
REVERT: B  455 ASP cc_start: 0.7946 (m-30) cc_final: 0.7567 (m-30)
REVERT: B  528 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7111 (ttt-90)
REVERT: C  346 ASP cc_start: 0.7862 (m-30) cc_final: 0.7252 (m-30)
REVERT: C  352 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.5889 (tttt)
  outliers start: 19
  outliers final: 12
  residues processed: 75
  average time/residue: 0.4959
  time to fit residues: 39.4455
Evaluate side-chains
  74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  418 LYS
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  528 ARG
Chi-restraints excluded: chain B residue  580 SER
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  127 ASP
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  352 LYS
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  429 THR
Chi-restraints excluded: chain C residue  462 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0570
   chunk 12 optimal weight:    0.0770
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.164068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.132784 restraints weight = 8014.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.96
r_work: 0.3678 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6913  Z= 0.121
  Angle     :  0.596   8.743   9586  Z= 0.310
  Chirality :  0.040   0.173   1086
  Planarity :  0.005   0.063   1063
  Dihedral  : 19.431 176.426   1435
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 35.15 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.05 (0.32), residues: 718
  helix:  1.65 (0.35), residues: 220
  sheet:  0.43 (0.44), residues: 156
  loop : -1.28 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  62 
 TYR   0.010   0.001   TYR C  54 
 PHE   0.007   0.001   PHE C 452 
 TRP   0.010   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6913)
  covalent geometry    : angle       0.59632 ( 9586)
  hydrogen bonds       : bond        0.03319 (  281)
  hydrogen bonds       : angle       4.26517 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: B  418 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6225 (tptp)
REVERT: B  455 ASP cc_start: 0.7946 (m-30) cc_final: 0.7540 (m-30)
REVERT: B  528 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7139 (ttt-90)
REVERT: C  119 ASN cc_start: 0.7399 (p0) cc_final: 0.6917 (m-40)
REVERT: C  346 ASP cc_start: 0.7805 (m-30) cc_final: 0.7253 (m-30)
REVERT: C  352 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.5944 (tttt)
  outliers start: 15
  outliers final: 10
  residues processed: 78
  average time/residue: 0.4714
  time to fit residues: 38.9642
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  418 LYS
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  528 ARG
Chi-restraints excluded: chain B residue  580 SER
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  127 ASP
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  352 LYS
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  462 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0060
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.7800

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.161689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130184 restraints weight = 7965.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.96
r_work: 0.3677 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6913  Z= 0.133
  Angle     :  0.607   9.737   9586  Z= 0.315
  Chirality :  0.041   0.166   1086
  Planarity :  0.005   0.065   1063
  Dihedral  : 19.438 176.972   1435
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 35.97 %
    Favored  : 61.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.04 (0.32), residues: 718
  helix:  1.62 (0.35), residues: 220
  sheet:  0.37 (0.44), residues: 159
  loop : -1.26 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 263 
 TYR   0.013   0.001   TYR C 341 
 PHE   0.008   0.001   PHE C 452 
 TRP   0.006   0.001   TRP B 502 
 HIS   0.002   0.001   HIS B 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6913)
  covalent geometry    : angle       0.60652 ( 9586)
  hydrogen bonds       : bond        0.03499 (  281)
  hydrogen bonds       : angle       4.30614 (  768)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: B  418 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6202 (tptp)
REVERT: B  455 ASP cc_start: 0.7943 (m-30) cc_final: 0.7552 (m-30)
REVERT: C  119 ASN cc_start: 0.7458 (p0) cc_final: 0.6931 (m-40)
REVERT: C  346 ASP cc_start: 0.7826 (m-30) cc_final: 0.7288 (m-30)
REVERT: C  352 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.5928 (tttt)
  outliers start: 14
  outliers final: 10
  residues processed: 72
  average time/residue: 0.4494
  time to fit residues: 34.4184
Evaluate side-chains
  73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  418 LYS
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  580 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  127 ASP
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  352 LYS
Chi-restraints excluded: chain C residue  407 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 558 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.158121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.127466 restraints weight = 8087.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.06
r_work: 0.3625 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6913  Z= 0.165
  Angle     :  0.642   9.945   9586  Z= 0.333
  Chirality :  0.043   0.193   1086
  Planarity :  0.005   0.066   1063
  Dihedral  : 19.555 176.697   1435
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 35.64 %
    Favored  : 61.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.12 (0.32), residues: 718
  helix:  1.39 (0.35), residues: 220
  sheet:  0.44 (0.44), residues: 155
  loop : -1.35 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 263 
 TYR   0.019   0.002   TYR C 341 
 PHE   0.009   0.001   PHE C 471 
 TRP   0.007   0.001   TRP C 377 
 HIS   0.002   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6913)
  covalent geometry    : angle       0.64242 ( 9586)
  hydrogen bonds       : bond        0.04042 (  281)
  hydrogen bonds       : angle       4.52776 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2277.56 seconds
wall clock time: 39 minutes 33.74 seconds (2373.74 seconds total)