Starting phenix.real_space_refine
on Tue Feb  3 18:07:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s1e_54446/02_2026/9s1e_54446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s1e_54446/02_2026/9s1e_54446.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s1e_54446/02_2026/9s1e_54446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s1e_54446/02_2026/9s1e_54446.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s1e_54446/02_2026/9s1e_54446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s1e_54446/02_2026/9s1e_54446.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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       5      5.49       5
     Mg      1      5.21       5
     S      31      5.16       5
     C    3689      2.51       5
     N    1008      2.21       5
     O    1072      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5806
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 103
          Classifications: {'RNA': 5}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 1, 'rna3p': 3}
    Chain: "B"
      Number of atoms: 5702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 717, 5702
          Classifications: {'peptide': 717}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 684}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 105
          Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 5, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 100
    Chain: "B"
      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: 1.25, per 1000 atoms: 0.22
  Number of scatterers: 5806
  At special positions: 0
  Unit cell: (75.8352, 79.9344, 116.827, 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      31     16.00
     P       5     15.00
     Mg      1     11.99
     O    1072      8.00
     N    1008      7.00
     C    3689      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: 0.41
  Conformation dependent library (CDL) restraints added in 156.8 milliseconds
  

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1358

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      34.9% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 143 through 152
    Processing helix  chain 'B' and resid 206 through 223
      removed outlier: 3.659A  pdb=" N   GLN B 211 " --> pdb=" O   PRO B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 288
    Processing helix  chain 'B' and resid 299 through 305
      removed outlier: 3.719A  pdb=" N   GLU B 303 " --> pdb=" O   GLN B 299 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU B 304 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE B 305 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 299 through 305'
    Processing helix  chain 'B' and resid 345 through 350
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 400 through 412
      removed outlier: 3.875A  pdb=" N   MET B 404 " --> pdb=" O   ASP B 400 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL B 409 " --> pdb=" O   LYS B 405 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   HIS B 410 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 432
      removed outlier: 4.102A  pdb=" N   LEU B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ILE B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 443
    Processing helix  chain 'B' and resid 505 through 524
      Proline residue:  B 521  - end of helix
    Processing helix  chain 'B' and resid 538 through 550
    Processing helix  chain 'B' and resid 565 through 579
      removed outlier: 3.682A  pdb=" N   TYR B 569 " --> pdb=" O   ARG B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 593
      removed outlier: 3.528A  pdb=" N   GLY B 593 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 590 through 593'
    Processing helix  chain 'B' and resid 594 through 614
      removed outlier: 4.371A  pdb=" N   MET B 599 " --> pdb=" O   GLN B 595 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   ALA B 600 " --> pdb=" O   GLN B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 691
    Processing helix  chain 'B' and resid 709 through 716
      removed outlier: 3.602A  pdb=" N   VAL B 714 " --> pdb=" O   LEU B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 726
    Processing helix  chain 'B' and resid 805 through 816
    Processing helix  chain 'B' and resid 817 through 819
      No H-bonds generated for 'chain 'B' and resid 817 through 819'
    Processing helix  chain 'B' and resid 830 through 846
    Processing helix  chain 'B' and resid 852 through 858
      removed outlier: 4.032A  pdb=" N   ASN B 857 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 659 through 664
      removed outlier: 4.964A  pdb=" N   ILE B 629 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU B 736 " --> pdb=" O   ASP B 800 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ASP B 800 " --> pdb=" O   LEU B 736 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 798 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LYS B 114 " --> pdb=" O   GLN B 752 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLN B 752 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG B 756 " --> pdb=" O   SER B 753 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 257 through 259
      removed outlier: 5.185A  pdb=" N   ILE B 264 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 164
      removed outlier: 5.619A  pdb=" N   LEU B 130 " --> pdb=" O   GLU B 201 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   GLU B 201 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   GLN B 132 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229
    Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229
    Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 319
    Processing sheet with id=AA7, first strand: chain 'B' and resid 463 through 464
      removed outlier: 3.749A  pdb=" N   ILE B 463 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 531 through 535
      removed outlier: 6.591A  pdb=" N   LEU B 498 " --> pdb=" O   VAL B 558 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   LEU B 560 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL B 557 " --> pdb=" O   GLN B 585 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL B 587 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   CYS B 559 " --> pdb=" O   VAL B 587 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    738 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.69

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1867
        1.34 -     1.46: 977
        1.46 -     1.57: 3040
        1.57 -     1.69: 9
        1.69 -     1.81: 46
  Bond restraints: 5939
  Sorted by residual:
  bond pdb=" P     C C   5 "
       pdb=" OP2   C C   5 "
    ideal  model  delta    sigma   weight residual
    1.485  1.515 -0.030 2.00e-02 2.50e+03 2.19e+00
  bond pdb=" P     C C   5 "
       pdb=" OP1   C C   5 "
    ideal  model  delta    sigma   weight residual
    1.485  1.514 -0.029 2.00e-02 2.50e+03 2.11e+00
  bond pdb=" P     C C   4 "
       pdb=" OP2   C C   4 "
    ideal  model  delta    sigma   weight residual
    1.485  1.513 -0.028 2.00e-02 2.50e+03 2.00e+00
  bond pdb=" CB  GLU B 692 "
       pdb=" CG  GLU B 692 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.91e+00
  bond pdb=" P     U C   2 "
       pdb=" OP2   U C   2 "
    ideal  model  delta    sigma   weight residual
    1.485  1.512 -0.027 2.00e-02 2.50e+03 1.83e+00
  ... (remaining 5934 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 7906
        1.56 -     3.12: 138
        3.12 -     4.68: 26
        4.68 -     6.24: 8
        6.24 -     7.79: 7
  Bond angle restraints: 8085
  Sorted by residual:
  angle pdb=" CA  GLU B 354 "
        pdb=" CB  GLU B 354 "
        pdb=" CG  GLU B 354 "
      ideal   model   delta    sigma   weight residual
     114.10  120.74   -6.64 2.00e+00 2.50e-01 1.10e+01
  angle pdb=" CA  GLU B 692 "
        pdb=" CB  GLU B 692 "
        pdb=" CG  GLU B 692 "
      ideal   model   delta    sigma   weight residual
     114.10  120.25   -6.15 2.00e+00 2.50e-01 9.46e+00
  angle pdb=" CB  GLU B 692 "
        pdb=" CG  GLU B 692 "
        pdb=" CD  GLU B 692 "
      ideal   model   delta    sigma   weight residual
     112.60  117.61   -5.01 1.70e+00 3.46e-01 8.69e+00
  angle pdb=" CG  ARG B 504 "
        pdb=" CD  ARG B 504 "
        pdb=" NE  ARG B 504 "
      ideal   model   delta    sigma   weight residual
     112.00  118.34   -6.34 2.20e+00 2.07e-01 8.30e+00
  angle pdb=" C   GLU B 354 "
        pdb=" CA  GLU B 354 "
        pdb=" CB  GLU B 354 "
      ideal   model   delta    sigma   weight residual
     109.72  113.38   -3.66 1.61e+00 3.86e-01 5.17e+00
  ... (remaining 8080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 3050
       17.75 -    35.50: 364
       35.50 -    53.24: 119
       53.24 -    70.99: 38
       70.99 -    88.74: 7
  Dihedral angle restraints: 3578
    sinusoidal: 1473
      harmonic: 2105
  Sorted by residual:
  dihedral pdb=" CA  ASP B 357 "
           pdb=" CB  ASP B 357 "
           pdb=" CG  ASP B 357 "
           pdb=" OD1 ASP B 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.41   56.41     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CA  ASP B 800 "
           pdb=" CB  ASP B 800 "
           pdb=" CG  ASP B 800 "
           pdb=" OD1 ASP B 800 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.67   55.67     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CB  GLU B 201 "
           pdb=" CG  GLU B 201 "
           pdb=" CD  GLU B 201 "
           pdb=" OE1 GLU B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.74   88.74     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3575 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 720
       0.048 -    0.096: 141
       0.096 -    0.144: 61
       0.144 -    0.192: 1
       0.192 -    0.240: 1
  Chirality restraints: 924
  Sorted by residual:
  chirality pdb=" P     U C   1 "
            pdb=" OP1   U C   1 "
            pdb=" OP2   U C   1 "
            pdb=" O5'   U C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.65   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  THR B 520 "
            pdb=" N   THR B 520 "
            pdb=" C   THR B 520 "
            pdb=" CB  THR B 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CA  VAL B 829 "
            pdb=" N   VAL B 829 "
            pdb=" C   VAL B 829 "
            pdb=" CB  VAL B 829 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 921 not shown)

  Planarity restraints: 1013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 829 "   -0.043 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO B 830 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 830 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 830 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 622 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO B 623 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 623 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 623 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 582 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO B 583 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 583 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 583 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1010 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 37
        2.51 -     3.11: 4067
        3.11 -     3.71: 8929
        3.71 -     4.30: 13064
        4.30 -     4.90: 21959
  Nonbonded interactions: 48056
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 862 "
            pdb="MG    MG B 901 "
     model   vdw
     1.914 2.170
  nonbonded pdb=" OP3   U C   1 "
            pdb="MG    MG B 901 "
     model   vdw
     2.074 2.170
  nonbonded pdb=" OP1   A C   3 "
            pdb="MG    MG B 901 "
     model   vdw
     2.110 2.170
  nonbonded pdb=" OE1 GLN B 608 "
            pdb="MG    MG B 901 "
     model   vdw
     2.123 2.170
  nonbonded pdb=" OXT LEU B 862 "
            pdb="MG    MG B 901 "
     model   vdw
     2.167 2.170
  ... (remaining 48051 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:             2.750
  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:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
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      :  0.004   0.053   5939  Z= 0.180
  Angle     :  0.593   7.794   8085  Z= 0.293
  Chirality :  0.045   0.240    924
  Planarity :  0.004   0.065   1013
  Dihedral  : 18.083  88.738   2220
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 33.07 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.54 (0.30), residues: 709
  helix: -0.32 (0.32), residues: 224
  sheet:  0.08 (0.38), residues: 173
  loop : -0.48 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 504 
 TYR   0.009   0.002   TYR B 776 
 PHE   0.011   0.002   PHE B 779 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.005   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 5939)
  covalent geometry    : angle       0.59326 ( 8085)
  hydrogen bonds       : bond        0.23597 (  255)
  hydrogen bonds       : angle       7.94955 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.4557
  time to fit residues: 32.6011
Evaluate side-chains
  54 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.0040
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN
B 505 ASN
B 691 ASN
B 818 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.123437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.096430 restraints weight = 10268.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.50
r_work: 0.3225 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5939  Z= 0.123
  Angle     :  0.552   7.507   8085  Z= 0.283
  Chirality :  0.045   0.164    924
  Planarity :  0.004   0.071   1013
  Dihedral  :  8.321  73.490    875
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.57 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.14 (0.31), residues: 709
  helix:  1.13 (0.35), residues: 223
  sheet: -0.38 (0.37), residues: 185
  loop : -0.24 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 504 
 TYR   0.011   0.001   TYR B 776 
 PHE   0.021   0.002   PHE B 283 
 TRP   0.007   0.001   TRP B 479 
 HIS   0.003   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5939)
  covalent geometry    : angle       0.55174 ( 8085)
  hydrogen bonds       : bond        0.04015 (  255)
  hydrogen bonds       : angle       5.12679 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 51
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  241 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8352 (m-30)
REVERT: B  470 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5432 (p90)
  outliers start: 31
  outliers final: 12
  residues processed: 76
  average time/residue: 0.4094
  time to fit residues: 32.8989
Evaluate side-chains
  59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  622 MET
Chi-restraints excluded: chain B residue  741 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0040
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
B 505 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.121013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.094449 restraints weight = 10275.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.48
r_work: 0.3171 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5939  Z= 0.191
  Angle     :  0.591  11.015   8085  Z= 0.297
  Chirality :  0.046   0.156    924
  Planarity :  0.005   0.074   1013
  Dihedral  :  8.216  73.404    870
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 27.29 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.31), residues: 709
  helix:  1.18 (0.35), residues: 223
  sheet: -0.64 (0.36), residues: 192
  loop : -0.22 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 437 
 TYR   0.011   0.002   TYR B 776 
 PHE   0.014   0.002   PHE B 648 
 TRP   0.009   0.002   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 5939)
  covalent geometry    : angle       0.59093 ( 8085)
  hydrogen bonds       : bond        0.04192 (  255)
  hydrogen bonds       : angle       4.99451 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 50
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  241 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8329 (m-30)
REVERT: B  298 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7478 (tp30)
REVERT: B  354 GLU cc_start: 0.6059 (tm-30) cc_final: 0.5817 (tm-30)
REVERT: B  355 ILE cc_start: 0.5712 (OUTLIER) cc_final: 0.5495 (tp)
  outliers start: 34
  outliers final: 15
  residues processed: 79
  average time/residue: 0.3534
  time to fit residues: 29.5699
Evaluate side-chains
  62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  554 THR
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 58 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
B 505 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.122679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.096135 restraints weight = 10357.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.49
r_work: 0.3193 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5939  Z= 0.143
  Angle     :  0.548   8.130   8085  Z= 0.277
  Chirality :  0.045   0.153    924
  Planarity :  0.004   0.075   1013
  Dihedral  :  8.078  73.403    870
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 27.93 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.09 (0.31), residues: 709
  helix:  1.36 (0.35), residues: 223
  sheet: -0.81 (0.35), residues: 195
  loop : -0.18 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 504 
 TYR   0.012   0.001   TYR B 776 
 PHE   0.023   0.002   PHE B 283 
 TRP   0.007   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5939)
  covalent geometry    : angle       0.54836 ( 8085)
  hydrogen bonds       : bond        0.03537 (  255)
  hydrogen bonds       : angle       4.72245 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 48
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7466 (mmm160)
REVERT: B  241 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8399 (m-30)
REVERT: B  284 MET cc_start: 0.8197 (ptt) cc_final: 0.7960 (ptp)
REVERT: B  298 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7371 (tp30)
  outliers start: 32
  outliers final: 16
  residues processed: 75
  average time/residue: 0.3969
  time to fit residues: 31.3835
Evaluate side-chains
  63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  622 MET
Chi-restraints excluded: chain B residue  741 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0470
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5280

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

Flipped N/Q/H residues before XYZ refinement:
B 263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.122596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.096234 restraints weight = 10406.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.50
r_work: 0.3200 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5939  Z= 0.131
  Angle     :  0.533   7.055   8085  Z= 0.269
  Chirality :  0.044   0.151    924
  Planarity :  0.004   0.076   1013
  Dihedral  :  8.011  73.389    870
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.21 %
    Favored  : 66.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.17 (0.31), residues: 709
  helix:  1.49 (0.35), residues: 223
  sheet: -0.79 (0.35), residues: 194
  loop : -0.18 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 319 
 TYR   0.013   0.001   TYR B 776 
 PHE   0.015   0.001   PHE B 648 
 TRP   0.007   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5939)
  covalent geometry    : angle       0.53270 ( 8085)
  hydrogen bonds       : bond        0.03326 (  255)
  hydrogen bonds       : angle       4.59090 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 47
  time to evaluate  : 0.151 
Fit side-chains
REVERT: B  174 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7469 (mmm160)
REVERT: B  241 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8425 (m-30)
REVERT: B  284 MET cc_start: 0.8222 (ptt) cc_final: 0.7946 (ptp)
REVERT: B  298 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7385 (tp30)
  outliers start: 25
  outliers final: 16
  residues processed: 68
  average time/residue: 0.3854
  time to fit residues: 27.7267
Evaluate side-chains
  63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.122058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.095654 restraints weight = 10388.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.50
r_work: 0.3189 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5939  Z= 0.155
  Angle     :  0.574  13.156   8085  Z= 0.285
  Chirality :  0.045   0.151    924
  Planarity :  0.004   0.076   1013
  Dihedral  :  8.055  73.377    870
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 29.05 %
    Favored  : 66.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.18 (0.31), residues: 709
  helix:  1.57 (0.34), residues: 217
  sheet: -0.84 (0.36), residues: 185
  loop : -0.18 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 756 
 TYR   0.012   0.001   TYR B 776 
 PHE   0.026   0.002   PHE B 401 
 TRP   0.009   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 5939)
  covalent geometry    : angle       0.57402 ( 8085)
  hydrogen bonds       : bond        0.03446 (  255)
  hydrogen bonds       : angle       4.61926 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 45
  time to evaluate  : 0.186 
Fit side-chains
REVERT: B  174 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7486 (mmm160)
REVERT: B  241 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8382 (m-30)
REVERT: B  284 MET cc_start: 0.8193 (ptt) cc_final: 0.7918 (ptp)
REVERT: B  298 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7358 (tp30)
REVERT: B  401 PHE cc_start: 0.8416 (t80) cc_final: 0.7102 (t80)
REVERT: B  405 LYS cc_start: 0.8637 (pttm) cc_final: 0.8170 (mtmm)
REVERT: B  421 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7326 (mp0)
  outliers start: 27
  outliers final: 17
  residues processed: 70
  average time/residue: 0.3226
  time to fit residues: 23.9829
Evaluate side-chains
  65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.121212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.094869 restraints weight = 10511.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.53
r_work: 0.3178 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5939  Z= 0.165
  Angle     :  0.577  12.004   8085  Z= 0.287
  Chirality :  0.045   0.150    924
  Planarity :  0.004   0.076   1013
  Dihedral  :  8.103  73.356    870
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 29.53 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.19 (0.31), residues: 709
  helix:  1.55 (0.34), residues: 218
  sheet: -0.81 (0.36), residues: 182
  loop : -0.18 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 756 
 TYR   0.011   0.001   TYR B 776 
 PHE   0.014   0.002   PHE B 401 
 TRP   0.009   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 5939)
  covalent geometry    : angle       0.57675 ( 8085)
  hydrogen bonds       : bond        0.03487 (  255)
  hydrogen bonds       : angle       4.65383 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 44
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7500 (mmm160)
REVERT: B  241 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8324 (m-30)
REVERT: B  284 MET cc_start: 0.8183 (ptt) cc_final: 0.7876 (ptp)
REVERT: B  298 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7277 (tp30)
REVERT: B  421 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7373 (mp0)
REVERT: B  528 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8072 (tttm)
  outliers start: 27
  outliers final: 16
  residues processed: 69
  average time/residue: 0.3390
  time to fit residues: 24.8059
Evaluate side-chains
  65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  174 ARG
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0040
   chunk 5 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.122467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.096113 restraints weight = 10427.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.54
r_work: 0.3205 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5939  Z= 0.129
  Angle     :  0.551  12.034   8085  Z= 0.273
  Chirality :  0.044   0.149    924
  Planarity :  0.004   0.075   1013
  Dihedral  :  8.065  73.358    870
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 29.86 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.26 (0.31), residues: 709
  helix:  1.72 (0.35), residues: 217
  sheet: -0.82 (0.36), residues: 183
  loop : -0.18 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 756 
 TYR   0.012   0.001   TYR B 776 
 PHE   0.025   0.002   PHE B 283 
 TRP   0.007   0.001   TRP B 479 
 HIS   0.003   0.000   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5939)
  covalent geometry    : angle       0.55125 ( 8085)
  hydrogen bonds       : bond        0.03176 (  255)
  hydrogen bonds       : angle       4.50029 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  241 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8399 (m-30)
REVERT: B  284 MET cc_start: 0.8178 (ptt) cc_final: 0.7884 (ptp)
REVERT: B  298 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7253 (tp30)
REVERT: B  401 PHE cc_start: 0.8557 (t80) cc_final: 0.8232 (t80)
REVERT: B  405 LYS cc_start: 0.8707 (pttm) cc_final: 0.8466 (pttp)
REVERT: B  421 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7383 (mp0)
  outliers start: 24
  outliers final: 16
  residues processed: 67
  average time/residue: 0.3649
  time to fit residues: 25.8358
Evaluate side-chains
  63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0970
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.122974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.096815 restraints weight = 10489.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.57
r_work: 0.3202 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5939  Z= 0.130
  Angle     :  0.556  11.913   8085  Z= 0.274
  Chirality :  0.044   0.150    924
  Planarity :  0.004   0.076   1013
  Dihedral  :  8.052  73.363    870
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 30.18 %
    Favored  : 66.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.29 (0.31), residues: 709
  helix:  1.73 (0.35), residues: 217
  sheet: -0.78 (0.36), residues: 180
  loop : -0.17 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 756 
 TYR   0.012   0.001   TYR B 776 
 PHE   0.022   0.002   PHE B 401 
 TRP   0.008   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5939)
  covalent geometry    : angle       0.55579 ( 8085)
  hydrogen bonds       : bond        0.03157 (  255)
  hydrogen bonds       : angle       4.48258 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: B  241 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8397 (m-30)
REVERT: B  284 MET cc_start: 0.8171 (ptt) cc_final: 0.7859 (ptp)
REVERT: B  298 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7269 (mm-30)
REVERT: B  421 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7323 (mp0)
REVERT: B  528 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8077 (tttm)
  outliers start: 20
  outliers final: 15
  residues processed: 64
  average time/residue: 0.3840
  time to fit residues: 25.9661
Evaluate side-chains
  63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 65 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 758 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.122285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.096009 restraints weight = 10492.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.55
r_work: 0.3203 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5939  Z= 0.143
  Angle     :  0.574  11.740   8085  Z= 0.283
  Chirality :  0.044   0.149    924
  Planarity :  0.004   0.076   1013
  Dihedral  :  8.067  73.352    870
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 30.82 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.23 (0.31), residues: 709
  helix:  1.63 (0.35), residues: 218
  sheet: -0.80 (0.36), residues: 180
  loop : -0.19 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 756 
 TYR   0.012   0.001   TYR B 776 
 PHE   0.025   0.002   PHE B 283 
 TRP   0.009   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5939)
  covalent geometry    : angle       0.57440 ( 8085)
  hydrogen bonds       : bond        0.03214 (  255)
  hydrogen bonds       : angle       4.52479 (  738)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: B  241 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (m-30)
REVERT: B  284 MET cc_start: 0.8158 (ptt) cc_final: 0.7853 (ptp)
REVERT: B  298 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7249 (mm-30)
REVERT: B  421 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7320 (mp0)
REVERT: B  528 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8076 (tttm)
  outliers start: 20
  outliers final: 15
  residues processed: 64
  average time/residue: 0.4153
  time to fit residues: 27.9922
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  511 SER
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain B residue  552 SER
Chi-restraints excluded: chain B residue  599 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  838 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 48 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 758 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.122293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.096019 restraints weight = 10291.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.53
r_work: 0.3201 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5939  Z= 0.131
  Angle     :  0.552  11.465   8085  Z= 0.274
  Chirality :  0.044   0.149    924
  Planarity :  0.004   0.076   1013
  Dihedral  :  8.040  73.358    870
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 30.02 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.27 (0.31), residues: 709
  helix:  1.73 (0.35), residues: 217
  sheet: -0.80 (0.36), residues: 180
  loop : -0.20 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 756 
 TYR   0.027   0.001   TYR B 313 
 PHE   0.022   0.002   PHE B 401 
 TRP   0.008   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5939)
  covalent geometry    : angle       0.55162 ( 8085)
  hydrogen bonds       : bond        0.03149 (  255)
  hydrogen bonds       : angle       4.49794 (  738)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1594.24 seconds
wall clock time: 27 minutes 54.90 seconds (1674.90 seconds total)