Starting phenix.real_space_refine
on Tue Feb 11 19:26:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xt9_38641/02_2025/8xt9_38641.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xt9_38641/02_2025/8xt9_38641.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xt9_38641/02_2025/8xt9_38641.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xt9_38641/02_2025/8xt9_38641.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xt9_38641/02_2025/8xt9_38641.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xt9_38641/02_2025/8xt9_38641.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4186      2.51       5
     N    1075      2.21       5
     O    1184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6479
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 5740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 737, 5740
          Classifications: {'peptide': 737}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 37, 'TRANS': 699}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 739
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 3, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 49
  Time building chain proxies: 4.19, per 1000 atoms: 0.65
  Number of scatterers: 6479
  At special positions: 0
  Unit cell: (69.615, 89.964, 171.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1184      8.00
     N    1075      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  29 " - pdb=" SG  CYS C  35 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  43 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 339 " - pdb=" SG  CYS C 364 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 618 " - pdb=" SG  CYS C 693 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 757 " - pdb=" SG  CYS C 761 " distance=2.57
    Simple disulfide: pdb=" SG  CYS A 428 " - pdb=" SG  CYS A 501 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 896.4 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1586

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 8 sheets defined
      34.1% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'C' and resid 121 through 127
      removed outlier: 3.588A  pdb=" N   ILE C 125 " --> pdb=" O   PRO C 121 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG C 126 " --> pdb=" O   SER C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 176
      removed outlier: 4.272A  pdb=" N   LEU C 176 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 247
    Processing helix  chain 'C' and resid 289 through 292
      removed outlier: 4.131A  pdb=" N   PHE C 292 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 289 through 292'
    Processing helix  chain 'C' and resid 337 through 342
    Processing helix  chain 'C' and resid 466 through 471
      removed outlier: 3.928A  pdb=" N   CYS C 470 " --> pdb=" O   TYR C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 566
    Processing helix  chain 'C' and resid 571 through 601
      removed outlier: 3.849A  pdb=" N   PHE C 586 " --> pdb=" O   VAL C 582 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   MET C 587 " --> pdb=" O   SER C 583 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 604 through 614
      removed outlier: 3.656A  pdb=" N   PHE C 608 " --> pdb=" O   ARG C 604 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE C 610 " --> pdb=" O   ALA C 606 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   TRP C 611 " --> pdb=" O   GLU C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 615 through 649
      removed outlier: 3.942A  pdb=" N   LYS C 619 " --> pdb=" O   GLY C 615 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 657 through 679
      removed outlier: 3.922A  pdb=" N   GLN C 661 " --> pdb=" O   ASN C 657 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 680 through 682
      No H-bonds generated for 'chain 'C' and resid 680 through 682'
    Processing helix  chain 'C' and resid 703 through 732
      removed outlier: 4.055A  pdb=" N   THR C 707 " --> pdb=" O   SER C 703 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 745 through 769
      Proline residue:  C 762  - end of helix
    Processing helix  chain 'C' and resid 770 through 772
      No H-bonds generated for 'chain 'C' and resid 770 through 772'
    Processing helix  chain 'C' and resid 778 through 790
    Processing helix  chain 'C' and resid 791 through 804
      Proline residue:  C 798  - end of helix
    Processing helix  chain 'C' and resid 805 through 821
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 467 through 470
      removed outlier: 4.124A  pdb=" N   LYS A 470 " --> pdb=" O   ASP A 467 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 467 through 470'
    Processing helix  chain 'A' and resid 492 through 496
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.790A  pdb=" N   ILE A 517 " --> pdb=" O   ASN A 514 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36
      removed outlier: 3.773A  pdb=" N   ARG C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LEU C 158 " --> pdb=" O   THR C 183 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASP C 231 " --> pdb=" O   LEU C 206 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'C' and resid 191 through 192
      removed outlier: 4.115A  pdb=" N   ILE C 192 " --> pdb=" O   SER C 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 262 through 263
    Processing sheet with id=AA5, first strand: chain 'C' and resid 300 through 304
      removed outlier: 6.527A  pdb=" N   LEU C 301 " --> pdb=" O   THR C 325 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   THR C 327 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ILE C 303 " --> pdb=" O   THR C 327 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU C 348 " --> pdb=" O   SER C 371 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   LEU C 418 " --> pdb=" O   LYS C 440 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 429
    Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 465
      removed outlier: 5.318A  pdb=" N   GLY A 453 " --> pdb=" O   ARG A 444 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   ARG A 444 " --> pdb=" O   GLY A 453 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 455 " --> pdb=" O   TRP A 442 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 465
      removed outlier: 5.318A  pdb=" N   GLY A 453 " --> pdb=" O   ARG A 444 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   ARG A 444 " --> pdb=" O   GLY A 453 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 455 " --> pdb=" O   TRP A 442 " (cutoff:3.500A)

    255 hydrogen bonds defined for protein.
    735 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: 2.09

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1039
        1.26 -     1.40: 1636
        1.40 -     1.55: 3898
        1.55 -     1.69: 12
        1.69 -     1.83: 45
  Bond restraints: 6630
  Sorted by residual:
  bond pdb=" N   PRO C 193 "
       pdb=" CD  PRO C 193 "
    ideal  model  delta    sigma   weight residual
    1.473  1.293  0.180 1.40e-02 5.10e+03 1.65e+02
  bond pdb=" C   GLN C 180 "
       pdb=" O   GLN C 180 "
    ideal  model  delta    sigma   weight residual
    1.235  1.120  0.115 1.24e-02 6.50e+03 8.64e+01
  bond pdb=" CA  ASP C 147 "
       pdb=" C   ASP C 147 "
    ideal  model  delta    sigma   weight residual
    1.525  1.647 -0.122 1.38e-02 5.25e+03 7.82e+01
  bond pdb=" C   CYS C 757 "
       pdb=" O   CYS C 757 "
    ideal  model  delta    sigma   weight residual
    1.237  1.137  0.100 1.16e-02 7.43e+03 7.42e+01
  bond pdb=" C   MET C 782 "
       pdb=" O   MET C 782 "
    ideal  model  delta    sigma   weight residual
    1.236  1.141  0.095 1.15e-02 7.56e+03 6.88e+01
  ... (remaining 6625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.91: 8799
        3.91 -     7.82: 188
        7.82 -    11.74: 25
       11.74 -    15.65: 6
       15.65 -    19.56: 3
  Bond angle restraints: 9021
  Sorted by residual:
  angle pdb=" N   SER C 148 "
        pdb=" CA  SER C 148 "
        pdb=" C   SER C 148 "
      ideal   model   delta    sigma   weight residual
     110.55   90.99   19.56 1.35e+00 5.49e-01 2.10e+02
  angle pdb=" N   GLU C 146 "
        pdb=" CA  GLU C 146 "
        pdb=" C   GLU C 146 "
      ideal   model   delta    sigma   weight residual
     111.11  125.81  -14.70 1.20e+00 6.94e-01 1.50e+02
  angle pdb=" N   ASN A 489 "
        pdb=" CA  ASN A 489 "
        pdb=" C   ASN A 489 "
      ideal   model   delta    sigma   weight residual
     109.50  127.94  -18.44 1.58e+00 4.01e-01 1.36e+02
  angle pdb=" C   ASP C 147 "
        pdb=" CA  ASP C 147 "
        pdb=" CB  ASP C 147 "
      ideal   model   delta    sigma   weight residual
     111.06   94.50   16.56 1.55e+00 4.16e-01 1.14e+02
  angle pdb=" N   VAL C 204 "
        pdb=" CA  VAL C 204 "
        pdb=" C   VAL C 204 "
      ideal   model   delta    sigma   weight residual
     111.81  119.89   -8.08 8.60e-01 1.35e+00 8.83e+01
  ... (remaining 9016 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 3355
       17.17 -    34.33: 421
       34.33 -    51.50: 127
       51.50 -    68.66: 34
       68.66 -    85.83: 4
  Dihedral angle restraints: 3941
    sinusoidal: 1501
      harmonic: 2440
  Sorted by residual:
  dihedral pdb=" CD  ARG C 275 "
           pdb=" NE  ARG C 275 "
           pdb=" CZ  ARG C 275 "
           pdb=" NH1 ARG C 275 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   67.65  -67.65     1      1.00e+01 1.00e-02 5.95e+01
  dihedral pdb=" C   ASP C 147 "
           pdb=" N   ASP C 147 "
           pdb=" CA  ASP C 147 "
           pdb=" CB  ASP C 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.56  -18.04     0      2.50e+00 1.60e-01 5.21e+01
  dihedral pdb=" C   ASP C 162 "
           pdb=" N   ASP C 162 "
           pdb=" CA  ASP C 162 "
           pdb=" CB  ASP C 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.53   17.93     0      2.50e+00 1.60e-01 5.14e+01
  ... (remaining 3938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 974
       0.135 -    0.269: 71
       0.269 -    0.404: 7
       0.404 -    0.538: 3
       0.538 -    0.672: 2
  Chirality restraints: 1057
  Sorted by residual:
  chirality pdb=" CA  ASP C 162 "
            pdb=" N   ASP C 162 "
            pdb=" C   ASP C 162 "
            pdb=" CB  ASP C 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" CA  GLU C 146 "
            pdb=" N   GLU C 146 "
            pdb=" C   GLU C 146 "
            pdb=" CB  GLU C 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" CA  ASP C 147 "
            pdb=" N   ASP C 147 "
            pdb=" C   ASP C 147 "
            pdb=" CB  ASP C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.03   -0.52 2.00e-01 2.50e+01 6.72e+00
  ... (remaining 1054 not shown)

  Planarity restraints: 1142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 275 "    1.003 9.50e-02 1.11e+02   4.50e-01 1.22e+02
        pdb=" NE  ARG C 275 "   -0.062 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 275 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 275 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 275 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 493 "   -0.027 2.00e-02 2.50e+03   4.97e-02 2.47e+01
        pdb=" C   PRO A 493 "    0.086 2.00e-02 2.50e+03
        pdb=" O   PRO A 493 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   GLU A 494 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 782 "   -0.024 2.00e-02 2.50e+03   4.91e-02 2.41e+01
        pdb=" C   MET C 782 "    0.085 2.00e-02 2.50e+03
        pdb=" O   MET C 782 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   LYS C 783 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 1139 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1655
        2.79 -     3.32: 6090
        3.32 -     3.85: 10590
        3.85 -     4.37: 12239
        4.37 -     4.90: 21019
  Nonbonded interactions: 51593
  Sorted by model distance:
  nonbonded pdb=" N   SER C 148 "
            pdb=" O   SER C 148 "
     model   vdw
     2.268 2.496
  nonbonded pdb=" O   HIS C 365 "
            pdb=" OG  SER C 390 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OE1 GLU C 686 "
            pdb=" OG  SER C 703 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   THR C 526 "
            pdb=" OG1 THR C 526 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" O   PRO A 447 "
            pdb=" NZ  LYS A 449 "
     model   vdw
     2.386 3.120
  ... (remaining 51588 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:             1.290
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     18.550
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
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      :  0.007   0.180   6630  Z= 0.424
  Angle     :  1.303  19.559   9021  Z= 0.859
  Chirality :  0.084   0.672   1057
  Planarity :  0.015   0.450   1142
  Dihedral  : 17.170  85.831   2337
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  6.01 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 26.83 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.63 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.29), residues: 832
  helix:  1.19 (0.33), residues: 247
  sheet: -0.72 (0.48), residues: 133
  loop : -1.14 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.022   0.001   PHE C 554 
 TYR   0.013   0.001   TYR C 725 
 ARG   0.003   0.000   ARG C 275 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 80
  time to evaluate  : 0.769 
Fit side-chains
REVERT: C  440 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8304 (mttp)
REVERT: C  659 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6850 (pt)
REVERT: A  445 GLN cc_start: 0.6414 (tp40) cc_final: 0.5246 (tp40)
REVERT: A  485 TYR cc_start: 0.8931 (m-80) cc_final: 0.8504 (m-80)
  outliers start: 43
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1751
  time to fit residues: 27.0239
Evaluate side-chains
  78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  373 GLN
Chi-restraints excluded: chain C residue  412 LEU
Chi-restraints excluded: chain C residue  464 VAL
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  538 SER
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  557 LEU
Chi-restraints excluded: chain C residue  575 LEU
Chi-restraints excluded: chain C residue  579 LEU
Chi-restraints excluded: chain C residue  641 VAL
Chi-restraints excluded: chain C residue  645 LEU
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  704 LEU
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0770
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
C 139 ASN
C 187 ASN
C 402 HIS
C 444 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.115903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.087138 restraints weight = 13064.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.19
r_work: 0.3239 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6630  Z= 0.196
  Angle     :  0.615   7.630   9021  Z= 0.304
  Chirality :  0.044   0.184   1057
  Planarity :  0.004   0.037   1142
  Dihedral  :  6.469  54.359    910
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.09 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.29), residues: 832
  helix:  1.73 (0.32), residues: 257
  sheet: -0.55 (0.48), residues: 135
  loop : -0.89 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 159 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.013   0.001   PHE C 808 
 TYR   0.009   0.001   TYR C 725 
 ARG   0.003   0.000   ARG C 817 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 0.713 
Fit side-chains
REVERT: C   71 GLN cc_start: 0.8679 (pp30) cc_final: 0.8241 (pp30)
REVERT: C  519 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7206 (tp)
REVERT: C  659 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6559 (pp)
REVERT: C  667 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8783 (tm)
REVERT: A  440 MET cc_start: 0.6868 (tmm) cc_final: 0.6566 (tmm)
REVERT: A  445 GLN cc_start: 0.7301 (tp40) cc_final: 0.6551 (tp40)
REVERT: A  459 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7880 (mm)
REVERT: A  485 TYR cc_start: 0.8719 (m-80) cc_final: 0.8503 (m-80)
  outliers start: 32
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1403
  time to fit residues: 18.8537
Evaluate side-chains
  78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  139 ASN
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  412 LEU
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  560 ILE
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  671 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 16 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.115934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.086388 restraints weight = 13368.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.28
r_work: 0.3219 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6630  Z= 0.201
  Angle     :  0.595   7.362   9021  Z= 0.293
  Chirality :  0.044   0.165   1057
  Planarity :  0.004   0.037   1142
  Dihedral  :  5.180  55.016    887
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 29.92 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.29), residues: 832
  helix:  1.95 (0.32), residues: 255
  sheet: -0.57 (0.47), residues: 135
  loop : -0.88 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.011   0.001   PHE C 808 
 TYR   0.009   0.001   TYR C 725 
 ARG   0.002   0.000   ARG A 444 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 59
  time to evaluate  : 0.760 
Fit side-chains
REVERT: C   71 GLN cc_start: 0.8690 (pp30) cc_final: 0.8261 (pp30)
REVERT: C  165 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7950 (pp)
REVERT: C  260 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8564 (tp)
REVERT: C  519 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7194 (tp)
REVERT: C  659 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6573 (pp)
REVERT: C  667 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8518 (tm)
REVERT: C  671 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8448 (mm)
REVERT: C  721 MET cc_start: 0.8767 (ptp) cc_final: 0.8512 (ptp)
REVERT: C  725 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7307 (m-80)
REVERT: A  445 GLN cc_start: 0.7362 (tp40) cc_final: 0.6827 (tp40)
REVERT: A  463 THR cc_start: 0.8770 (p) cc_final: 0.8224 (m)
REVERT: A  485 TYR cc_start: 0.8712 (m-80) cc_final: 0.8497 (m-80)
  outliers start: 28
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1347
  time to fit residues: 16.4546
Evaluate side-chains
  78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  560 ILE
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  671 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 66 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.112945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.083548 restraints weight = 13228.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 3.24
r_work: 0.3170 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6630  Z= 0.307
  Angle     :  0.621   7.205   9021  Z= 0.307
  Chirality :  0.045   0.165   1057
  Planarity :  0.004   0.042   1142
  Dihedral  :  5.090  54.597    885
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 27.81 %
    Favored  : 66.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.29), residues: 832
  helix:  2.00 (0.32), residues: 255
  sheet: -0.50 (0.47), residues: 133
  loop : -0.85 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 159 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.011   0.001   PHE C 473 
 TYR   0.011   0.001   TYR C 725 
 ARG   0.003   0.000   ARG C 542 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 57
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: C   71 GLN cc_start: 0.8693 (pp30) cc_final: 0.8286 (pp30)
REVERT: C  165 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7991 (pp)
REVERT: C  367 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8774 (tp)
REVERT: C  519 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7194 (tp)
REVERT: C  659 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6870 (pp)
REVERT: C  667 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8621 (tm)
REVERT: C  671 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8451 (mm)
REVERT: C  725 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7320 (m-80)
REVERT: A  445 GLN cc_start: 0.7508 (tp40) cc_final: 0.7113 (tp40)
REVERT: A  485 TYR cc_start: 0.8739 (m-80) cc_final: 0.8518 (m-80)
  outliers start: 40
  outliers final: 21
  residues processed: 87
  average time/residue: 0.1404
  time to fit residues: 18.5255
Evaluate side-chains
  85 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  367 LEU
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  560 ILE
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  618 CYS
Chi-restraints excluded: chain C residue  637 MET
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  671 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  501 CYS
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 78 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C 658 HIS
C 714 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.114496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.084645 restraints weight = 13395.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 3.33
r_work: 0.3216 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6630  Z= 0.214
  Angle     :  0.587   8.210   9021  Z= 0.287
  Chirality :  0.043   0.152   1057
  Planarity :  0.004   0.046   1142
  Dihedral  :  4.905  54.213    885
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 27.25 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.29), residues: 832
  helix:  2.26 (0.32), residues: 250
  sheet: -0.51 (0.49), residues: 126
  loop : -0.83 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.010   0.001   PHE C 760 
 TYR   0.010   0.001   TYR C 725 
 ARG   0.002   0.000   ARG C 542 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 59
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: C   62 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7262 (tt)
REVERT: C   66 MET cc_start: 0.8816 (mpp) cc_final: 0.8515 (mpp)
REVERT: C   71 GLN cc_start: 0.8672 (pp30) cc_final: 0.8228 (pp30)
REVERT: C   83 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8524 (tt)
REVERT: C  165 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7942 (pp)
REVERT: C  381 LYS cc_start: 0.9295 (mttt) cc_final: 0.8997 (mtpp)
REVERT: C  519 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7130 (tp)
REVERT: C  659 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6920 (pp)
REVERT: C  667 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8545 (tm)
REVERT: C  725 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7341 (m-80)
REVERT: A  445 GLN cc_start: 0.7364 (tp40) cc_final: 0.7013 (tp40)
REVERT: A  463 THR cc_start: 0.8788 (p) cc_final: 0.8386 (m)
REVERT: A  485 TYR cc_start: 0.8911 (m-80) cc_final: 0.8682 (m-80)
  outliers start: 38
  outliers final: 21
  residues processed: 88
  average time/residue: 0.1323
  time to fit residues: 17.3539
Evaluate side-chains
  85 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  560 ILE
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  645 LEU
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  681 LEU
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.112635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.082596 restraints weight = 13222.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 3.30
r_work: 0.3176 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6630  Z= 0.335
  Angle     :  0.644   7.575   9021  Z= 0.315
  Chirality :  0.046   0.190   1057
  Planarity :  0.004   0.046   1142
  Dihedral  :  5.068  52.871    885
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 27.25 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.29), residues: 832
  helix:  2.02 (0.32), residues: 256
  sheet: -0.46 (0.50), residues: 123
  loop : -0.89 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 159 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.012   0.001   PHE C 808 
 TYR   0.011   0.001   TYR C 725 
 ARG   0.003   0.000   ARG C 542 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 57
  time to evaluate  : 0.749 
Fit side-chains
REVERT: C   62 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7304 (tt)
REVERT: C   66 MET cc_start: 0.8795 (mpp) cc_final: 0.8526 (mpp)
REVERT: C   71 GLN cc_start: 0.8696 (pp30) cc_final: 0.8264 (pp30)
REVERT: C   83 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8590 (tt)
REVERT: C  165 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7966 (pp)
REVERT: C  344 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8572 (mtm)
REVERT: C  381 LYS cc_start: 0.9347 (mttt) cc_final: 0.9050 (mtpp)
REVERT: C  519 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: C  659 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7187 (pp)
REVERT: C  667 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8735 (tm)
REVERT: C  721 MET cc_start: 0.8832 (ptp) cc_final: 0.8515 (ptp)
REVERT: C  725 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7214 (m-80)
REVERT: C  775 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5977 (mp)
REVERT: A  445 GLN cc_start: 0.7441 (tp40) cc_final: 0.7033 (tp40)
REVERT: A  485 TYR cc_start: 0.8921 (m-80) cc_final: 0.8688 (m-80)
REVERT: A  498 MET cc_start: 0.7374 (tpt) cc_final: 0.7164 (tpt)
  outliers start: 40
  outliers final: 22
  residues processed: 89
  average time/residue: 0.1390
  time to fit residues: 18.3102
Evaluate side-chains
  88 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 57
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  367 LEU
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  560 ILE
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  618 CYS
Chi-restraints excluded: chain C residue  637 MET
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  775 ILE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 73 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.113987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.084940 restraints weight = 12993.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.20
r_work: 0.3224 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6630  Z= 0.209
  Angle     :  0.598   8.154   9021  Z= 0.289
  Chirality :  0.043   0.146   1057
  Planarity :  0.004   0.048   1142
  Dihedral  :  4.869  51.576    885
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 26.69 %
    Favored  : 67.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.30), residues: 832
  helix:  2.09 (0.32), residues: 256
  sheet: -0.51 (0.49), residues: 126
  loop : -0.80 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.010   0.001   PHE C 760 
 TYR   0.012   0.001   TYR C 725 
 ARG   0.001   0.000   ARG C 542 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 61
  time to evaluate  : 0.723 
Fit side-chains
REVERT: C   62 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7291 (tt)
REVERT: C   66 MET cc_start: 0.8843 (mpp) cc_final: 0.8581 (mpp)
REVERT: C   71 GLN cc_start: 0.8675 (pp30) cc_final: 0.8196 (pp30)
REVERT: C  165 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7923 (pp)
REVERT: C  344 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8478 (mtm)
REVERT: C  354 ASN cc_start: 0.8269 (p0) cc_final: 0.7830 (p0)
REVERT: C  381 LYS cc_start: 0.9310 (mttt) cc_final: 0.8992 (mtpp)
REVERT: C  519 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7093 (tp)
REVERT: C  659 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7142 (pp)
REVERT: C  667 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8853 (tm)
REVERT: C  725 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7193 (m-80)
REVERT: A  445 GLN cc_start: 0.7302 (tp40) cc_final: 0.6899 (tp40)
REVERT: A  463 THR cc_start: 0.8782 (p) cc_final: 0.8402 (m)
REVERT: A  498 MET cc_start: 0.7307 (tpt) cc_final: 0.7032 (tpt)
  outliers start: 40
  outliers final: 24
  residues processed: 94
  average time/residue: 0.1493
  time to fit residues: 20.6197
Evaluate side-chains
  89 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 58
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  367 LEU
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  637 MET
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  645 LEU
Chi-restraints excluded: chain C residue  659 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  681 LEU
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  489 ASN
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 60 optimal weight:    0.0670
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7322

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.114241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.084626 restraints weight = 13259.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 3.29
r_work: 0.3213 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6630  Z= 0.223
  Angle     :  0.620   9.269   9021  Z= 0.298
  Chirality :  0.044   0.178   1057
  Planarity :  0.004   0.049   1142
  Dihedral  :  4.850  50.883    885
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 26.97 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.29), residues: 832
  helix:  2.25 (0.32), residues: 250
  sheet: -0.50 (0.50), residues: 126
  loop : -0.76 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.011   0.001   PHE A 518 
 TYR   0.012   0.001   TYR C 725 
 ARG   0.008   0.000   ARG C 214 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 57
  time to evaluate  : 0.740 
Fit side-chains
REVERT: C   62 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7269 (tt)
REVERT: C   66 MET cc_start: 0.8877 (mpp) cc_final: 0.8579 (mpp)
REVERT: C   71 GLN cc_start: 0.8629 (pp30) cc_final: 0.8187 (pp30)
REVERT: C   83 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8593 (tt)
REVERT: C  165 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7940 (pp)
REVERT: C  344 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8517 (mtm)
REVERT: C  381 LYS cc_start: 0.9288 (mttt) cc_final: 0.8986 (mtpp)
REVERT: C  519 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7059 (tp)
REVERT: C  667 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8820 (tm)
REVERT: C  721 MET cc_start: 0.8912 (ptp) cc_final: 0.8372 (ptp)
REVERT: C  725 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7246 (m-80)
REVERT: A  445 GLN cc_start: 0.7330 (tp40) cc_final: 0.6878 (tp40)
REVERT: A  463 THR cc_start: 0.8830 (p) cc_final: 0.8465 (m)
REVERT: A  498 MET cc_start: 0.7429 (tpt) cc_final: 0.7130 (tpt)
  outliers start: 37
  outliers final: 23
  residues processed: 88
  average time/residue: 0.1333
  time to fit residues: 17.5023
Evaluate side-chains
  86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 56
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  192 ILE
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  367 LEU
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  637 MET
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  645 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0980
   chunk 67 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0970
   chunk 68 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    0.1980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
C 140 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.116321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.086954 restraints weight = 13567.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 3.34
r_work: 0.3257 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6630  Z= 0.166
  Angle     :  0.610   8.859   9021  Z= 0.292
  Chirality :  0.043   0.190   1057
  Planarity :  0.004   0.050   1142
  Dihedral  :  4.550  49.593    883
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 27.11 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.29), residues: 832
  helix:  2.29 (0.32), residues: 249
  sheet: -0.58 (0.48), residues: 131
  loop : -0.70 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.010   0.001   PHE A 518 
 TYR   0.013   0.001   TYR C 725 
 ARG   0.007   0.000   ARG C 214 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 58
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: C   62 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7203 (tt)
REVERT: C   66 MET cc_start: 0.8839 (mpp) cc_final: 0.8552 (mpp)
REVERT: C   71 GLN cc_start: 0.8567 (pp30) cc_final: 0.8119 (pp30)
REVERT: C   83 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8580 (tt)
REVERT: C  165 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7875 (pp)
REVERT: C  344 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8458 (mtm)
REVERT: C  354 ASN cc_start: 0.8166 (p0) cc_final: 0.7700 (p0)
REVERT: C  381 LYS cc_start: 0.9230 (mttt) cc_final: 0.8810 (mtpp)
REVERT: C  519 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7031 (tp)
REVERT: C  667 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8783 (tm)
REVERT: C  725 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7286 (m-80)
REVERT: C  775 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5954 (mp)
REVERT: A  445 GLN cc_start: 0.7285 (tp40) cc_final: 0.6949 (tp40)
REVERT: A  484 LEU cc_start: 0.7265 (tp) cc_final: 0.7023 (tp)
REVERT: A  498 MET cc_start: 0.7383 (tpt) cc_final: 0.7118 (tpt)
  outliers start: 34
  outliers final: 21
  residues processed: 86
  average time/residue: 0.1350
  time to fit residues: 17.0060
Evaluate side-chains
  86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  645 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  681 LEU
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  775 ILE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain A residue  439 CYS
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0770
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN
C 140 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.115153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.085617 restraints weight = 13512.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 3.34
r_work: 0.3231 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6630  Z= 0.202
  Angle     :  0.620   8.637   9021  Z= 0.296
  Chirality :  0.043   0.190   1057
  Planarity :  0.004   0.049   1142
  Dihedral  :  4.564  49.518    883
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 27.25 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.29), residues: 832
  helix:  2.30 (0.32), residues: 249
  sheet: -0.59 (0.48), residues: 131
  loop : -0.71 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 442 
 HIS   0.006   0.001   HIS C 256 
 PHE   0.009   0.001   PHE C 760 
 TYR   0.012   0.001   TYR C 725 
 ARG   0.007   0.000   ARG C 214 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: C   62 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7254 (tt)
REVERT: C   66 MET cc_start: 0.8814 (mpp) cc_final: 0.8537 (mpp)
REVERT: C   71 GLN cc_start: 0.8589 (pp30) cc_final: 0.8130 (pp30)
REVERT: C   83 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8554 (tt)
REVERT: C  165 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7920 (pp)
REVERT: C  344 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8500 (mtm)
REVERT: C  354 ASN cc_start: 0.8175 (p0) cc_final: 0.7730 (p0)
REVERT: C  381 LYS cc_start: 0.9272 (mttt) cc_final: 0.8949 (mtpp)
REVERT: C  519 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7008 (tp)
REVERT: C  554 PHE cc_start: 0.8541 (m-10) cc_final: 0.7719 (t80)
REVERT: C  667 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8803 (tm)
REVERT: C  725 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7324 (m-80)
REVERT: C  775 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5982 (mp)
REVERT: A  445 GLN cc_start: 0.7333 (tp40) cc_final: 0.6886 (tp40)
REVERT: A  498 MET cc_start: 0.7418 (tpt) cc_final: 0.7124 (tpt)
  outliers start: 32
  outliers final: 22
  residues processed: 87
  average time/residue: 0.1368
  time to fit residues: 18.5518
Evaluate side-chains
  89 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  165 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  367 LEU
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  519 ILE
Chi-restraints excluded: chain C residue  532 CYS
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  640 THR
Chi-restraints excluded: chain C residue  644 SER
Chi-restraints excluded: chain C residue  645 LEU
Chi-restraints excluded: chain C residue  667 LEU
Chi-restraints excluded: chain C residue  678 CYS
Chi-restraints excluded: chain C residue  683 HIS
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  725 TYR
Chi-restraints excluded: chain C residue  768 PHE
Chi-restraints excluded: chain C residue  775 ILE
Chi-restraints excluded: chain C residue  792 LEU
Chi-restraints excluded: chain C residue  815 LEU
Chi-restraints excluded: chain A residue  439 CYS
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 60 optimal weight:    0.0010
   chunk 6 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 78 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.114529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.085512 restraints weight = 13447.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.27
r_work: 0.3240 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6630  Z= 0.210
  Angle     :  0.621   8.517   9021  Z= 0.298
  Chirality :  0.044   0.192   1057
  Planarity :  0.004   0.049   1142
  Dihedral  :  4.587  49.424    883
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 27.11 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 832
  helix:  2.27 (0.32), residues: 249
  sheet: -0.57 (0.48), residues: 131
  loop : -0.69 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 442 
 HIS   0.005   0.001   HIS C 256 
 PHE   0.010   0.001   PHE C 754 
 TYR   0.012   0.001   TYR C 725 
 ARG   0.007   0.000   ARG C 214 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3251.00 seconds
wall clock time: 58 minutes 27.42 seconds (3507.42 seconds total)