Starting phenix.real_space_refine
on Thu Jul  2 02:07:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jp0_36465/07_2026/8jp0_36465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jp0_36465/07_2026/8jp0_36465.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jp0_36465/07_2026/8jp0_36465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jp0_36465/07_2026/8jp0_36465.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jp0_36465/07_2026/8jp0_36465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jp0_36465/07_2026/8jp0_36465.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3691      2.51       5
     N     910      2.21       5
     O    1044      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5671
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 719, 5644
          Classifications: {'peptide': 719}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 23, 'TRANS': 695}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'EKY': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.62, per 1000 atoms: 0.29
  Number of scatterers: 5671
  At special positions: 0
  Unit cell: (139.4, 68.88, 108.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     F       2      9.00
     O    1044      8.00
     N     910      7.00
     C    3691      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: 0.61
  Conformation dependent library (CDL) restraints added in 264.1 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:  1324

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 7 sheets defined
      45.1% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 104
    Processing helix  chain 'A' and resid 134 through 139
    Processing helix  chain 'A' and resid 142 through 145
    Processing helix  chain 'A' and resid 146 through 159
      removed outlier: 4.299A  pdb=" N   SER A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   VAL A 156 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   CYS A 157 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 188
      removed outlier: 4.750A  pdb=" N   ILE A 183 " --> pdb=" O   MET A 179 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ALA A 184 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 224
      removed outlier: 3.549A  pdb=" N   PHE A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   VAL A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TYR A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR A 216 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   TYR A 219 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE A 220 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 259
      removed outlier: 3.777A  pdb=" N   PHE A 239 " --> pdb=" O   GLY A 235 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   PHE A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      Proline residue:  A 243  - end of helix
      removed outlier: 4.743A  pdb=" N   ARG A 254 " --> pdb=" O   TRP A 250 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 256 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TYR A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 665
    Processing helix  chain 'A' and resid 683 through 697
    Processing helix  chain 'A' and resid 713 through 720
    Processing helix  chain 'A' and resid 737 through 744
      removed outlier: 3.975A  pdb=" N   VAL A 741 " --> pdb=" O   CYS A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 756
      removed outlier: 3.653A  pdb=" N   PHE A 755 " --> pdb=" O   VAL A 751 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   VAL A 756 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 769
      removed outlier: 4.323A  pdb=" N   PHE A 768 " --> pdb=" O   GLY A 764 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE A 769 " --> pdb=" O   TRP A 765 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 764 through 769'
    Processing helix  chain 'A' and resid 770 through 790
    Processing helix  chain 'A' and resid 796 through 804
      removed outlier: 3.757A  pdb=" N   THR A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ALA A 801 " --> pdb=" O   ASP A 797 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL A 802 " --> pdb=" O   SER A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 810
      removed outlier: 3.807A  pdb=" N   GLY A 808 " --> pdb=" O   PHE A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 824
      removed outlier: 3.818A  pdb=" N   THR A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 860
      removed outlier: 4.239A  pdb=" N   VAL A 834 " --> pdb=" O   SER A 830 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 842 " --> pdb=" O   ASN A 838 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN A 860 " --> pdb=" O   TYR A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 890
      removed outlier: 3.876A  pdb=" N   LEU A 890 " --> pdb=" O   VAL A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 897
    Processing helix  chain 'A' and resid 904 through 932
      removed outlier: 4.495A  pdb=" N   SER A 912 " --> pdb=" O   LYS A 908 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   CYS A 913 " --> pdb=" O   LEU A 909 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 116
    Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268
      removed outlier: 3.792A  pdb=" N   TYR A 263 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 472 through 478
      removed outlier: 5.663A  pdb=" N   SER A 407 " --> pdb=" O   CYS A 520 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 419
      removed outlier: 5.694A  pdb=" N   TYR A 416 " --> pdb=" O   THR A 530 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   PHE A 532 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   CYS A 418 " --> pdb=" O   PHE A 532 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   VAL A 498 " --> pdb=" O   PHE A 441 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE A 441 " --> pdb=" O   VAL A 498 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL A 500 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   THR A 439 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 605 through 609
    Processing sheet with id=AA6, first strand: chain 'A' and resid 546 through 550
    Processing sheet with id=AA7, first strand: chain 'A' and resid 593 through 597

    272 hydrogen bonds defined for protein.
    786 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: 0.89

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 921
        1.31 -     1.43: 1619
        1.43 -     1.56: 3229
        1.56 -     1.68: 0
        1.68 -     1.81: 34
  Bond restraints: 5803
  Sorted by residual:
  bond pdb=" CA  SER A 145 "
       pdb=" CB  SER A 145 "
    ideal  model  delta    sigma   weight residual
    1.528  1.461  0.066 1.35e-02 5.49e+03 2.42e+01
  bond pdb=" C   PRO A 545 "
       pdb=" O   PRO A 545 "
    ideal  model  delta    sigma   weight residual
    1.239  1.185  0.054 1.27e-02 6.20e+03 1.78e+01
  bond pdb=" C12 EKY A1001 "
       pdb=" N06 EKY A1001 "
    ideal  model  delta    sigma   weight residual
    1.380  1.450 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" N   GLU A 544 "
       pdb=" CA  GLU A 544 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.031 9.20e-03 1.18e+04 1.16e+01
  bond pdb=" N   VAL A 546 "
       pdb=" CA  VAL A 546 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.22e-02 6.72e+03 9.77e+00
  ... (remaining 5798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 7749
        2.76 -     5.51: 108
        5.51 -     8.27: 14
        8.27 -    11.02: 1
       11.02 -    13.78: 1
  Bond angle restraints: 7873
  Sorted by residual:
  angle pdb=" C   ASN A 178 "
        pdb=" CA  ASN A 178 "
        pdb=" CB  ASN A 178 "
      ideal   model   delta    sigma   weight residual
     110.96   97.18   13.78 1.54e+00 4.22e-01 8.00e+01
  angle pdb=" N   PRO A 524 "
        pdb=" CA  PRO A 524 "
        pdb=" CB  PRO A 524 "
      ideal   model   delta    sigma   weight residual
     103.25  111.42   -8.17 1.05e+00 9.07e-01 6.05e+01
  angle pdb=" N   ILE A 831 "
        pdb=" CA  ILE A 831 "
        pdb=" C   ILE A 831 "
      ideal   model   delta    sigma   weight residual
     112.96  107.63    5.33 1.00e+00 1.00e+00 2.85e+01
  angle pdb=" N   GLY A 538 "
        pdb=" CA  GLY A 538 "
        pdb=" C   GLY A 538 "
      ideal   model   delta    sigma   weight residual
     111.35  117.07   -5.72 1.20e+00 6.94e-01 2.28e+01
  angle pdb=" CA  THR A 547 "
        pdb=" C   THR A 547 "
        pdb=" O   THR A 547 "
      ideal   model   delta    sigma   weight residual
     121.40  116.05    5.35 1.13e+00 7.83e-01 2.24e+01
  ... (remaining 7868 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 3301
       35.27 -    70.53: 59
       70.53 -   105.80: 4
      105.80 -   141.06: 1
      141.06 -   176.33: 2
  Dihedral angle restraints: 3367
    sinusoidal: 1306
      harmonic: 2061
  Sorted by residual:
  dihedral pdb=" C   ASN A 178 "
           pdb=" N   ASN A 178 "
           pdb=" CA  ASN A 178 "
           pdb=" CB  ASN A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.48  -16.12     0      2.50e+00 1.60e-01 4.16e+01
  dihedral pdb=" C22 EKY A1001 "
           pdb=" C07 EKY A1001 "
           pdb=" C09 EKY A1001 "
           pdb=" O03 EKY A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
       5.40 -170.93  176.33     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C21 EKY A1001 "
           pdb=" C07 EKY A1001 "
           pdb=" C09 EKY A1001 "
           pdb=" O03 EKY A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     184.92    9.58  175.34     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 3364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 769
       0.072 -    0.143: 118
       0.143 -    0.215: 7
       0.215 -    0.286: 2
       0.286 -    0.358: 3
  Chirality restraints: 899
  Sorted by residual:
  chirality pdb=" CA  ASN A 178 "
            pdb=" N   ASN A 178 "
            pdb=" C   ASN A 178 "
            pdb=" CB  ASN A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" CB  ILE A 555 "
            pdb=" CA  ILE A 555 "
            pdb=" CG1 ILE A 555 "
            pdb=" CG2 ILE A 555 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" CA  GLU A 544 "
            pdb=" N   GLU A 544 "
            pdb=" C   GLU A 544 "
            pdb=" CB  GLU A 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 896 not shown)

  Planarity restraints: 985
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 572 "   -0.047 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO A 573 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 573 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 573 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 757 "   -0.042 5.00e-02 4.00e+02   6.30e-02 6.36e+00
        pdb=" N   PRO A 758 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 758 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 758 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 903 "   -0.041 5.00e-02 4.00e+02   6.15e-02 6.05e+00
        pdb=" N   PRO A 904 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 904 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 904 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 982 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 533
        2.74 -     3.28: 6069
        3.28 -     3.82: 9195
        3.82 -     4.36: 10925
        4.36 -     4.90: 18291
  Nonbonded interactions: 45013
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 450 "
            pdb=" OD1 ASN A 490 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OE2 GLU A 148 "
            pdb=" OG1 THR A 809 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   GLY A 423 "
            pdb=" N   ILE A 479 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" N   GLU A 132 "
            pdb=" OE2 GLU A 277 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" O   HIS A 788 "
            pdb=" OG1 THR A 792 "
     model   vdw
     2.281 3.040
  ... (remaining 45008 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.910
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   5803  Z= 0.250
  Angle     :  0.824  13.777   7873  Z= 0.488
  Chirality :  0.054   0.358    899
  Planarity :  0.006   0.072    985
  Dihedral  : 15.248 176.329   2043
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.74 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.49 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.30), residues: 709
  helix: -1.42 (0.28), residues: 288
  sheet: -1.02 (0.40), residues: 160
  loop : -2.67 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 582 
 TYR   0.019   0.002   TYR A 215 
 PHE   0.033   0.002   PHE A 744 
 TRP   0.022   0.002   TRP A 749 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.25 ( 5803)
  covalent geometry    : angle       0.82352 /  0.49 ( 7873)
  hydrogen bonds       : bond        0.12823 /  8.66 (  272)
  hydrogen bonds       : angle       7.33122 /  5.14 (  786)

*********************** 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
  97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.7746 (mt) cc_final: 0.7493 (mp)
REVERT: A   88 MET cc_start: 0.7147 (mmp) cc_final: 0.6947 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0857
  time to fit residues: 10.3505
Evaluate side-chains
  62 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:   40.0000
   overall best weight:    0.5318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 536 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.173496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.137839 restraints weight = 12524.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.140498 restraints weight = 6086.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.142096 restraints weight = 3871.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.142790 restraints weight = 2985.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.143461 restraints weight = 2624.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5803  Z= 0.133
  Angle     :  0.644   7.663   7873  Z= 0.340
  Chirality :  0.047   0.337    899
  Planarity :  0.006   0.066    985
  Dihedral  : 12.151 163.483    780
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.90 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.39 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.31), residues: 709
  helix: -0.54 (0.30), residues: 290
  sheet: -0.81 (0.41), residues: 152
  loop : -2.34 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 905 
 TYR   0.016   0.002   TYR A 215 
 PHE   0.021   0.001   PHE A 744 
 TRP   0.013   0.001   TRP A 250 
 HIS   0.003   0.001   HIS A 536 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 5803)
  covalent geometry    : angle       0.64406 /  0.34 ( 7873)
  hydrogen bonds       : bond        0.04437 /  2.94 (  272)
  hydrogen bonds       : angle       5.85084 /  4.18 (  786)

*********************** 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
  71 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 MET cc_start: 0.6958 (mmp) cc_final: 0.6753 (mmt)
REVERT: A  541 THR cc_start: 0.7859 (m) cc_final: 0.7650 (p)
  outliers start: 8
  outliers final: 3
  residues processed: 69
  average time/residue: 0.0737
  time to fit residues: 6.8639
Evaluate side-chains
  57 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  612 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 35 optimal weight:    0.1980
   chunk 28 optimal weight:   40.0000
   chunk 23 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.173611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.138361 restraints weight = 12513.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.140884 restraints weight = 6125.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.142299 restraints weight = 3903.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.143325 restraints weight = 3033.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.143964 restraints weight = 2591.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5803  Z= 0.125
  Angle     :  0.591   8.193   7873  Z= 0.311
  Chirality :  0.044   0.200    899
  Planarity :  0.005   0.068    985
  Dihedral  : 11.147 169.704    780
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.33 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.83 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.32), residues: 709
  helix:  0.00 (0.31), residues: 277
  sheet: -0.74 (0.41), residues: 154
  loop : -2.18 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 905 
 TYR   0.012   0.001   TYR A 215 
 PHE   0.015   0.001   PHE A 744 
 TRP   0.012   0.001   TRP A 250 
 HIS   0.002   0.000   HIS A 857 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 5803)
  covalent geometry    : angle       0.59140 /  0.31 ( 7873)
  hydrogen bonds       : bond        0.04166 /  2.75 (  272)
  hydrogen bonds       : angle       5.57253 /  4.00 (  786)

*********************** 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
  68 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.7896 (mp) cc_final: 0.7687 (mt)
REVERT: A   87 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7381 (t80)
REVERT: A  541 THR cc_start: 0.7950 (m) cc_final: 0.7735 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.0657
  time to fit residues: 5.9214
Evaluate side-chains
  56 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  745 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:   40.0000
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.0786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.171906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.136073 restraints weight = 12477.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.138769 restraints weight = 6162.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.140285 restraints weight = 3955.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.141071 restraints weight = 3070.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.141630 restraints weight = 2701.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5803  Z= 0.149
  Angle     :  0.602   6.753   7873  Z= 0.317
  Chirality :  0.045   0.197    899
  Planarity :  0.005   0.070    985
  Dihedral  : 10.915 179.089    780
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.46 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.98 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.32), residues: 709
  helix: -0.08 (0.31), residues: 277
  sheet: -0.71 (0.41), residues: 162
  loop : -2.12 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 905 
 TYR   0.016   0.001   TYR A 215 
 PHE   0.014   0.001   PHE A 755 
 TRP   0.013   0.001   TRP A 250 
 HIS   0.002   0.001   HIS A 536 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 5803)
  covalent geometry    : angle       0.60216 /  0.32 ( 7873)
  hydrogen bonds       : bond        0.04298 /  2.86 (  272)
  hydrogen bonds       : angle       5.52704 /  3.98 (  786)

*********************** 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
  68 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7509 (t80)
REVERT: A  541 THR cc_start: 0.7956 (m) cc_final: 0.7742 (p)
  outliers start: 14
  outliers final: 7
  residues processed: 67
  average time/residue: 0.0595
  time to fit residues: 5.6652
Evaluate side-chains
  59 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  250 TRP
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain A residue  842 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:   50.0000
   chunk 17 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.6584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.169194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.132659 restraints weight = 12767.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.135115 restraints weight = 6321.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.136613 restraints weight = 4059.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.137329 restraints weight = 3159.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.138018 restraints weight = 2793.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5803  Z= 0.196
  Angle     :  0.663   9.042   7873  Z= 0.345
  Chirality :  0.047   0.192    899
  Planarity :  0.005   0.072    985
  Dihedral  : 10.702 170.818    780
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.89 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.46 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.32), residues: 709
  helix: -0.29 (0.31), residues: 277
  sheet: -0.71 (0.42), residues: 158
  loop : -2.15 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 905 
 TYR   0.018   0.002   TYR A 219 
 PHE   0.019   0.002   PHE A 755 
 TRP   0.015   0.002   TRP A 250 
 HIS   0.002   0.001   HIS A 857 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.20 ( 5803)
  covalent geometry    : angle       0.66295 /  0.35 ( 7873)
  hydrogen bonds       : bond        0.04678 /  3.12 (  272)
  hydrogen bonds       : angle       5.66020 /  4.06 (  786)

*********************** 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
  73 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.7944 (mp) cc_final: 0.7729 (mt)
REVERT: A   87 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7609 (t80)
REVERT: A  541 THR cc_start: 0.8024 (m) cc_final: 0.7817 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0547
  time to fit residues: 5.3696
Evaluate side-chains
  64 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  250 TRP
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  842 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 31 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0980
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:   20.0000
   chunk 58 optimal weight:    0.4980
   chunk 26 optimal weight:   50.0000
   chunk 1 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.173134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.138209 restraints weight = 12609.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.140901 restraints weight = 6101.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.142471 restraints weight = 3899.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.143209 restraints weight = 3012.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 64)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.143890 restraints weight = 2649.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5803  Z= 0.125
  Angle     :  0.603   8.608   7873  Z= 0.314
  Chirality :  0.044   0.183    899
  Planarity :  0.005   0.071    985
  Dihedral  :  9.812 157.926    780
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.91 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.44 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.32), residues: 709
  helix: -0.08 (0.31), residues: 284
  sheet: -0.59 (0.42), residues: 158
  loop : -2.05 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 582 
 TYR   0.013   0.001   TYR A 215 
 PHE   0.011   0.001   PHE A 768 
 TRP   0.012   0.001   TRP A 250 
 HIS   0.002   0.000   HIS A 536 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 5803)
  covalent geometry    : angle       0.60331 /  0.31 ( 7873)
  hydrogen bonds       : bond        0.04013 /  2.60 (  272)
  hydrogen bonds       : angle       5.45625 /  3.94 (  786)

*********************** 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
  76 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7481 (t80)
REVERT: A  541 THR cc_start: 0.7966 (m) cc_final: 0.7748 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0591
  time to fit residues: 6.0302
Evaluate side-chains
  65 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  885 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.2986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.171225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.135967 restraints weight = 12672.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.138635 restraints weight = 6118.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.140196 restraints weight = 3896.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.140934 restraints weight = 3011.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.141590 restraints weight = 2651.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5803  Z= 0.168
  Angle     :  0.644   9.606   7873  Z= 0.338
  Chirality :  0.046   0.174    899
  Planarity :  0.005   0.071    985
  Dihedral  :  9.677 151.620    780
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.18 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.60 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.32), residues: 709
  helix: -0.16 (0.30), residues: 283
  sheet: -0.56 (0.42), residues: 158
  loop : -2.13 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 582 
 TYR   0.015   0.001   TYR A 215 
 PHE   0.014   0.001   PHE A 755 
 TRP   0.014   0.002   TRP A 217 
 HIS   0.002   0.001   HIS A 857 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 ( 5803)
  covalent geometry    : angle       0.64381 /  0.34 ( 7873)
  hydrogen bonds       : bond        0.04393 /  2.87 (  272)
  hydrogen bonds       : angle       5.50851 /  3.96 (  786)

*********************** 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
  72 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 53
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.7926 (mp) cc_final: 0.7691 (mt)
REVERT: A   87 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7592 (t80)
REVERT: A  541 THR cc_start: 0.8042 (m) cc_final: 0.7819 (p)
REVERT: A  755 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.5816 (m-10)
  outliers start: 19
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0642
  time to fit residues: 6.1716
Evaluate side-chains
  66 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  250 TRP
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain A residue  755 PHE
Chi-restraints excluded: chain A residue  842 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:   30.0000
   chunk 53 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.9184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.172063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.136932 restraints weight = 12477.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.139358 restraints weight = 6049.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.140744 restraints weight = 3828.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.141730 restraints weight = 3009.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.142189 restraints weight = 2606.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5803  Z= 0.140
  Angle     :  0.632  15.036   7873  Z= 0.322
  Chirality :  0.045   0.170    899
  Planarity :  0.005   0.070    985
  Dihedral  :  9.155 141.855    780
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.05 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.93 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.32), residues: 709
  helix: -0.10 (0.31), residues: 283
  sheet: -0.50 (0.42), residues: 158
  loop : -2.05 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 582 
 TYR   0.013   0.001   TYR A 215 
 PHE   0.012   0.001   PHE A 755 
 TRP   0.013   0.001   TRP A 217 
 HIS   0.002   0.001   HIS A 536 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 5803)
  covalent geometry    : angle       0.63155 /  0.32 ( 7873)
  hydrogen bonds       : bond        0.04098 /  2.65 (  272)
  hydrogen bonds       : angle       5.43152 /  3.91 (  786)

*********************** 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
  71 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.7942 (mp) cc_final: 0.7704 (mt)
REVERT: A   87 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7552 (t80)
REVERT: A  541 THR cc_start: 0.7974 (m) cc_final: 0.7755 (p)
REVERT: A  755 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.5660 (m-10)
  outliers start: 18
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0639
  time to fit residues: 5.8691
Evaluate side-chains
  67 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  250 TRP
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain A residue  755 PHE
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  885 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 27 optimal weight:   30.0000
   chunk 17 optimal weight:    0.0570
   chunk 45 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.4856

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.167833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.130545 restraints weight = 12493.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.133669 restraints weight = 5677.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.135621 restraints weight = 3440.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.136592 restraints weight = 2558.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.137380 restraints weight = 2196.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5803  Z= 0.118
  Angle     :  0.612  14.391   7873  Z= 0.308
  Chirality :  0.044   0.174    899
  Planarity :  0.005   0.065    985
  Dihedral  :  8.255 122.084    780
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.35 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 19.60 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.32), residues: 709
  helix:  0.25 (0.31), residues: 288
  sheet: -0.47 (0.42), residues: 158
  loop : -1.94 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 582 
 TYR   0.009   0.001   TYR A 215 
 PHE   0.010   0.001   PHE A 755 
 TRP   0.016   0.001   TRP A 217 
 HIS   0.002   0.000   HIS A 536 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 5803)
  covalent geometry    : angle       0.61169 /  0.31 ( 7873)
  hydrogen bonds       : bond        0.03796 /  2.44 (  272)
  hydrogen bonds       : angle       5.25510 /  3.81 (  786)

*********************** 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
  80 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.8000 (mp) cc_final: 0.7753 (mt)
REVERT: A   87 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7543 (t80)
REVERT: A  102 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8658 (m)
REVERT: A  755 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.5571 (m-10)
  outliers start: 22
  outliers final: 16
  residues processed: 74
  average time/residue: 0.0627
  time to fit residues: 6.5563
Evaluate side-chains
  71 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  263 TYR
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  755 PHE
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  885 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0020
   chunk 60 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 65 optimal weight:    0.1980
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.167322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.130168 restraints weight = 13062.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.133299 restraints weight = 5973.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.135282 restraints weight = 3617.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.136259 restraints weight = 2669.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.136952 restraints weight = 2289.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5803  Z= 0.123
  Angle     :  0.628  14.435   7873  Z= 0.314
  Chirality :  0.043   0.162    899
  Planarity :  0.005   0.062    985
  Dihedral  :  7.985 107.958    780
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.63 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.25 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.32), residues: 709
  helix:  0.21 (0.31), residues: 294
  sheet: -0.43 (0.42), residues: 156
  loop : -1.92 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 582 
 TYR   0.035   0.001   TYR A 215 
 PHE   0.016   0.001   PHE A 239 
 TRP   0.027   0.001   TRP A 217 
 HIS   0.002   0.001   HIS A 536 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.12 ( 5803)
  covalent geometry    : angle       0.62831 /  0.31 ( 7873)
  hydrogen bonds       : bond        0.03831 /  2.49 (  272)
  hydrogen bonds       : angle       5.24762 /  3.81 (  786)

********************** 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
  74 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.8015 (mp) cc_final: 0.7763 (mt)
REVERT: A   87 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7530 (t80)
  outliers start: 18
  outliers final: 16
  residues processed: 68
  average time/residue: 0.0552
  time to fit residues: 5.5343
Evaluate side-chains
  71 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  263 TYR
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  885 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.9586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.169588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.133246 restraints weight = 12531.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.135867 restraints weight = 6254.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.137384 restraints weight = 4051.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.138089 restraints weight = 3163.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.138790 restraints weight = 2807.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5803  Z= 0.224
  Angle     :  0.715  15.066   7873  Z= 0.366
  Chirality :  0.046   0.158    899
  Planarity :  0.005   0.066    985
  Dihedral  :  8.718 102.900    780
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.60 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.09 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.31), residues: 709
  helix: -0.37 (0.29), residues: 296
  sheet: -0.37 (0.42), residues: 154
  loop : -2.19 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 582 
 TYR   0.032   0.002   TYR A 215 
 PHE   0.019   0.002   PHE A 755 
 TRP   0.023   0.002   TRP A 217 
 HIS   0.003   0.001   HIS A 857 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00526 /  0.22 ( 5803)
  covalent geometry    : angle       0.71482 /  0.37 ( 7873)
  hydrogen bonds       : bond        0.04716 /  3.12 (  272)
  hydrogen bonds       : angle       5.52152 /  3.96 (  786)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1252.39 seconds
wall clock time: 22 minutes 14.17 seconds (1334.17 seconds total)