Starting phenix.real_space_refine
on Thu Jul  2 02:43:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q74_18203/07_2026/8q74_18203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q74_18203/07_2026/8q74_18203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q74_18203/07_2026/8q74_18203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q74_18203/07_2026/8q74_18203.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q74_18203/07_2026/8q74_18203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q74_18203/07_2026/8q74_18203.map"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
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
     Cu      1      5.60       5
     S      34      5.16       5
     C    3812      2.51       5
     N     988      2.21       5
     O    1108      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 5943
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 5942
          Classifications: {'peptide': 783}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 745}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 0
          Ad-hoc single atom residues: {' CU': 1}
          Chain breaks: 1

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3243  SG  CYS A 597      27.486  24.901  48.334  1.00140.08           S
  ATOM   3256  SG  CYS A 599      28.127  29.237  48.453  1.00142.78           S

  Time building chain proxies: 1.60, per 1000 atoms: 0.27
  Number of scatterers: 5943
  At special positions: 0
  Unit cell: (80.408, 86.3328, 141.349, 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)
     Cu      1     28.99
     S      34     16.00
     O    1108      8.00
     N     988      7.00
     C    3812      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 436.3 milliseconds
  

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1448

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      53.6% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 197 through 209
      removed outlier: 4.285A  pdb=" N   ARG A 207 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 248
      removed outlier: 3.599A  pdb=" N   ALA A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 296
      removed outlier: 3.793A  pdb=" N   PHE A 286 " --> pdb=" O   TRP A 282 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 297 through 300
    Processing helix  chain 'A' and resid 302 through 308
    Processing helix  chain 'A' and resid 317 through 332
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 6.499A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 377
      removed outlier: 3.696A  pdb=" N   LEU A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 420
      removed outlier: 4.094A  pdb=" N   ILE A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 531
      removed outlier: 3.635A  pdb=" N   GLN A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 545
    Processing helix  chain 'A' and resid 546 through 567
      removed outlier: 3.520A  pdb=" N   TRP A 561 " --> pdb=" O   THR A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 594
      removed outlier: 3.638A  pdb=" N   LEU A 593 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 618
      removed outlier: 4.010A  pdb=" N   MET A 610 " --> pdb=" O   PRO A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 634
    Processing helix  chain 'A' and resid 682 through 693
      removed outlier: 4.373A  pdb=" N   THR A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 691 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 743 through 756
      removed outlier: 3.825A  pdb=" N   GLU A 747 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 768
    Processing helix  chain 'A' and resid 782 through 794
    Processing helix  chain 'A' and resid 804 through 816
    Processing helix  chain 'A' and resid 825 through 839
    Processing helix  chain 'A' and resid 849 through 851
      No H-bonds generated for 'chain 'A' and resid 849 through 851'
    Processing helix  chain 'A' and resid 852 through 859
    Processing helix  chain 'A' and resid 869 through 876
      removed outlier: 3.900A  pdb=" N   ILE A 873 " --> pdb=" O   THR A 869 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 875 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 922
      removed outlier: 4.123A  pdb=" N   ILE A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR A 890 " --> pdb=" O   GLU A 886 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A 913 " --> pdb=" O   ALA A 909 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 915 " --> pdb=" O   GLY A 911 " (cutoff:3.500A)
      Proline residue:  A 918  - end of helix
    Processing helix  chain 'A' and resid 924 through 929
    Processing helix  chain 'A' and resid 933 through 954
      removed outlier: 4.146A  pdb=" N   ALA A 939 " --> pdb=" O   TRP A 935 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A 940 " --> pdb=" O   LEU A 936 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 941 " --> pdb=" O   ALA A 937 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 954 " --> pdb=" O   CYS A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 958
    Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312
      removed outlier: 3.628A  pdb=" N   VAL A 311 " --> pdb=" O   MET A 315 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   MET A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425
    Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455
      removed outlier: 4.082A  pdb=" N   CYS A 504 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821
      removed outlier: 8.929A  pdb=" N   PHE A 821 " --> pdb=" O   SER A 797 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET A 799 " --> pdb=" O   PHE A 821 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA A 637 " --> pdb=" O   ALA A 844 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    831 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: 0.87

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1893
        1.34 -     1.46: 801
        1.46 -     1.57: 3309
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6057
  Sorted by residual:
  bond pdb=" CA  CYS A 597 "
       pdb=" C   CYS A 597 "
    ideal  model  delta    sigma   weight residual
    1.524  1.474  0.050 1.26e-02 6.30e+03 1.59e+01
  bond pdb=" CA  CYS A 599 "
       pdb=" C   CYS A 599 "
    ideal  model  delta    sigma   weight residual
    1.527  1.495  0.032 1.30e-02 5.92e+03 5.93e+00
  bond pdb=" CA  MET A 352 "
       pdb=" C   MET A 352 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.28e-02 6.10e+03 4.59e+00
  bond pdb=" N   ALA A 600 "
       pdb=" CA  ALA A 600 "
    ideal  model  delta    sigma   weight residual
    1.458  1.433  0.026 1.26e-02 6.30e+03 4.14e+00
  bond pdb=" CA  ASP A 353 "
       pdb=" C   ASP A 353 "
    ideal  model  delta    sigma   weight residual
    1.525  1.499  0.026 1.37e-02 5.33e+03 3.62e+00
  ... (remaining 6052 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 7903
        2.42 -     4.85: 279
        4.85 -     7.27: 38
        7.27 -     9.69: 4
        9.69 -    12.12: 2
  Bond angle restraints: 8226
  Sorted by residual:
  angle pdb=" N   ALA A 600 "
        pdb=" CA  ALA A 600 "
        pdb=" C   ALA A 600 "
      ideal   model   delta    sigma   weight residual
     111.69  103.10    8.59 1.23e+00 6.61e-01 4.88e+01
  angle pdb=" C   THR A 656 "
        pdb=" N   LYS A 657 "
        pdb=" CA  LYS A 657 "
      ideal   model   delta    sigma   weight residual
     122.11  112.10   10.01 1.59e+00 3.96e-01 3.97e+01
  angle pdb=" N   VAL A 311 "
        pdb=" CA  VAL A 311 "
        pdb=" C   VAL A 311 "
      ideal   model   delta    sigma   weight residual
     113.53  108.53    5.00 9.80e-01 1.04e+00 2.60e+01
  angle pdb=" C   LYS A 657 "
        pdb=" N   VAL A 658 "
        pdb=" CA  VAL A 658 "
      ideal   model   delta    sigma   weight residual
     120.13  128.17   -8.04 1.58e+00 4.01e-01 2.59e+01
  angle pdb=" N   TRP A 335 "
        pdb=" CA  TRP A 335 "
        pdb=" C   TRP A 335 "
      ideal   model   delta    sigma   weight residual
     113.43  107.54    5.89 1.26e+00 6.30e-01 2.18e+01
  ... (remaining 8221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3320
       17.59 -    35.18: 277
       35.18 -    52.77: 34
       52.77 -    70.36: 13
       70.36 -    87.95: 8
  Dihedral angle restraints: 3652
    sinusoidal: 1403
      harmonic: 2249
  Sorted by residual:
  dihedral pdb=" CA  PRO A 250 "
           pdb=" C   PRO A 250 "
           pdb=" N   PRO A 251 "
           pdb=" CA  PRO A 251 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.23   40.77     0      5.00e+00 4.00e-02 6.65e+01
  dihedral pdb=" CA  ASN A 721 "
           pdb=" C   ASN A 721 "
           pdb=" N   VAL A 722 "
           pdb=" CA  VAL A 722 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -144.73  -35.27     0      5.00e+00 4.00e-02 4.98e+01
  dihedral pdb=" CA  GLY A 724 "
           pdb=" C   GLY A 724 "
           pdb=" N   LYS A 725 "
           pdb=" CA  LYS A 725 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.04  -26.96     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 3649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 705
       0.048 -    0.096: 209
       0.096 -    0.144: 50
       0.144 -    0.192: 8
       0.192 -    0.240: 2
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CB  ILE A 704 "
            pdb=" CA  ILE A 704 "
            pdb=" CG1 ILE A 704 "
            pdb=" CG2 ILE A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  THR A 656 "
            pdb=" N   THR A 656 "
            pdb=" C   THR A 656 "
            pdb=" CB  THR A 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.31e-01
  chirality pdb=" CB  ILE A 662 "
            pdb=" CA  ILE A 662 "
            pdb=" CG1 ILE A 662 "
            pdb=" CG2 ILE A 662 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1041
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 662 "   -0.050 5.00e-02 4.00e+02   7.66e-02 9.38e+00
        pdb=" N   PRO A 663 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 663 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 663 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 570 "   -0.047 5.00e-02 4.00e+02   7.02e-02 7.88e+00
        pdb=" N   PRO A 571 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 571 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 571 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 740 "    0.043 5.00e-02 4.00e+02   6.53e-02 6.83e+00
        pdb=" N   PRO A 741 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 741 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 741 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1038 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 11
        2.29 -     2.94: 2791
        2.94 -     3.59: 9756
        3.59 -     4.25: 14043
        4.25 -     4.90: 22453
  Nonbonded interactions: 49054
  Sorted by model distance:
  nonbonded pdb=" CE  MET A 352 "
            pdb="CU    CU A1001 "
     model   vdw
     1.633 3.400
  nonbonded pdb=" SG  CYS A 597 "
            pdb="CU    CU A1001 "
     model   vdw
     2.079 3.340
  nonbonded pdb=" SD  MET A 352 "
            pdb="CU    CU A1001 "
     model   vdw
     2.087 3.340
  nonbonded pdb=" O   VAL A 687 "
            pdb=" OG1 THR A 690 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OE1 GLU A 476 "
            pdb=" N   MET A 478 "
     model   vdw
     2.183 3.120
  ... (remaining 49049 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=0.00 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:             3.310
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
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   0.124   6058  Z= 0.287
  Angle     :  1.020  12.117   8226  Z= 0.613
  Chirality :  0.048   0.240    974
  Planarity :  0.008   0.077   1041
  Dihedral  : 14.005  87.951   2204
  Min Nonbonded Distance : 1.633

Molprobity Statistics.
  All-atom Clashscore : 20.98
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 15.88 %
    Favored  : 83.23 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.23 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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: -2.37 (0.30), residues: 781
  helix:  0.65 (0.28), residues: 366
  sheet: -3.40 (0.73), residues: 30
  loop : -3.90 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 322 
 TYR   0.028   0.002   TYR A 689 
 PHE   0.020   0.002   PHE A 582 
 TRP   0.023   0.002   TRP A 558 
 HIS   0.009   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.24 ( 6057)
  covalent geometry    : angle       1.02032 /  0.61 ( 8226)
  hydrogen bonds       : bond        0.19672 / 12.62 (  283)
  hydrogen bonds       : angle       6.81073 /  4.69 (  831)
  Misc. bond           : bond        0.12434 /  6.54 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9357 (m-80) cc_final: 0.9065 (m-80)
REVERT: A  315 MET cc_start: 0.9055 (ppp) cc_final: 0.8799 (tmm)
REVERT: A  319 MET cc_start: 0.8325 (mpp) cc_final: 0.8016 (mtp)
REVERT: A  331 PHE cc_start: 0.7861 (m-80) cc_final: 0.7285 (m-80)
REVERT: A  686 ILE cc_start: 0.9548 (mt) cc_final: 0.9235 (mt)
REVERT: A  790 LEU cc_start: 0.9583 (mt) cc_final: 0.9329 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0585
  time to fit residues: 6.5880
Evaluate side-chains
  46 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    2.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 GLN
A 721 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.100324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.061309 restraints weight = 24091.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.063011 restraints weight = 11006.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.063906 restraints weight = 7328.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.064287 restraints weight = 6073.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.064368 restraints weight = 5648.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6058  Z= 0.235
  Angle     :  0.884  10.227   8226  Z= 0.460
  Chirality :  0.048   0.175    974
  Planarity :  0.007   0.067   1041
  Dihedral  :  6.661  38.961    826
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 21.40
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 16.39 %
    Favored  : 82.84 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.94 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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: -2.08 (0.30), residues: 781
  helix:  0.61 (0.26), residues: 387
  sheet: -3.05 (0.76), residues: 31
  loop : -3.68 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 322 
 TYR   0.015   0.002   TYR A 253 
 PHE   0.024   0.003   PHE A 293 
 TRP   0.024   0.002   TRP A 558 
 HIS   0.012   0.002   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.24 ( 6057)
  covalent geometry    : angle       0.88361 /  0.46 ( 8226)
  hydrogen bonds       : bond        0.06287 /  4.04 (  283)
  hydrogen bonds       : angle       5.59813 /  3.80 (  831)
  Misc. bond           : bond        0.00084 /  0.04 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9214 (m-80) cc_final: 0.8636 (m-80)
REVERT: A  319 MET cc_start: 0.8529 (mpp) cc_final: 0.8238 (mpp)
REVERT: A  331 PHE cc_start: 0.8162 (m-10) cc_final: 0.7530 (m-80)
REVERT: A  601 LEU cc_start: 0.9210 (mm) cc_final: 0.8938 (mm)
REVERT: A  689 TYR cc_start: 0.9122 (p90) cc_final: 0.8763 (p90)
REVERT: A  799 MET cc_start: 0.9001 (ppp) cc_final: 0.8376 (ppp)
  outliers start: 15
  outliers final: 13
  residues processed: 56
  average time/residue: 0.0447
  time to fit residues: 3.8469
Evaluate side-chains
  52 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 54 optimal weight:   30.0000
   chunk 51 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 64 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN
A 448 GLN
A 721 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.101554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.061754 restraints weight = 23473.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.063613 restraints weight = 10383.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.064561 restraints weight = 6776.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 72)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.065052 restraints weight = 5608.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.065232 restraints weight = 5113.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6058  Z= 0.159
  Angle     :  0.788   8.723   8226  Z= 0.409
  Chirality :  0.047   0.248    974
  Planarity :  0.006   0.063   1041
  Dihedral  :  6.426  36.084    826
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 18.81
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 14.08 %
    Favored  : 85.15 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.48 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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: -1.72 (0.30), residues: 781
  helix:  0.97 (0.27), residues: 390
  sheet: -2.62 (0.82), residues: 31
  loop : -3.64 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 322 
 TYR   0.015   0.001   TYR A 253 
 PHE   0.019   0.002   PHE A 293 
 TRP   0.015   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.16 ( 6057)
  covalent geometry    : angle       0.78767 /  0.41 ( 8226)
  hydrogen bonds       : bond        0.05216 /  3.33 (  283)
  hydrogen bonds       : angle       5.07490 /  3.42 (  831)
  Misc. bond           : bond        0.00236 /  0.12 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9292 (tmm) cc_final: 0.9044 (tmm)
REVERT: A  319 MET cc_start: 0.8415 (mpp) cc_final: 0.8116 (mpp)
REVERT: A  331 PHE cc_start: 0.8149 (m-10) cc_final: 0.7586 (m-80)
REVERT: A  601 LEU cc_start: 0.9106 (mm) cc_final: 0.8905 (mm)
REVERT: A  689 TYR cc_start: 0.9004 (p90) cc_final: 0.8601 (p90)
REVERT: A  799 MET cc_start: 0.8931 (ppp) cc_final: 0.8555 (ppp)
REVERT: A  845 MET cc_start: 0.7781 (ptp) cc_final: 0.7581 (ppp)
  outliers start: 17
  outliers final: 10
  residues processed: 64
  average time/residue: 0.0410
  time to fit residues: 4.0204
Evaluate side-chains
  52 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0870
   chunk 29 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0870
   chunk 0 optimal weight:   30.0000
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.4340

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 837 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.101981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.061755 restraints weight = 24047.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.063641 restraints weight = 10674.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.064655 restraints weight = 6997.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.065101 restraints weight = 5756.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.065244 restraints weight = 5255.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6058  Z= 0.164
  Angle     :  0.776  10.871   8226  Z= 0.396
  Chirality :  0.046   0.201    974
  Planarity :  0.005   0.061   1041
  Dihedral  :  6.257  37.508    826
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 14.34 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.79 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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: -1.63 (0.30), residues: 781
  helix:  1.20 (0.26), residues: 387
  sheet: -2.46 (0.86), residues: 31
  loop : -3.78 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 322 
 TYR   0.019   0.001   TYR A 689 
 PHE   0.012   0.002   PHE A 286 
 TRP   0.012   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 ( 6057)
  covalent geometry    : angle       0.77646 /  0.40 ( 8226)
  hydrogen bonds       : bond        0.04788 /  3.08 (  283)
  hydrogen bonds       : angle       5.00189 /  3.38 (  831)
  Misc. bond           : bond        0.00003 /  0.00 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8445 (mpp) cc_final: 0.8144 (mpp)
REVERT: A  331 PHE cc_start: 0.8203 (m-10) cc_final: 0.7751 (m-80)
REVERT: A  657 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6743 (mmtt)
REVERT: A  705 MET cc_start: 0.8773 (ppp) cc_final: 0.8350 (ppp)
REVERT: A  799 MET cc_start: 0.8975 (ppp) cc_final: 0.8698 (tmm)
REVERT: A  845 MET cc_start: 0.7956 (ptp) cc_final: 0.7679 (ppp)
  outliers start: 21
  outliers final: 13
  residues processed: 60
  average time/residue: 0.0586
  time to fit residues: 5.0564
Evaluate side-chains
  55 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 3 optimal weight:   30.0000
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.101667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.062141 restraints weight = 24580.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.063989 restraints weight = 10905.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.064991 restraints weight = 7141.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.065390 restraints weight = 5881.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 70)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.065651 restraints weight = 5426.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6058  Z= 0.156
  Angle     :  0.759   8.516   8226  Z= 0.390
  Chirality :  0.046   0.177    974
  Planarity :  0.005   0.059   1041
  Dihedral  :  6.119  38.094    826
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.19 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.95 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.48 (0.30), residues: 781
  helix:  1.30 (0.27), residues: 388
  sheet: -2.32 (0.88), residues: 31
  loop : -3.69 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 322 
 TYR   0.014   0.001   TYR A 253 
 PHE   0.011   0.002   PHE A 293 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 6057)
  covalent geometry    : angle       0.75885 /  0.39 ( 8226)
  hydrogen bonds       : bond        0.04598 /  2.95 (  283)
  hydrogen bonds       : angle       4.91004 /  3.32 (  831)
  Misc. bond           : bond        0.00045 /  0.02 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9441 (t80) cc_final: 0.9224 (t80)
REVERT: A  315 MET cc_start: 0.9253 (tmm) cc_final: 0.8973 (tmm)
REVERT: A  319 MET cc_start: 0.8457 (mpp) cc_final: 0.8165 (mpp)
REVERT: A  331 PHE cc_start: 0.8289 (m-10) cc_final: 0.7713 (m-80)
REVERT: A  705 MET cc_start: 0.8800 (ppp) cc_final: 0.8242 (ppp)
REVERT: A  799 MET cc_start: 0.8963 (ppp) cc_final: 0.8694 (tmm)
REVERT: A  845 MET cc_start: 0.7998 (ptp) cc_final: 0.7644 (ppp)
  outliers start: 21
  outliers final: 18
  residues processed: 60
  average time/residue: 0.0651
  time to fit residues: 5.6032
Evaluate side-chains
  58 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:   30.0000
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 53 optimal weight:   50.0000
   chunk 11 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0470
   chunk 43 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.7282

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 ASN
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.103308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.063201 restraints weight = 24622.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.065191 restraints weight = 10708.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.066216 restraints weight = 7018.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.066701 restraints weight = 5705.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.066819 restraints weight = 5229.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6058  Z= 0.137
  Angle     :  0.753  10.894   8226  Z= 0.381
  Chirality :  0.045   0.147    974
  Planarity :  0.005   0.058   1041
  Dihedral  :  5.996  38.392    826
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.93 %
    Favored  : 86.17 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.80 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.40 (0.31), residues: 781
  helix:  1.37 (0.27), residues: 390
  sheet: -2.31 (0.88), residues: 31
  loop : -3.68 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 322 
 TYR   0.039   0.001   TYR A 689 
 PHE   0.011   0.001   PHE A 710 
 TRP   0.009   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.14 ( 6057)
  covalent geometry    : angle       0.75343 /  0.38 ( 8226)
  hydrogen bonds       : bond        0.04093 /  2.62 (  283)
  hydrogen bonds       : angle       4.74074 /  3.19 (  831)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9490 (t80) cc_final: 0.9262 (t80)
REVERT: A  315 MET cc_start: 0.9276 (tmm) cc_final: 0.8951 (tmm)
REVERT: A  319 MET cc_start: 0.8407 (mpp) cc_final: 0.8126 (mpp)
REVERT: A  579 MET cc_start: 0.9186 (pmm) cc_final: 0.8947 (pmm)
REVERT: A  657 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6922 (mmtt)
REVERT: A  705 MET cc_start: 0.8906 (ppp) cc_final: 0.8532 (ppp)
REVERT: A  799 MET cc_start: 0.9001 (ppp) cc_final: 0.8720 (tmm)
REVERT: A  845 MET cc_start: 0.7927 (ptp) cc_final: 0.7493 (ppp)
REVERT: A  863 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8149 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 59
  average time/residue: 0.0547
  time to fit residues: 4.6152
Evaluate side-chains
  54 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0770
   chunk 66 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 32 optimal weight:   50.0000
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.4742

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.102467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.061941 restraints weight = 24337.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.063856 restraints weight = 10883.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.064866 restraints weight = 7140.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.065230 restraints weight = 5838.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.065492 restraints weight = 5425.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6058  Z= 0.154
  Angle     :  0.754  10.608   8226  Z= 0.386
  Chirality :  0.045   0.142    974
  Planarity :  0.005   0.057   1041
  Dihedral  :  5.898  38.632    826
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.16 %
    Favored  : 86.94 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.95 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.45 (0.31), residues: 781
  helix:  1.33 (0.27), residues: 393
  sheet: -2.71 (0.72), residues: 41
  loop : -3.72 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 322 
 TYR   0.014   0.001   TYR A 689 
 PHE   0.012   0.001   PHE A 395 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.010   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 6057)
  covalent geometry    : angle       0.75440 /  0.39 ( 8226)
  hydrogen bonds       : bond        0.04548 /  2.94 (  283)
  hydrogen bonds       : angle       4.86438 /  3.32 (  831)
  Misc. bond           : bond        0.00035 /  0.02 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9805 (mmtm) cc_final: 0.9321 (tppt)
REVERT: A  319 MET cc_start: 0.8487 (mpp) cc_final: 0.8183 (mpp)
REVERT: A  331 PHE cc_start: 0.8311 (m-10) cc_final: 0.7615 (m-80)
REVERT: A  657 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6997 (mmtt)
REVERT: A  705 MET cc_start: 0.8849 (ppp) cc_final: 0.8500 (ppp)
REVERT: A  799 MET cc_start: 0.8975 (ppp) cc_final: 0.8695 (tmm)
REVERT: A  845 MET cc_start: 0.8095 (ptp) cc_final: 0.7586 (ppp)
REVERT: A  863 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8193 (tt)
  outliers start: 21
  outliers final: 18
  residues processed: 58
  average time/residue: 0.0590
  time to fit residues: 4.8985
Evaluate side-chains
  61 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:   20.0000
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.102505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.062181 restraints weight = 24301.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.064121 restraints weight = 10815.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.065090 restraints weight = 7060.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.065556 restraints weight = 5770.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.065685 restraints weight = 5298.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6058  Z= 0.148
  Angle     :  0.760  12.556   8226  Z= 0.384
  Chirality :  0.046   0.374    974
  Planarity :  0.005   0.064   1041
  Dihedral  :  5.851  38.760    826
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.80 %
    Favored  : 86.30 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.26 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.45 (0.31), residues: 781
  helix:  1.35 (0.27), residues: 393
  sheet: -2.70 (0.71), residues: 41
  loop : -3.73 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 322 
 TYR   0.040   0.001   TYR A 689 
 PHE   0.011   0.001   PHE A 395 
 TRP   0.009   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 6057)
  covalent geometry    : angle       0.76038 /  0.38 ( 8226)
  hydrogen bonds       : bond        0.04352 /  2.78 (  283)
  hydrogen bonds       : angle       4.81187 /  3.26 (  831)
  Misc. bond           : bond        0.00040 /  0.02 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9825 (mmtm) cc_final: 0.9352 (tppt)
REVERT: A  315 MET cc_start: 0.9300 (tmm) cc_final: 0.9007 (tmm)
REVERT: A  319 MET cc_start: 0.8457 (mpp) cc_final: 0.8162 (mpp)
REVERT: A  331 PHE cc_start: 0.8356 (m-10) cc_final: 0.7655 (m-80)
REVERT: A  657 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7285 (mmtt)
REVERT: A  705 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8624 (ppp)
REVERT: A  799 MET cc_start: 0.8982 (ppp) cc_final: 0.8705 (tmm)
REVERT: A  845 MET cc_start: 0.8104 (ptp) cc_final: 0.7598 (ppp)
REVERT: A  863 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8191 (tt)
  outliers start: 20
  outliers final: 17
  residues processed: 57
  average time/residue: 0.0533
  time to fit residues: 4.3716
Evaluate side-chains
  60 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
A 536 GLN
A 587 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.101537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.060511 restraints weight = 24699.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.062351 restraints weight = 11187.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.063316 restraints weight = 7257.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.063650 restraints weight = 5951.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.063922 restraints weight = 5525.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6058  Z= 0.196
  Angle     :  0.797  14.423   8226  Z= 0.406
  Chirality :  0.046   0.327    974
  Planarity :  0.005   0.072   1041
  Dihedral  :  5.862  38.426    826
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.32 %
    Favored  : 85.79 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.72 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.55 (0.31), residues: 781
  helix:  1.16 (0.27), residues: 393
  sheet: -2.57 (0.84), residues: 33
  loop : -3.65 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 322 
 TYR   0.036   0.002   TYR A 689 
 PHE   0.015   0.002   PHE A 303 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.20 ( 6057)
  covalent geometry    : angle       0.79718 /  0.41 ( 8226)
  hydrogen bonds       : bond        0.05097 /  3.30 (  283)
  hydrogen bonds       : angle       5.03666 /  3.42 (  831)
  Misc. bond           : bond        0.00058 /  0.03 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9821 (mmtm) cc_final: 0.9349 (tppt)
REVERT: A  315 MET cc_start: 0.9293 (tmm) cc_final: 0.8965 (tmm)
REVERT: A  319 MET cc_start: 0.8506 (mpp) cc_final: 0.8193 (mpp)
REVERT: A  705 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8626 (ppp)
REVERT: A  799 MET cc_start: 0.8999 (ppp) cc_final: 0.8697 (tmm)
REVERT: A  845 MET cc_start: 0.8227 (ptp) cc_final: 0.7640 (ppp)
REVERT: A  863 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8221 (tt)
  outliers start: 22
  outliers final: 19
  residues processed: 60
  average time/residue: 0.0628
  time to fit residues: 5.4136
Evaluate side-chains
  63 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 53 optimal weight:   40.0000
   chunk 70 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 205 GLN
A 249 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.103867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.062915 restraints weight = 24489.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.064908 restraints weight = 10738.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.065920 restraints weight = 7012.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.066384 restraints weight = 5689.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.066503 restraints weight = 5216.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6058  Z= 0.135
  Angle     :  0.758  10.374   8226  Z= 0.383
  Chirality :  0.045   0.286    974
  Planarity :  0.005   0.076   1041
  Dihedral  :  5.774  38.553    826
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.42 %
    Favored  : 86.68 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.18 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 (0.31), residues: 781
  helix:  1.26 (0.27), residues: 393
  sheet: -2.51 (0.83), residues: 33
  loop : -3.59 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 322 
 TYR   0.033   0.001   TYR A 689 
 PHE   0.010   0.001   PHE A 659 
 TRP   0.008   0.001   TRP A 335 
 HIS   0.011   0.001   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 6057)
  covalent geometry    : angle       0.75806 /  0.38 ( 8226)
  hydrogen bonds       : bond        0.04233 /  2.70 (  283)
  hydrogen bonds       : angle       4.76658 /  3.21 (  831)
  Misc. bond           : bond        0.00024 /  0.01 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9822 (mmtm) cc_final: 0.9377 (tppt)
REVERT: A  315 MET cc_start: 0.9279 (tmm) cc_final: 0.9027 (tmm)
REVERT: A  331 PHE cc_start: 0.8350 (m-10) cc_final: 0.7641 (m-80)
REVERT: A  332 ILE cc_start: 0.8866 (tp) cc_final: 0.8508 (pt)
REVERT: A  705 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8600 (ppp)
REVERT: A  799 MET cc_start: 0.9002 (ppp) cc_final: 0.8724 (tmm)
REVERT: A  831 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9320 (pm20)
REVERT: A  845 MET cc_start: 0.8009 (ptp) cc_final: 0.7553 (ppp)
REVERT: A  863 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8229 (tt)
  outliers start: 21
  outliers final: 16
  residues processed: 59
  average time/residue: 0.0636
  time to fit residues: 5.3977
Evaluate side-chains
  59 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  488 LYS
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  831 GLU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0270
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5240

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 205 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.103154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.063106 restraints weight = 24342.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.065067 restraints weight = 10584.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.066076 restraints weight = 6911.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.066472 restraints weight = 5660.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 69)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.066762 restraints weight = 5236.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.121   6058  Z= 0.217
  Angle     :  1.138  59.176   8226  Z= 0.642
  Chirality :  0.051   0.728    974
  Planarity :  0.007   0.139   1041
  Dihedral  :  5.766  38.581    826
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.55 %
    Favored  : 86.56 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.34 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.44 (0.31), residues: 781
  helix:  1.23 (0.27), residues: 393
  sheet: -2.48 (0.83), residues: 33
  loop : -3.59 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.043   0.001   ARG A 269 
 TYR   0.036   0.001   TYR A 689 
 PHE   0.009   0.001   PHE A 710 
 TRP   0.007   0.001   TRP A 335 
 HIS   0.012   0.002   HIS A 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.22 ( 6057)
  covalent geometry    : angle       1.13829 /  0.64 ( 8226)
  hydrogen bonds       : bond        0.04302 /  2.73 (  283)
  hydrogen bonds       : angle       4.75862 /  3.21 (  831)
  Misc. bond           : bond        0.00014 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1481.41 seconds
wall clock time: 26 minutes 11.62 seconds (1571.62 seconds total)