Starting phenix.real_space_refine
on Fri Aug 22 16:39:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q73_18202/08_2025/8q73_18202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q73_18202/08_2025/8q73_18202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q73_18202/08_2025/8q73_18202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q73_18202/08_2025/8q73_18202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q73_18202/08_2025/8q73_18202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q73_18202/08_2025/8q73_18202.cif"
  }
  resolution = 3.58
  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: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    3792      2.51       5
     N     982      2.21       5
     O    1101      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5909
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 779, 5909
          Classifications: {'peptide': 779}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 742}
  Time building chain proxies: 1.58, per 1000 atoms: 0.27
  Number of scatterers: 5909
  At special positions: 0
  Unit cell: (80.9998, 93.0636, 144.766, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1101      8.00
     N     982      7.00
     C    3792      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 363.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1440

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      52.2% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 4.172A  pdb=" N   ILE A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 264 through 297
      removed outlier: 3.548A  pdb=" N   PHE A 286 " --> pdb=" O   TRP A 282 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
      removed outlier: 4.073A  pdb=" N   SER A 294 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET A 295 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 297 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 309
    Processing helix  chain 'A' and resid 317 through 325
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.652A  pdb=" N   GLN A 330 " --> pdb=" O   CYS A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 3.720A  pdb=" N   TYR A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   HIS A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA A 344 " --> pdb=" O   GLY A 340 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ARG A 347 " --> pdb=" O   HIS A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 377
      removed outlier: 3.780A  pdb=" N   LEU A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ALA A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR A 364 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 412
      removed outlier: 3.539A  pdb=" N   ALA A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 4.794A  pdb=" N   LYS A 416 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 515
      removed outlier: 3.743A  pdb=" N   GLU A 515 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 512 through 515'
    Processing helix  chain 'A' and resid 516 through 529
    Processing helix  chain 'A' and resid 534 through 567
      removed outlier: 3.939A  pdb=" N   LEU A 538 " --> pdb=" O   PRO A 534 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 545 " --> pdb=" O   ARG A 541 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   VAL A 547 " --> pdb=" O   SER A 543 " (cutoff:3.500A)
      Proline residue:  A 548  - end of helix
      removed outlier: 3.658A  pdb=" N   THR A 557 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TRP A 558 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 591
      removed outlier: 3.665A  pdb=" N   LEU A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 620
    Processing helix  chain 'A' and resid 625 through 632
      removed outlier: 3.628A  pdb=" N   LEU A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 676
    Processing helix  chain 'A' and resid 680 through 698
    Processing helix  chain 'A' and resid 731 through 738
    Processing helix  chain 'A' and resid 743 through 757
      removed outlier: 3.906A  pdb=" N   GLU A 747 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A 756 " --> pdb=" O   GLU A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 794
      removed outlier: 4.187A  pdb=" N   SER A 788 " --> pdb=" O   GLY A 784 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR A 789 " --> pdb=" O   ARG A 785 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER A 791 " --> pdb=" O   ILE A 787 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   SER A 792 " --> pdb=" O   SER A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 815
      removed outlier: 3.898A  pdb=" N   VAL A 815 " --> pdb=" O   ILE A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 840
      removed outlier: 3.525A  pdb=" N   GLY A 840 " --> pdb=" O   LEU A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 859
      removed outlier: 3.548A  pdb=" N   LEU A 856 " --> pdb=" O   ASP A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 869 through 874
      removed outlier: 4.170A  pdb=" N   ILE A 873 " --> pdb=" O   THR A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 913
      removed outlier: 4.225A  pdb=" N   ILE A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A 890 " --> pdb=" O   GLU A 886 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 894 " --> pdb=" O   THR A 890 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 903 " --> pdb=" O   LEU A 899 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 910 " --> pdb=" O   TYR A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 937 through 942
      removed outlier: 3.523A  pdb=" N   ALA A 942 " --> pdb=" O   GLY A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 954
      removed outlier: 5.032A  pdb=" N   VAL A 948 " --> pdb=" O   SER A 944 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   VAL A 949 " --> pdb=" O   SER A 945 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312
      removed outlier: 3.518A  pdb=" N   VAL A 311 " --> pdb=" O   MET A 315 " (cutoff:3.500A)
      removed outlier: 7.024A  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 429
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.571A  pdb=" N   GLY A 465 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP A 492 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 484 through 488
      removed outlier: 6.229A  pdb=" N   ASN A 475 " --> pdb=" O   ASN A 500 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ASN A 500 " --> pdb=" O   ASN A 475 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 621 through 623
      removed outlier: 3.781A  pdb=" N   VAL A 879 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 820 through 821
      removed outlier: 8.678A  pdb=" N   PHE A 821 " --> pdb=" O   SER A 797 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   MET A 799 " --> pdb=" O   PHE A 821 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   ILE A 638 " --> pdb=" O   ILE A 798 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL A 800 " --> pdb=" O   ILE A 638 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   MET A 845 " --> pdb=" O   LEU A 863 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 655
      removed outlier: 6.782A  pdb=" N   SER A 774 " --> pdb=" O   VAL A 654 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 729
      removed outlier: 4.984A  pdb=" N   VAL A 763 " --> pdb=" O   CYS A 770 " (cutoff:3.500A)

    281 hydrogen bonds defined for protein.
    816 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: 0.97

  Time building geometry restraints manager: 0.68 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: 1882
        1.34 -     1.46: 844
        1.46 -     1.58: 3243
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6023
  Sorted by residual:
  bond pdb=" N   PRO A 457 "
       pdb=" CD  PRO A 457 "
    ideal  model  delta    sigma   weight residual
    1.473  1.425  0.048 1.40e-02 5.10e+03 1.17e+01
  bond pdb=" CA  PRO A 457 "
       pdb=" CB  PRO A 457 "
    ideal  model  delta    sigma   weight residual
    1.532  1.569 -0.037 1.34e-02 5.57e+03 7.60e+00
  bond pdb=" CG  PRO A 457 "
       pdb=" CD  PRO A 457 "
    ideal  model  delta    sigma   weight residual
    1.503  1.567 -0.064 3.40e-02 8.65e+02 3.56e+00
  bond pdb=" C   HIS A 680 "
       pdb=" N   PRO A 681 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.28e-02 6.10e+03 3.21e+00
  bond pdb=" C   ASP A 825 "
       pdb=" N   PRO A 826 "
    ideal  model  delta    sigma   weight residual
    1.333  1.355 -0.021 1.44e-02 4.82e+03 2.21e+00
  ... (remaining 6018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 8043
        2.88 -     5.76: 116
        5.76 -     8.64: 19
        8.64 -    11.52: 1
       11.52 -    14.40: 1
  Bond angle restraints: 8180
  Sorted by residual:
  angle pdb=" N   VAL A 594 "
        pdb=" CA  VAL A 594 "
        pdb=" C   VAL A 594 "
      ideal   model   delta    sigma   weight residual
     113.71  106.73    6.98 9.50e-01 1.11e+00 5.40e+01
  angle pdb=" CA  PRO A 457 "
        pdb=" N   PRO A 457 "
        pdb=" CD  PRO A 457 "
      ideal   model   delta    sigma   weight residual
     112.00  104.27    7.73 1.40e+00 5.10e-01 3.05e+01
  angle pdb=" C   GLY A 816 "
        pdb=" N   ILE A 817 "
        pdb=" CA  ILE A 817 "
      ideal   model   delta    sigma   weight residual
     121.97  131.34   -9.37 1.80e+00 3.09e-01 2.71e+01
  angle pdb=" N   LEU A 915 "
        pdb=" CA  LEU A 915 "
        pdb=" C   LEU A 915 "
      ideal   model   delta    sigma   weight residual
     114.16  106.62    7.54 1.48e+00 4.57e-01 2.60e+01
  angle pdb=" N   CYS A 599 "
        pdb=" CA  CYS A 599 "
        pdb=" C   CYS A 599 "
      ideal   model   delta    sigma   weight residual
     114.09  106.91    7.18 1.55e+00 4.16e-01 2.15e+01
  ... (remaining 8175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 3308
       17.80 -    35.60: 264
       35.60 -    53.39: 31
       53.39 -    71.19: 18
       71.19 -    88.99: 11
  Dihedral angle restraints: 3632
    sinusoidal: 1395
      harmonic: 2237
  Sorted by residual:
  dihedral pdb=" CA  VAL A 914 "
           pdb=" C   VAL A 914 "
           pdb=" N   LEU A 915 "
           pdb=" CA  LEU A 915 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.74   34.26     0      5.00e+00 4.00e-02 4.69e+01
  dihedral pdb=" CA  SER A 301 "
           pdb=" C   SER A 301 "
           pdb=" N   PRO A 302 "
           pdb=" CA  PRO A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  LYS A 780 "
           pdb=" C   LYS A 780 "
           pdb=" N   PRO A 781 "
           pdb=" CA  PRO A 781 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.76  -22.24     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 3629 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 596
       0.035 -    0.070: 240
       0.070 -    0.105: 95
       0.105 -    0.140: 30
       0.140 -    0.175: 8
  Chirality restraints: 969
  Sorted by residual:
  chirality pdb=" CA  VAL A 648 "
            pdb=" N   VAL A 648 "
            pdb=" C   VAL A 648 "
            pdb=" CB  VAL A 648 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  VAL A 474 "
            pdb=" N   VAL A 474 "
            pdb=" C   VAL A 474 "
            pdb=" CB  VAL A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  VAL A 635 "
            pdb=" N   VAL A 635 "
            pdb=" C   VAL A 635 "
            pdb=" CB  VAL A 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.32e-01
  ... (remaining 966 not shown)

  Planarity restraints: 1035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 597 "   -0.052 5.00e-02 4.00e+02   7.84e-02 9.83e+00
        pdb=" N   PRO A 598 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 598 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 598 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 662 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO A 663 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 663 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 663 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 301 "   -0.040 5.00e-02 4.00e+02   6.08e-02 5.91e+00
        pdb=" N   PRO A 302 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 302 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 302 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1032 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1093
        2.77 -     3.31: 6313
        3.31 -     3.84: 9865
        3.84 -     4.37: 10963
        4.37 -     4.90: 18243
  Nonbonded interactions: 46477
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 415 "
            pdb=" OE2 GLU A 419 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ILE A 824 "
            pdb=" NZ  LYS A 829 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   LYS A 615 "
            pdb=" NE2 GLN A 619 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   GLY A 784 "
            pdb=" OG  SER A 788 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" NE2 HIS A 749 "
            pdb=" OG  SER A 774 "
     model   vdw
     2.285 3.120
  ... (remaining 46472 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.320
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6023  Z= 0.194
  Angle     :  0.916  14.404   8180  Z= 0.547
  Chirality :  0.047   0.175    969
  Planarity :  0.008   0.078   1035
  Dihedral  : 14.497  88.988   2192
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  : 12.61 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -2.53 (0.29), residues: 777
  helix: -0.23 (0.27), residues: 378
  sheet: -3.91 (0.80), residues: 28
  loop : -3.17 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 896 
 TYR   0.013   0.001   TYR A 570 
 PHE   0.017   0.001   PHE A 385 
 TRP   0.030   0.002   TRP A 282 
 HIS   0.008   0.002   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6023)
  covalent geometry    : angle       0.91574 ( 8180)
  hydrogen bonds       : bond        0.16727 (  281)
  hydrogen bonds       : angle       7.60107 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.8617 (m-80) cc_final: 0.8126 (m-80)
REVERT: A  299 MET cc_start: 0.8658 (mmt) cc_final: 0.8365 (mmm)
REVERT: A  315 MET cc_start: 0.8356 (tpt) cc_final: 0.8044 (tpt)
REVERT: A  351 ASN cc_start: 0.7838 (p0) cc_final: 0.7599 (p0)
REVERT: A  353 ASP cc_start: 0.7850 (m-30) cc_final: 0.7153 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0547
  time to fit residues: 7.3410
Evaluate side-chains
  60 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 619 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.105574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.067725 restraints weight = 26963.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.068821 restraints weight = 16272.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.069610 restraints weight = 11707.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.070235 restraints weight = 9625.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.070417 restraints weight = 8794.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6023  Z= 0.144
  Angle     :  0.756  10.997   8180  Z= 0.384
  Chirality :  0.047   0.161    969
  Planarity :  0.006   0.056   1035
  Dihedral  :  5.679  35.535    822
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  : 12.23 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  8.37 %
    Favored  : 89.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -2.10 (0.29), residues: 777
  helix:  0.29 (0.27), residues: 379
  sheet: -3.56 (0.81), residues: 30
  loop : -3.18 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 758 
 TYR   0.018   0.002   TYR A 789 
 PHE   0.018   0.002   PHE A 291 
 TRP   0.018   0.002   TRP A 282 
 HIS   0.007   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6023)
  covalent geometry    : angle       0.75627 ( 8180)
  hydrogen bonds       : bond        0.04712 (  281)
  hydrogen bonds       : angle       5.75282 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 MET cc_start: 0.9152 (tmm) cc_final: 0.8521 (ppp)
REVERT: A  293 PHE cc_start: 0.8847 (m-80) cc_final: 0.8048 (m-80)
REVERT: A  299 MET cc_start: 0.8738 (mmt) cc_final: 0.8390 (mmm)
REVERT: A  353 ASP cc_start: 0.8384 (m-30) cc_final: 0.7709 (m-30)
REVERT: A  391 MET cc_start: 0.9151 (ptm) cc_final: 0.8795 (ppp)
REVERT: A  838 MET cc_start: 0.8103 (ptm) cc_final: 0.7198 (ppp)
  outliers start: 11
  outliers final: 5
  residues processed: 72
  average time/residue: 0.0580
  time to fit residues: 6.1249
Evaluate side-chains
  67 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 25 optimal weight:   30.0000
   chunk 20 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:   30.0000
   chunk 76 optimal weight:    0.6980
   chunk 54 optimal weight:   20.0000
   chunk 75 optimal weight:    0.0030
   chunk 31 optimal weight:    0.0010
   chunk 0 optimal weight:   30.0000
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.7400

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.103542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.065815 restraints weight = 26790.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.066788 restraints weight = 17005.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.067483 restraints weight = 12496.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.068080 restraints weight = 10700.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.068347 restraints weight = 9633.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6023  Z= 0.152
  Angle     :  0.707  12.693   8180  Z= 0.364
  Chirality :  0.045   0.155    969
  Planarity :  0.005   0.054   1035
  Dihedral  :  5.431  31.776    822
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  : 12.23 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.61 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.83 (0.30), residues: 777
  helix:  0.47 (0.26), residues: 385
  sheet: -3.67 (0.77), residues: 30
  loop : -3.01 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 758 
 TYR   0.017   0.001   TYR A 789 
 PHE   0.014   0.001   PHE A 821 
 TRP   0.011   0.002   TRP A 282 
 HIS   0.008   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6023)
  covalent geometry    : angle       0.70695 ( 8180)
  hydrogen bonds       : bond        0.04288 (  281)
  hydrogen bonds       : angle       5.55520 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 MET cc_start: 0.9038 (tmm) cc_final: 0.8553 (ppp)
REVERT: A  293 PHE cc_start: 0.8888 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  299 MET cc_start: 0.8688 (mmt) cc_final: 0.8324 (mmm)
REVERT: A  838 MET cc_start: 0.8178 (ptm) cc_final: 0.7495 (ppp)
REVERT: A  941 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7874 (tpt)
  outliers start: 12
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0435
  time to fit residues: 4.8065
Evaluate side-chains
  71 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  941 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 HIS ** 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 = 0.4223 r_free = 0.4223 target = 0.100247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.062629 restraints weight = 27337.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.063706 restraints weight = 17452.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.064397 restraints weight = 13013.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.064980 restraints weight = 11070.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.065224 restraints weight = 10205.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6023  Z= 0.207
  Angle     :  0.745  12.576   8180  Z= 0.386
  Chirality :  0.046   0.149    969
  Planarity :  0.005   0.055   1035
  Dihedral  :  5.433  30.990    822
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.23 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.40 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.92 (0.30), residues: 777
  helix:  0.40 (0.26), residues: 384
  sheet: -3.51 (0.79), residues: 30
  loop : -3.06 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 882 
 TYR   0.013   0.002   TYR A 789 
 PHE   0.022   0.002   PHE A 821 
 TRP   0.011   0.002   TRP A 908 
 HIS   0.008   0.002   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6023)
  covalent geometry    : angle       0.74493 ( 8180)
  hydrogen bonds       : bond        0.04395 (  281)
  hydrogen bonds       : angle       5.72098 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 MET cc_start: 0.9179 (tmm) cc_final: 0.8742 (ppp)
REVERT: A  293 PHE cc_start: 0.8977 (m-80) cc_final: 0.8170 (m-80)
REVERT: A  299 MET cc_start: 0.8754 (mmt) cc_final: 0.8400 (mmm)
REVERT: A  391 MET cc_start: 0.9469 (ptm) cc_final: 0.9078 (ppp)
REVERT: A  412 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8813 (p0)
REVERT: A  610 MET cc_start: 0.8758 (ppp) cc_final: 0.8506 (ppp)
REVERT: A  845 MET cc_start: 0.6435 (ptm) cc_final: 0.5836 (ppp)
REVERT: A  885 LEU cc_start: 0.9625 (tt) cc_final: 0.9392 (mt)
REVERT: A  941 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8119 (tpt)
  outliers start: 18
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0559
  time to fit residues: 5.9425
Evaluate side-chains
  67 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  941 MET
Chi-restraints excluded: chain A residue  953 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:   40.0000
   chunk 12 optimal weight:    0.0170
   chunk 2 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.3424

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 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 = 0.4256 r_free = 0.4256 target = 0.102299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.064440 restraints weight = 27482.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.065488 restraints weight = 17139.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.066221 restraints weight = 12613.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.066704 restraints weight = 10723.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.066882 restraints weight = 9782.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6023  Z= 0.132
  Angle     :  0.701  10.380   8180  Z= 0.350
  Chirality :  0.045   0.149    969
  Planarity :  0.005   0.056   1035
  Dihedral  :  5.284  31.837    822
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 11.71 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.50 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.61 (0.30), residues: 777
  helix:  0.65 (0.27), residues: 385
  sheet: -3.43 (0.80), residues: 30
  loop : -2.92 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 694 
 TYR   0.009   0.001   TYR A 789 
 PHE   0.016   0.001   PHE A 291 
 TRP   0.010   0.001   TRP A 574 
 HIS   0.009   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6023)
  covalent geometry    : angle       0.70083 ( 8180)
  hydrogen bonds       : bond        0.03771 (  281)
  hydrogen bonds       : angle       5.41329 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 MET cc_start: 0.9139 (tmm) cc_final: 0.8823 (ppp)
REVERT: A  293 PHE cc_start: 0.8895 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  299 MET cc_start: 0.8796 (mmt) cc_final: 0.8450 (mmm)
REVERT: A  320 LEU cc_start: 0.9404 (tp) cc_final: 0.9176 (pp)
REVERT: A  391 MET cc_start: 0.9488 (ptm) cc_final: 0.9077 (ppp)
REVERT: A  412 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8804 (p0)
REVERT: A  610 MET cc_start: 0.8812 (ppp) cc_final: 0.8573 (ppp)
REVERT: A  838 MET cc_start: 0.8261 (ppp) cc_final: 0.7802 (ppp)
REVERT: A  845 MET cc_start: 0.6403 (ptm) cc_final: 0.5818 (ppp)
REVERT: A  885 LEU cc_start: 0.9619 (tt) cc_final: 0.9354 (mt)
REVERT: A  941 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8036 (tpt)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0481
  time to fit residues: 5.1300
Evaluate side-chains
  68 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  941 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0270
   chunk 20 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:   40.0000
   chunk 2 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 53 optimal weight:   50.0000
   overall best weight:    2.3844

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
** A 330 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 = 0.4238 r_free = 0.4238 target = 0.100856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.063230 restraints weight = 27430.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.064139 restraints weight = 18115.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.064936 restraints weight = 13153.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.065236 restraints weight = 10994.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.065668 restraints weight = 9959.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6023  Z= 0.175
  Angle     :  0.725   9.625   8180  Z= 0.365
  Chirality :  0.045   0.148    969
  Planarity :  0.005   0.056   1035
  Dihedral  :  5.274  29.506    822
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.10 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.35 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.57 (0.30), residues: 777
  helix:  0.67 (0.27), residues: 383
  sheet: -3.09 (0.83), residues: 30
  loop : -2.89 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 882 
 TYR   0.009   0.001   TYR A 789 
 PHE   0.016   0.002   PHE A 385 
 TRP   0.012   0.002   TRP A 574 
 HIS   0.009   0.002   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6023)
  covalent geometry    : angle       0.72541 ( 8180)
  hydrogen bonds       : bond        0.03903 (  281)
  hydrogen bonds       : angle       5.54287 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9010 (m-80) cc_final: 0.8646 (m-80)
REVERT: A  299 MET cc_start: 0.8806 (mmt) cc_final: 0.8456 (mmm)
REVERT: A  391 MET cc_start: 0.9466 (ptm) cc_final: 0.9086 (ppp)
REVERT: A  412 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8872 (p0)
REVERT: A  838 MET cc_start: 0.8412 (ppp) cc_final: 0.7984 (ppp)
REVERT: A  845 MET cc_start: 0.6538 (ptm) cc_final: 0.5988 (ppp)
REVERT: A  885 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9409 (mt)
REVERT: A  941 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8206 (tpt)
  outliers start: 22
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0637
  time to fit residues: 7.1156
Evaluate side-chains
  77 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  941 MET
Chi-restraints excluded: chain A residue  953 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 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 = 0.4212 r_free = 0.4212 target = 0.099044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.061270 restraints weight = 27671.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.062276 restraints weight = 17688.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.062985 restraints weight = 13469.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.063483 restraints weight = 11478.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.063632 restraints weight = 10539.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6023  Z= 0.221
  Angle     :  0.764   8.459   8180  Z= 0.389
  Chirality :  0.046   0.216    969
  Planarity :  0.005   0.057   1035
  Dihedral  :  5.417  28.786    822
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.74 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.74 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.30), residues: 777
  helix:  0.59 (0.27), residues: 375
  sheet: -3.03 (0.86), residues: 30
  loop : -2.91 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 694 
 TYR   0.013   0.002   TYR A 789 
 PHE   0.020   0.002   PHE A 291 
 TRP   0.012   0.002   TRP A 574 
 HIS   0.010   0.002   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6023)
  covalent geometry    : angle       0.76432 ( 8180)
  hydrogen bonds       : bond        0.04182 (  281)
  hydrogen bonds       : angle       5.74242 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9064 (m-80) cc_final: 0.8732 (m-80)
REVERT: A  299 MET cc_start: 0.8821 (mmt) cc_final: 0.8485 (mmm)
REVERT: A  391 MET cc_start: 0.9500 (ptm) cc_final: 0.9094 (ppp)
REVERT: A  412 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8923 (p0)
REVERT: A  838 MET cc_start: 0.8479 (ppp) cc_final: 0.8085 (ppp)
REVERT: A  845 MET cc_start: 0.6698 (ptm) cc_final: 0.6172 (ppp)
REVERT: A  941 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8245 (tpt)
  outliers start: 24
  outliers final: 15
  residues processed: 74
  average time/residue: 0.0592
  time to fit residues: 6.5039
Evaluate side-chains
  77 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  941 MET
Chi-restraints excluded: chain A residue  953 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0770
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0980
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    1.6344

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 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 = 0.4243 r_free = 0.4243 target = 0.101278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.063371 restraints weight = 27962.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.064362 restraints weight = 17274.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.065071 restraints weight = 12751.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.065624 restraints weight = 10772.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.065759 restraints weight = 9939.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6023  Z= 0.139
  Angle     :  0.738  14.574   8180  Z= 0.359
  Chirality :  0.045   0.149    969
  Planarity :  0.005   0.057   1035
  Dihedral  :  5.315  30.154    822
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  : 11.58 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.21 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.48 (0.30), residues: 777
  helix:  0.75 (0.27), residues: 382
  sheet: -3.07 (0.85), residues: 30
  loop : -2.84 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 882 
 TYR   0.012   0.001   TYR A 789 
 PHE   0.015   0.001   PHE A 291 
 TRP   0.011   0.001   TRP A 574 
 HIS   0.010   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6023)
  covalent geometry    : angle       0.73770 ( 8180)
  hydrogen bonds       : bond        0.03741 (  281)
  hydrogen bonds       : angle       5.45700 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.8936 (m-80) cc_final: 0.8647 (m-80)
REVERT: A  299 MET cc_start: 0.8805 (mmt) cc_final: 0.8459 (mmm)
REVERT: A  364 TYR cc_start: 0.8975 (t80) cc_final: 0.8698 (t80)
REVERT: A  391 MET cc_start: 0.9411 (ptm) cc_final: 0.9028 (ppp)
REVERT: A  412 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8844 (p0)
REVERT: A  838 MET cc_start: 0.8428 (ppp) cc_final: 0.8056 (ppp)
REVERT: A  845 MET cc_start: 0.6658 (ptm) cc_final: 0.6128 (ppp)
REVERT: A  941 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8386 (tpt)
  outliers start: 20
  outliers final: 15
  residues processed: 76
  average time/residue: 0.0593
  time to fit residues: 6.6015
Evaluate side-chains
  79 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  941 MET
Chi-restraints excluded: chain A residue  953 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 26 optimal weight:   30.0000
   chunk 33 optimal weight:    0.1980
   chunk 71 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.101640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.063050 restraints weight = 28020.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.064439 restraints weight = 17380.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.065376 restraints weight = 13212.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.065747 restraints weight = 11253.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.065998 restraints weight = 10378.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6023  Z= 0.131
  Angle     :  0.756  17.053   8180  Z= 0.361
  Chirality :  0.046   0.209    969
  Planarity :  0.005   0.057   1035
  Dihedral  :  5.201  29.964    822
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  : 11.58 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.60 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.31), residues: 777
  helix:  0.82 (0.27), residues: 383
  sheet: -3.20 (0.81), residues: 30
  loop : -2.78 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 694 
 TYR   0.007   0.001   TYR A 349 
 PHE   0.021   0.001   PHE A 291 
 TRP   0.012   0.001   TRP A 574 
 HIS   0.009   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6023)
  covalent geometry    : angle       0.75585 ( 8180)
  hydrogen bonds       : bond        0.03644 (  281)
  hydrogen bonds       : angle       5.33480 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.8920 (m-80) cc_final: 0.8613 (m-80)
REVERT: A  299 MET cc_start: 0.8824 (mmt) cc_final: 0.8474 (mmm)
REVERT: A  364 TYR cc_start: 0.8933 (t80) cc_final: 0.8642 (t80)
REVERT: A  391 MET cc_start: 0.9402 (ptm) cc_final: 0.9009 (ppp)
REVERT: A  412 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8826 (p0)
REVERT: A  838 MET cc_start: 0.8417 (ppp) cc_final: 0.8026 (ppp)
REVERT: A  845 MET cc_start: 0.6667 (ptm) cc_final: 0.6145 (ppp)
REVERT: A  941 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8391 (tpt)
  outliers start: 14
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0577
  time to fit residues: 6.1804
Evaluate side-chains
  76 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  941 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 64 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:   30.0000
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.101821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.063911 restraints weight = 28046.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.064974 restraints weight = 17355.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.065668 restraints weight = 12718.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.066240 restraints weight = 10686.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.066477 restraints weight = 9641.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6023  Z= 0.129
  Angle     :  0.759  18.001   8180  Z= 0.362
  Chirality :  0.046   0.160    969
  Planarity :  0.005   0.057   1035
  Dihedral  :  5.139  29.790    822
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 11.07 %
    Favored  : 88.03 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.76 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.31), residues: 777
  helix:  0.89 (0.28), residues: 377
  sheet: -3.30 (0.78), residues: 35
  loop : -2.71 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 347 
 TYR   0.016   0.001   TYR A 789 
 PHE   0.020   0.001   PHE A 291 
 TRP   0.013   0.001   TRP A 574 
 HIS   0.010   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6023)
  covalent geometry    : angle       0.75877 ( 8180)
  hydrogen bonds       : bond        0.03563 (  281)
  hydrogen bonds       : angle       5.26250 (  816)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9036 (m-80) cc_final: 0.8695 (m-80)
REVERT: A  299 MET cc_start: 0.8818 (mmt) cc_final: 0.8452 (mmm)
REVERT: A  364 TYR cc_start: 0.8989 (t80) cc_final: 0.8667 (t80)
REVERT: A  391 MET cc_start: 0.9497 (ptm) cc_final: 0.9065 (ppp)
REVERT: A  412 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8789 (p0)
REVERT: A  593 LEU cc_start: 0.9240 (mp) cc_final: 0.8377 (tp)
REVERT: A  838 MET cc_start: 0.8438 (ppp) cc_final: 0.8057 (ppp)
REVERT: A  845 MET cc_start: 0.6608 (ptm) cc_final: 0.6077 (ppp)
REVERT: A  941 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8297 (tpt)
  outliers start: 14
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0570
  time to fit residues: 6.3008
Evaluate side-chains
  75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  412 ASP
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  941 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:   40.0000
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0570
   chunk 28 optimal weight:   20.0000
   chunk 12 optimal weight:    0.0020
   overall best weight:    0.5106

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.103933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.067793 restraints weight = 31320.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.069291 restraints weight = 17593.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.070093 restraints weight = 12467.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.070642 restraints weight = 10415.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.071014 restraints weight = 9577.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6023  Z= 0.117
  Angle     :  0.759  16.092   8180  Z= 0.358
  Chirality :  0.045   0.145    969
  Planarity :  0.005   0.057   1035
  Dihedral  :  5.032  30.236    822
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 10.30 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.69 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.25 (0.31), residues: 777
  helix:  0.99 (0.28), residues: 381
  sheet: -3.32 (0.78), residues: 35
  loop : -2.71 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 265 
 TYR   0.030   0.001   TYR A 789 
 PHE   0.022   0.001   PHE A 291 
 TRP   0.012   0.001   TRP A 574 
 HIS   0.010   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6023)
  covalent geometry    : angle       0.75945 ( 8180)
  hydrogen bonds       : bond        0.03395 (  281)
  hydrogen bonds       : angle       5.13010 (  816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1904.43 seconds
wall clock time: 33 minutes 18.97 seconds (1998.97 seconds total)