Starting phenix.real_space_refine
on Tue Aug  4 22:35:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zqb_60381/08_2026/8zqb_60381.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zqb_60381/08_2026/8zqb_60381.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2026/8zqb_60381.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2026/8zqb_60381.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2026/8zqb_60381.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2026/8zqb_60381.map"
  }
  resolution = 3.65
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     S      24      5.16       5
     C    4390      2.51       5
     N    1333      2.21       5
     O    1437      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7222
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6412
          Classifications: {'peptide': 787}
          Link IDs: {'PTRANS': 28, 'TRANS': 758}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 810
          Classifications: {'RNA': 38}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 17}
          Link IDs: {'rna2p': 3, 'rna3p': 34}
  Time building chain proxies: 1.87, per 1000 atoms: 0.26
  Number of scatterers: 7222
  At special positions: 0
  Unit cell: (95.04, 96.36, 100.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      38     15.00
     O    1437      8.00
     N    1333      7.00
     C    4390      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 418.3 milliseconds
  

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      48.0% alpha, 17.8% beta
      14 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 39
      removed outlier: 4.548A  pdb=" N   HIS A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 69
    Processing helix  chain 'A' and resid 76 through 88
      removed outlier: 3.584A  pdb=" N   LEU A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 96
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 187 through 199
    Processing helix  chain 'A' and resid 211 through 252
    Processing helix  chain 'A' and resid 255 through 270
      removed outlier: 3.525A  pdb=" N   GLU A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 4.373A  pdb=" N   LEU A 303 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 330
      removed outlier: 3.862A  pdb=" N   VAL A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   TYR A 322 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
    Processing helix  chain 'A' and resid 447 through 454
      removed outlier: 3.606A  pdb=" N   LYS A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLY A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 553
      removed outlier: 4.069A  pdb=" N   ARG A 541 " --> pdb=" O   PHE A 537 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 566
      removed outlier: 3.926A  pdb=" N   ALA A 560 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 572
    Processing helix  chain 'A' and resid 579 through 606
    Processing helix  chain 'A' and resid 607 through 609
      No H-bonds generated for 'chain 'A' and resid 607 through 609'
    Processing helix  chain 'A' and resid 612 through 616
    Processing helix  chain 'A' and resid 620 through 641
      removed outlier: 4.252A  pdb=" N   PHE A 624 " --> pdb=" O   SER A 620 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASN A 635 " --> pdb=" O   LYS A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 688
      removed outlier: 3.730A  pdb=" N   GLU A 688 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 720
      removed outlier: 3.801A  pdb=" N   LEU A 719 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 736
    Processing helix  chain 'A' and resid 782 through 797
    Processing helix  chain 'A' and resid 820 through 831
      removed outlier: 3.524A  pdb=" N   LEU A 827 " --> pdb=" O   GLU A 823 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 885
    Processing helix  chain 'A' and resid 888 through 898
    Processing helix  chain 'A' and resid 899 through 903
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11
      removed outlier: 3.583A  pdb=" N   LYS A   5 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR A 439 " --> pdb=" O   LYS A   5 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TYR A 433 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLU A 423 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASN A 440 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   VAL A 421 " --> pdb=" O   ASN A 440 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 11
      removed outlier: 3.583A  pdb=" N   LYS A   5 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR A 439 " --> pdb=" O   LYS A   5 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TYR A 433 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLU A 423 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASN A 440 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   VAL A 421 " --> pdb=" O   ASN A 440 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ARG A 415 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 419 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 365
    Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 517
      removed outlier: 4.048A  pdb=" N   SER A 513 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG A 517 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 486 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA A 488 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU A 697 " --> pdb=" O   ILE A 477 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   LEU A 479 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   VAL A 743 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   MET A 696 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503
      removed outlier: 4.444A  pdb=" N   VAL A 503 " --> pdb=" O   GLU A 507 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   GLU A 507 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 761
      removed outlier: 3.579A  pdb=" N   TYR A 760 " --> pdb=" O   TYR A 770 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 845 through 848
      removed outlier: 3.793A  pdb=" N   SER A 845 " --> pdb=" O   THR A 841 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TYR A 814 " --> pdb=" O   LEU A 838 " (cutoff:3.500A)

    333 hydrogen bonds defined for protein.
    942 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      37 hydrogen bonds
      66 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2162
        1.33 -     1.45: 1280
        1.45 -     1.57: 3880
        1.57 -     1.69: 75
        1.69 -     1.81: 37
  Bond restraints: 7434
  Sorted by residual:
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.13e+00
  bond pdb=" C8    G B -36 "
       pdb=" N7    G B -36 "
    ideal  model  delta    sigma   weight residual
    1.305  1.295  0.010 6.00e-03 2.78e+04 2.53e+00
  bond pdb=" CG  LEU A 670 "
       pdb=" CD2 LEU A 670 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.76e+00
  bond pdb=" CA  THR A 837 "
       pdb=" C   THR A 837 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.016 1.23e-02 6.61e+03 1.60e+00
  bond pdb=" C   THR A 837 "
       pdb=" N   LEU A 838 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.015 1.29e-02 6.01e+03 1.43e+00
  ... (remaining 7429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 9712
        1.40 -     2.81: 398
        2.81 -     4.21: 66
        4.21 -     5.62: 13
        5.62 -     7.02: 2
  Bond angle restraints: 10191
  Sorted by residual:
  angle pdb=" O5'   U B -25 "
        pdb=" C5'   U B -25 "
        pdb=" C4'   U B -25 "
      ideal   model   delta    sigma   weight residual
     109.40  112.30   -2.90 8.00e-01 1.56e+00 1.32e+01
  angle pdb=" N   ASN A 482 "
        pdb=" CA  ASN A 482 "
        pdb=" C   ASN A 482 "
      ideal   model   delta    sigma   weight residual
     112.35  107.68    4.67 1.34e+00 5.57e-01 1.22e+01
  angle pdb=" N   VAL A 743 "
        pdb=" CA  VAL A 743 "
        pdb=" C   VAL A 743 "
      ideal   model   delta    sigma   weight residual
     108.45  113.57   -5.12 1.48e+00 4.57e-01 1.20e+01
  angle pdb=" O5'   G B -31 "
        pdb=" C5'   G B -31 "
        pdb=" C4'   G B -31 "
      ideal   model   delta    sigma   weight residual
     109.40  112.09   -2.69 8.00e-01 1.56e+00 1.13e+01
  angle pdb=" O5'   C B  -1 "
        pdb=" C5'   C B  -1 "
        pdb=" C4'   C B  -1 "
      ideal   model   delta    sigma   weight residual
     109.40  112.06   -2.66 8.00e-01 1.56e+00 1.10e+01
  ... (remaining 10186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 4359
       35.87 -    71.74: 215
       71.74 -   107.62: 18
      107.62 -   143.49: 1
      143.49 -   179.36: 1
  Dihedral angle restraints: 4594
    sinusoidal: 2303
      harmonic: 2291
  Sorted by residual:
  dihedral pdb=" O4'   U B -32 "
           pdb=" C1'   U B -32 "
           pdb=" N1    U B -32 "
           pdb=" C2    U B -32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.64  179.36     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   A B -21 "
           pdb=" C1'   A B -21 "
           pdb=" N9    A B -21 "
           pdb=" C4    A B -21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -18.62  -71.38     1      2.00e+01 2.50e-03 1.63e+01
  dihedral pdb=" CA  ARG A 873 "
           pdb=" C   ARG A 873 "
           pdb=" N   HIS A 874 "
           pdb=" CA  HIS A 874 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 778
       0.033 -    0.065: 226
       0.065 -    0.098: 74
       0.098 -    0.131: 53
       0.131 -    0.164: 3
  Chirality restraints: 1134
  Sorted by residual:
  chirality pdb=" CA  PRO A 310 "
            pdb=" N   PRO A 310 "
            pdb=" C   PRO A 310 "
            pdb=" CB  PRO A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CA  ILE A 780 "
            pdb=" N   ILE A 780 "
            pdb=" C   ILE A 780 "
            pdb=" CB  ILE A 780 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  VAL A 385 "
            pdb=" N   VAL A 385 "
            pdb=" C   VAL A 385 "
            pdb=" CB  VAL A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  ... (remaining 1131 not shown)

  Planarity restraints: 1181
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 903 "   -0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO A 904 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 904 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 904 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B -36 "   -0.016 2.00e-02 2.50e+03   7.84e-03 1.84e+00
        pdb=" N9    G B -36 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    G B -36 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    G B -36 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    G B -36 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B -36 "   -0.000 2.00e-02 2.50e+03
        pdb=" O6    G B -36 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G B -36 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G B -36 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B -36 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B -36 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G B -36 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 734 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.80e+00
        pdb=" C   LYS A 734 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   LYS A 734 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN A 735 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1178 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1030
        2.75 -     3.29: 7543
        3.29 -     3.83: 12503
        3.83 -     4.36: 14418
        4.36 -     4.90: 23219
  Nonbonded interactions: 58713
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  40 "
            pdb=" NH1 ARG A  40 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" O   PRO A 870 "
            pdb=" OG1 THR A 880 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASN A 785 "
            pdb=" OD1 ASN A 789 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   ASP A 341 "
            pdb=" OG  SER A 345 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OD1 ASP A 497 "
            pdb=" N   GLY A 498 "
     model   vdw
     2.237 3.120
  ... (remaining 58708 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.380
  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:             0.010
  Load rotamer database and sin/cos tables:1.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
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      :  0.003   0.046   7434  Z= 0.178
  Angle     :  0.641   7.021  10191  Z= 0.420
  Chirality :  0.041   0.164   1134
  Planarity :  0.004   0.050   1181
  Dihedral  : 19.010 179.362   3110
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 19.41 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.31), residues: 769
  helix:  0.63 (0.30), residues: 309
  sheet: -0.46 (0.54), residues: 109
  loop : -2.03 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 613 
 TYR   0.013   0.001   TYR A 542 
 PHE   0.019   0.001   PHE A 771 
 TRP   0.014   0.001   TRP A 229 
 HIS   0.010   0.002   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.18 ( 7434)
  covalent geometry    : angle       0.64084 /  0.42 (10191)
  hydrogen bonds       : bond        0.16657 / 10.95 (  358)
  hydrogen bonds       : angle       6.72235 /  4.85 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 185
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  477 ILE cc_start: 0.8688 (mm) cc_final: 0.8441 (mm)
REVERT: A  623 TYR cc_start: 0.7488 (m-80) cc_final: 0.7283 (m-80)
REVERT: A  793 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8280 (mtt180)
  outliers start: 7
  outliers final: 1
  residues processed: 186
  average time/residue: 0.1231
  time to fit residues: 28.4546
Evaluate side-chains
  118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 530 HIS
A 773 GLN
A 789 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.085756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.070774 restraints weight = 31617.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.073309 restraints weight = 16426.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.074907 restraints weight = 10183.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.076062 restraints weight = 7169.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.076853 restraints weight = 5482.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7434  Z= 0.190
  Angle     :  0.818  13.578  10191  Z= 0.422
  Chirality :  0.045   0.186   1134
  Planarity :  0.006   0.046   1181
  Dihedral  : 17.430 178.812   1501
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 22.06 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.30), residues: 769
  helix:  0.60 (0.29), residues: 333
  sheet: -0.44 (0.48), residues: 115
  loop : -1.83 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 615 
 TYR   0.043   0.003   TYR A 308 
 PHE   0.026   0.003   PHE A 604 
 TRP   0.049   0.004   TRP A 640 
 HIS   0.010   0.002   HIS A 884 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.19 ( 7434)
  covalent geometry    : angle       0.81833 /  0.42 (10191)
  hydrogen bonds       : bond        0.05250 /  3.57 (  358)
  hydrogen bonds       : angle       5.26084 /  3.78 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.8183 (m-80) cc_final: 0.7800 (m-80)
REVERT: A  343 ASP cc_start: 0.8864 (m-30) cc_final: 0.8287 (p0)
REVERT: A  391 TRP cc_start: 0.8453 (t-100) cc_final: 0.8179 (t-100)
REVERT: A  438 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8549 (p0)
REVERT: A  607 ARG cc_start: 0.8798 (ptt-90) cc_final: 0.8179 (ptt-90)
REVERT: A  608 TYR cc_start: 0.8370 (m-80) cc_final: 0.7702 (m-80)
REVERT: A  735 ASN cc_start: 0.8946 (p0) cc_final: 0.8677 (p0)
REVERT: A  799 ARG cc_start: 0.8701 (tpt90) cc_final: 0.8487 (mmm160)
REVERT: A  872 TYR cc_start: 0.6397 (m-80) cc_final: 0.6076 (m-80)
  outliers start: 24
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1127
  time to fit residues: 19.2438
Evaluate side-chains
  119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  742 GLU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  837 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 689 HIS
A 789 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.082811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.068171 restraints weight = 32745.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.070506 restraints weight = 17167.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.072127 restraints weight = 10822.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.073253 restraints weight = 7629.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.073986 restraints weight = 5805.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7434  Z= 0.191
  Angle     :  0.737   9.124  10191  Z= 0.383
  Chirality :  0.043   0.195   1134
  Planarity :  0.006   0.079   1181
  Dihedral  : 17.217 176.642   1497
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.88 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.31), residues: 769
  helix:  0.94 (0.29), residues: 328
  sheet: -0.50 (0.48), residues: 108
  loop : -1.80 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  40 
 TYR   0.029   0.002   TYR A 308 
 PHE   0.021   0.002   PHE A 571 
 TRP   0.016   0.002   TRP A 741 
 HIS   0.008   0.002   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.19 ( 7434)
  covalent geometry    : angle       0.73731 /  0.38 (10191)
  hydrogen bonds       : bond        0.04783 /  3.23 (  358)
  hydrogen bonds       : angle       4.86881 /  3.50 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.8260 (m-80) cc_final: 0.7702 (m-80)
REVERT: A  242 GLU cc_start: 0.9381 (tm-30) cc_final: 0.9174 (pp20)
REVERT: A  328 TRP cc_start: 0.9116 (t60) cc_final: 0.8808 (t60)
REVERT: A  343 ASP cc_start: 0.8881 (m-30) cc_final: 0.8280 (p0)
REVERT: A  345 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8404 (p)
REVERT: A  391 TRP cc_start: 0.8588 (t-100) cc_final: 0.8271 (t-100)
REVERT: A  548 LYS cc_start: 0.8752 (tttt) cc_final: 0.8337 (tttm)
REVERT: A  641 ASN cc_start: 0.8714 (t0) cc_final: 0.8513 (t0)
REVERT: A  696 MET cc_start: 0.9347 (ptp) cc_final: 0.8648 (pmm)
REVERT: A  735 ASN cc_start: 0.8971 (p0) cc_final: 0.8720 (p0)
REVERT: A  741 TRP cc_start: 0.6814 (t-100) cc_final: 0.5593 (t-100)
REVERT: A  774 ASP cc_start: 0.9317 (m-30) cc_final: 0.8961 (p0)
REVERT: A  837 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8894 (t)
REVERT: A  869 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8911 (mm-30)
REVERT: A  872 TYR cc_start: 0.6878 (m-80) cc_final: 0.6589 (m-80)
  outliers start: 31
  outliers final: 21
  residues processed: 137
  average time/residue: 0.1005
  time to fit residues: 17.7960
Evaluate side-chains
  130 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  187 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  661 LYS
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  742 GLU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  837 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.7586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.082490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067839 restraints weight = 33136.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.070191 restraints weight = 17328.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.071687 restraints weight = 10875.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.072786 restraints weight = 7723.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.073335 restraints weight = 5946.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7434  Z= 0.177
  Angle     :  0.706   9.356  10191  Z= 0.370
  Chirality :  0.043   0.204   1134
  Planarity :  0.004   0.039   1181
  Dihedral  : 17.194 177.405   1497
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 20.74 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.31), residues: 769
  helix:  0.81 (0.28), residues: 337
  sheet: -0.54 (0.45), residues: 123
  loop : -1.68 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 607 
 TYR   0.030   0.002   TYR A 308 
 PHE   0.016   0.002   PHE A 571 
 TRP   0.012   0.002   TRP A 640 
 HIS   0.009   0.001   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.18 ( 7434)
  covalent geometry    : angle       0.70564 /  0.37 (10191)
  hydrogen bonds       : bond        0.04454 /  3.03 (  358)
  hydrogen bonds       : angle       4.71633 /  3.39 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.8319 (m-80) cc_final: 0.7642 (m-80)
REVERT: A   95 LYS cc_start: 0.7514 (tptp) cc_final: 0.7308 (tptp)
REVERT: A  328 TRP cc_start: 0.9121 (t60) cc_final: 0.8818 (t60)
REVERT: A  343 ASP cc_start: 0.8872 (m-30) cc_final: 0.8286 (p0)
REVERT: A  345 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8397 (p)
REVERT: A  391 TRP cc_start: 0.8578 (t-100) cc_final: 0.8234 (t-100)
REVERT: A  641 ASN cc_start: 0.8722 (t0) cc_final: 0.8469 (t0)
REVERT: A  658 ASP cc_start: 0.6274 (p0) cc_final: 0.5582 (t70)
REVERT: A  661 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.7998 (pttm)
REVERT: A  696 MET cc_start: 0.9317 (ptp) cc_final: 0.8619 (pmm)
REVERT: A  735 ASN cc_start: 0.8942 (p0) cc_final: 0.8657 (p0)
REVERT: A  741 TRP cc_start: 0.6872 (t-100) cc_final: 0.5466 (t-100)
REVERT: A  774 ASP cc_start: 0.9304 (m-30) cc_final: 0.8964 (p0)
REVERT: A  793 ARG cc_start: 0.9159 (mtt180) cc_final: 0.8955 (mtt180)
REVERT: A  851 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8291 (mt)
REVERT: A  869 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8905 (mm-30)
REVERT: A  872 TYR cc_start: 0.7021 (m-80) cc_final: 0.6712 (m-80)
  outliers start: 35
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1054
  time to fit residues: 17.7619
Evaluate side-chains
  127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  661 LYS
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  742 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   overall best weight:    2.2784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.080937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.066198 restraints weight = 32993.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.068459 restraints weight = 17403.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.070012 restraints weight = 11015.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.071011 restraints weight = 7855.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.071807 restraints weight = 6094.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7434  Z= 0.199
  Angle     :  0.708   8.802  10191  Z= 0.369
  Chirality :  0.043   0.270   1134
  Planarity :  0.004   0.036   1181
  Dihedral  : 17.163 177.498   1497
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 21.03 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.31), residues: 769
  helix:  0.90 (0.28), residues: 337
  sheet: -0.57 (0.44), residues: 125
  loop : -1.66 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 820 
 TYR   0.027   0.002   TYR A 308 
 PHE   0.022   0.002   PHE A 265 
 TRP   0.010   0.002   TRP A 640 
 HIS   0.018   0.002   HIS A 530 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.20 ( 7434)
  covalent geometry    : angle       0.70751 /  0.37 (10191)
  hydrogen bonds       : bond        0.04484 /  3.09 (  358)
  hydrogen bonds       : angle       4.61880 /  3.33 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 102
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.8434 (m-80) cc_final: 0.7832 (m-80)
REVERT: A  242 GLU cc_start: 0.9379 (tm-30) cc_final: 0.9175 (pp20)
REVERT: A  328 TRP cc_start: 0.9144 (t60) cc_final: 0.8841 (t60)
REVERT: A  345 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8072 (p)
REVERT: A  391 TRP cc_start: 0.8621 (t-100) cc_final: 0.8355 (t-100)
REVERT: A  641 ASN cc_start: 0.8807 (t0) cc_final: 0.8502 (t0)
REVERT: A  694 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8374 (p)
REVERT: A  696 MET cc_start: 0.9307 (ptp) cc_final: 0.8628 (pmm)
REVERT: A  735 ASN cc_start: 0.8871 (p0) cc_final: 0.8576 (p0)
REVERT: A  774 ASP cc_start: 0.9275 (m-30) cc_final: 0.8945 (p0)
REVERT: A  851 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8298 (mt)
REVERT: A  872 TYR cc_start: 0.7230 (m-80) cc_final: 0.6849 (m-80)
  outliers start: 39
  outliers final: 30
  residues processed: 127
  average time/residue: 0.0980
  time to fit residues: 16.3915
Evaluate side-chains
  135 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  26 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 = 0.3786 r_free = 0.3786 target = 0.082161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.067395 restraints weight = 32664.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.069737 restraints weight = 17126.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.071324 restraints weight = 10744.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.072465 restraints weight = 7555.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.073248 restraints weight = 5761.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7434  Z= 0.144
  Angle     :  0.682  10.680  10191  Z= 0.352
  Chirality :  0.042   0.273   1134
  Planarity :  0.004   0.034   1181
  Dihedral  : 17.241 177.860   1497
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 21.03 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.31), residues: 769
  helix:  1.01 (0.28), residues: 336
  sheet: -0.58 (0.45), residues: 127
  loop : -1.63 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 326 
 TYR   0.025   0.002   TYR A 308 
 PHE   0.021   0.002   PHE A 202 
 TRP   0.013   0.001   TRP A 229 
 HIS   0.010   0.002   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 7434)
  covalent geometry    : angle       0.68196 /  0.35 (10191)
  hydrogen bonds       : bond        0.04070 /  2.84 (  358)
  hydrogen bonds       : angle       4.58025 /  3.32 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7659 (mmt90)
REVERT: A   64 PHE cc_start: 0.8466 (m-80) cc_final: 0.7807 (m-80)
REVERT: A  242 GLU cc_start: 0.9360 (tm-30) cc_final: 0.9154 (pp20)
REVERT: A  328 TRP cc_start: 0.9150 (t60) cc_final: 0.8857 (t60)
REVERT: A  343 ASP cc_start: 0.8861 (m-30) cc_final: 0.8334 (p0)
REVERT: A  391 TRP cc_start: 0.8612 (t-100) cc_final: 0.8309 (t-100)
REVERT: A  608 TYR cc_start: 0.8155 (m-80) cc_final: 0.7939 (m-80)
REVERT: A  641 ASN cc_start: 0.8739 (t0) cc_final: 0.8391 (t0)
REVERT: A  658 ASP cc_start: 0.7098 (m-30) cc_final: 0.6775 (p0)
REVERT: A  672 MET cc_start: 0.7415 (tpp) cc_final: 0.7201 (tpp)
REVERT: A  694 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8435 (p)
REVERT: A  696 MET cc_start: 0.9257 (ptp) cc_final: 0.8615 (pmm)
REVERT: A  717 LEU cc_start: 0.8986 (pt) cc_final: 0.8658 (mm)
REVERT: A  730 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8505 (pp20)
REVERT: A  735 ASN cc_start: 0.8772 (p0) cc_final: 0.8472 (p0)
REVERT: A  774 ASP cc_start: 0.9244 (m-30) cc_final: 0.8914 (p0)
REVERT: A  851 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8254 (mt)
  outliers start: 39
  outliers final: 26
  residues processed: 133
  average time/residue: 0.0977
  time to fit residues: 17.0024
Evaluate side-chains
  130 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  742 GLU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 63 optimal weight:    0.0000
   chunk 22 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 66 optimal weight:    0.4980
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.5586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.083066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.068276 restraints weight = 32368.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.070626 restraints weight = 16881.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.072255 restraints weight = 10644.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.073385 restraints weight = 7474.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.073945 restraints weight = 5712.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7434  Z= 0.136
  Angle     :  0.697   9.640  10191  Z= 0.356
  Chirality :  0.042   0.291   1134
  Planarity :  0.005   0.061   1181
  Dihedral  : 17.237 177.912   1497
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 21.18 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.31), residues: 769
  helix:  1.16 (0.29), residues: 330
  sheet: -0.46 (0.45), residues: 127
  loop : -1.57 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  49 
 TYR   0.023   0.001   TYR A 308 
 PHE   0.027   0.002   PHE A 202 
 TRP   0.012   0.001   TRP A 229 
 HIS   0.010   0.001   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 7434)
  covalent geometry    : angle       0.69693 /  0.36 (10191)
  hydrogen bonds       : bond        0.03950 /  2.77 (  358)
  hydrogen bonds       : angle       4.45126 /  3.24 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7601 (mmt90)
REVERT: A   64 PHE cc_start: 0.8466 (m-80) cc_final: 0.7793 (m-80)
REVERT: A  242 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9131 (pp20)
REVERT: A  328 TRP cc_start: 0.9156 (t60) cc_final: 0.8875 (t60)
REVERT: A  391 TRP cc_start: 0.8609 (t-100) cc_final: 0.8377 (t-100)
REVERT: A  506 MET cc_start: 0.8949 (mmt) cc_final: 0.8627 (mmt)
REVERT: A  641 ASN cc_start: 0.8685 (t0) cc_final: 0.8309 (t0)
REVERT: A  672 MET cc_start: 0.7411 (tpp) cc_final: 0.7193 (tpp)
REVERT: A  694 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8374 (p)
REVERT: A  696 MET cc_start: 0.9199 (ptp) cc_final: 0.8742 (pmm)
REVERT: A  717 LEU cc_start: 0.8950 (pt) cc_final: 0.8649 (mm)
REVERT: A  730 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8474 (pp20)
REVERT: A  735 ASN cc_start: 0.8706 (p0) cc_final: 0.8426 (p0)
REVERT: A  774 ASP cc_start: 0.9233 (m-30) cc_final: 0.8892 (p0)
REVERT: A  851 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8220 (mt)
  outliers start: 32
  outliers final: 23
  residues processed: 125
  average time/residue: 0.1003
  time to fit residues: 16.3839
Evaluate side-chains
  124 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    1.3586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.082026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066959 restraints weight = 33556.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.069299 restraints weight = 17613.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.070878 restraints weight = 11065.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.071780 restraints weight = 7866.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.072721 restraints weight = 6258.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7434  Z= 0.158
  Angle     :  0.703   9.792  10191  Z= 0.361
  Chirality :  0.042   0.241   1134
  Planarity :  0.004   0.049   1181
  Dihedral  : 17.201 177.865   1497
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 22.35 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.31), residues: 769
  helix:  1.12 (0.29), residues: 336
  sheet: -0.51 (0.47), residues: 116
  loop : -1.54 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 326 
 TYR   0.030   0.002   TYR A 760 
 PHE   0.025   0.002   PHE A 202 
 TRP   0.018   0.001   TRP A 741 
 HIS   0.011   0.002   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 7434)
  covalent geometry    : angle       0.70294 /  0.36 (10191)
  hydrogen bonds       : bond        0.03979 /  2.78 (  358)
  hydrogen bonds       : angle       4.46805 /  3.26 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7513 (mmt90)
REVERT: A  328 TRP cc_start: 0.9208 (t60) cc_final: 0.8932 (t60)
REVERT: A  391 TRP cc_start: 0.8674 (t-100) cc_final: 0.8450 (t-100)
REVERT: A  506 MET cc_start: 0.9058 (mmt) cc_final: 0.8691 (mmt)
REVERT: A  625 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7664 (tpp-160)
REVERT: A  641 ASN cc_start: 0.8816 (t0) cc_final: 0.8439 (t0)
REVERT: A  694 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8363 (p)
REVERT: A  696 MET cc_start: 0.9313 (ptp) cc_final: 0.8779 (pmm)
REVERT: A  717 LEU cc_start: 0.9013 (pt) cc_final: 0.8720 (mm)
REVERT: A  730 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8478 (pp20)
REVERT: A  735 ASN cc_start: 0.8743 (p0) cc_final: 0.8504 (p0)
REVERT: A  774 ASP cc_start: 0.9289 (m-30) cc_final: 0.8937 (p0)
REVERT: A  793 ARG cc_start: 0.9142 (mtt180) cc_final: 0.8662 (mtt180)
REVERT: A  851 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8223 (mt)
  outliers start: 33
  outliers final: 27
  residues processed: 119
  average time/residue: 0.0998
  time to fit residues: 15.6979
Evaluate side-chains
  127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   overall best weight:    1.3586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.081866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.066854 restraints weight = 32939.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.069171 restraints weight = 17454.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.070689 restraints weight = 11013.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.071808 restraints weight = 7876.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.072585 restraints weight = 6084.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7434  Z= 0.152
  Angle     :  0.700  11.338  10191  Z= 0.358
  Chirality :  0.041   0.189   1134
  Planarity :  0.004   0.054   1181
  Dihedral  : 17.195 177.897   1497
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 22.06 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.31), residues: 769
  helix:  1.16 (0.29), residues: 330
  sheet: -0.40 (0.49), residues: 110
  loop : -1.53 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 326 
 TYR   0.021   0.002   TYR A 308 
 PHE   0.026   0.002   PHE A 202 
 TRP   0.015   0.001   TRP A 741 
 HIS   0.011   0.001   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 ( 7434)
  covalent geometry    : angle       0.69997 /  0.36 (10191)
  hydrogen bonds       : bond        0.03946 /  2.76 (  358)
  hydrogen bonds       : angle       4.49565 /  3.29 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7549 (mmt90)
REVERT: A   64 PHE cc_start: 0.8642 (m-80) cc_final: 0.8375 (m-80)
REVERT: A  328 TRP cc_start: 0.9197 (t60) cc_final: 0.8913 (t60)
REVERT: A  391 TRP cc_start: 0.8676 (t-100) cc_final: 0.8451 (t-100)
REVERT: A  506 MET cc_start: 0.9034 (mmt) cc_final: 0.8687 (mmt)
REVERT: A  641 ASN cc_start: 0.8827 (t0) cc_final: 0.8430 (t0)
REVERT: A  672 MET cc_start: 0.7599 (tpp) cc_final: 0.7336 (tpp)
REVERT: A  694 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8444 (p)
REVERT: A  696 MET cc_start: 0.9307 (ptp) cc_final: 0.8788 (pmm)
REVERT: A  730 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8456 (pp20)
REVERT: A  735 ASN cc_start: 0.8677 (p0) cc_final: 0.8437 (p0)
REVERT: A  774 ASP cc_start: 0.9277 (m-30) cc_final: 0.8926 (p0)
REVERT: A  793 ARG cc_start: 0.9134 (mtt180) cc_final: 0.8885 (mtp180)
REVERT: A  851 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8214 (mt)
  outliers start: 32
  outliers final: 25
  residues processed: 125
  average time/residue: 0.0981
  time to fit residues: 16.2201
Evaluate side-chains
  132 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue  898 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 49 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 496 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 = 0.3783 r_free = 0.3783 target = 0.081792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066670 restraints weight = 32701.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.068984 restraints weight = 17294.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.070541 restraints weight = 10975.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.071674 restraints weight = 7836.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.072557 restraints weight = 6054.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.5286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7434  Z= 0.156
  Angle     :  0.708  12.256  10191  Z= 0.363
  Chirality :  0.042   0.177   1134
  Planarity :  0.005   0.057   1181
  Dihedral  : 17.199 178.089   1497
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 23.09 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.31), residues: 769
  helix:  1.08 (0.29), residues: 336
  sheet: -0.44 (0.49), residues: 110
  loop : -1.57 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 615 
 TYR   0.019   0.002   TYR A 308 
 PHE   0.021   0.002   PHE A 202 
 TRP   0.013   0.001   TRP A 229 
 HIS   0.011   0.001   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 7434)
  covalent geometry    : angle       0.70828 /  0.36 (10191)
  hydrogen bonds       : bond        0.03952 /  2.77 (  358)
  hydrogen bonds       : angle       4.51179 /  3.31 ( 1008)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7674 (ttm170)
REVERT: A   64 PHE cc_start: 0.8719 (m-80) cc_final: 0.8362 (m-80)
REVERT: A  328 TRP cc_start: 0.9193 (t60) cc_final: 0.8910 (t60)
REVERT: A  391 TRP cc_start: 0.8675 (t-100) cc_final: 0.8453 (t-100)
REVERT: A  506 MET cc_start: 0.8998 (mmt) cc_final: 0.8653 (mmt)
REVERT: A  641 ASN cc_start: 0.8819 (t0) cc_final: 0.8423 (t0)
REVERT: A  672 MET cc_start: 0.7661 (tpp) cc_final: 0.7387 (tpp)
REVERT: A  694 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8473 (p)
REVERT: A  696 MET cc_start: 0.9256 (ptp) cc_final: 0.8764 (pmm)
REVERT: A  730 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8452 (pp20)
REVERT: A  735 ASN cc_start: 0.8633 (p0) cc_final: 0.8396 (p0)
REVERT: A  774 ASP cc_start: 0.9256 (m-30) cc_final: 0.8905 (p0)
REVERT: A  793 ARG cc_start: 0.9123 (mtt180) cc_final: 0.8859 (mtp180)
REVERT: A  851 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8197 (mt)
  outliers start: 28
  outliers final: 25
  residues processed: 119
  average time/residue: 0.1027
  time to fit residues: 16.1297
Evaluate side-chains
  130 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    1.2386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.081974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.066731 restraints weight = 32781.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.069129 restraints weight = 17426.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.070664 restraints weight = 10970.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.071807 restraints weight = 7852.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.072629 restraints weight = 6093.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.5421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7434  Z= 0.148
  Angle     :  0.694  12.207  10191  Z= 0.355
  Chirality :  0.041   0.176   1134
  Planarity :  0.005   0.057   1181
  Dihedral  : 17.177 178.239   1497
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.09 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.31), residues: 769
  helix:  1.18 (0.29), residues: 336
  sheet: -0.62 (0.47), residues: 117
  loop : -1.56 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 615 
 TYR   0.019   0.002   TYR A 417 
 PHE   0.019   0.002   PHE A 202 
 TRP   0.014   0.001   TRP A 229 
 HIS   0.011   0.001   HIS A 747 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 ( 7434)
  covalent geometry    : angle       0.69430 /  0.35 (10191)
  hydrogen bonds       : bond        0.03857 /  2.70 (  358)
  hydrogen bonds       : angle       4.45086 /  3.25 ( 1008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1461.30 seconds
wall clock time: 25 minutes 59.20 seconds (1559.20 seconds total)