Starting phenix.real_space_refine
on Fri Aug 22 19:24:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zqb_60381/08_2025/8zqb_60381.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zqb_60381/08_2025/8zqb_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_2025/8zqb_60381.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2025/8zqb_60381.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2025/8zqb_60381.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zqb_60381/08_2025/8zqb_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-2.0-5787/lib/python3.9/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: 2.06, per 1000 atoms: 0.29
  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: 0.70
  Conformation dependent library (CDL) restraints added in 390.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 1.12
  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: 1.34

  Time building geometry restraints manager: 0.91 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=" 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
  bond pdb=" C   VAL A 743 "
       pdb=" O   VAL A 743 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.01e-02 9.80e+03 9.46e-01
  ... (remaining 7429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 9819
        1.40 -     2.81: 291
        2.81 -     4.21: 66
        4.21 -     5.62: 13
        5.62 -     7.02: 2
  Bond angle restraints: 10191
  Sorted by residual:
  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=" N   SER A   6 "
        pdb=" CA  SER A   6 "
        pdb=" C   SER A   6 "
      ideal   model   delta    sigma   weight residual
     108.55  113.87   -5.32 1.62e+00 3.81e-01 1.08e+01
  angle pdb=" N   ILE A 481 "
        pdb=" CA  ILE A 481 "
        pdb=" C   ILE A 481 "
      ideal   model   delta    sigma   weight residual
     111.62  109.08    2.54 7.90e-01 1.60e+00 1.04e+01
  angle pdb=" CB  LYS A  94 "
        pdb=" CG  LYS A  94 "
        pdb=" CD  LYS A  94 "
      ideal   model   delta    sigma   weight residual
     111.30  118.32   -7.02 2.30e+00 1.89e-01 9.32e+00
  ... (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: 791
       0.033 -    0.065: 249
       0.065 -    0.098: 60
       0.098 -    0.131: 31
       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:             5.120
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.870
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
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= 0.152
  Angle     :  0.608   7.021  10191  Z= 0.341
  Chirality :  0.037   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 aren 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
  covalent geometry    : bond        0.00304 ( 7434)
  covalent geometry    : angle       0.60776 (10191)
  hydrogen bonds       : bond        0.16657 (  358)
  hydrogen bonds       : angle       6.72235 ( 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  : 0.287 
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: 0.1368
  time to fit residues: 31.2706
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  : 0.295 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 641 ASN
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 = 0.085759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.070906 restraints weight = 31568.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.073376 restraints weight = 16321.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.075015 restraints weight = 10222.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.076162 restraints weight = 7174.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.076916 restraints weight = 5433.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7434  Z= 0.163
  Angle     :  0.750  11.682  10191  Z= 0.383
  Chirality :  0.043   0.185   1134
  Planarity :  0.005   0.065   1181
  Dihedral  : 17.326 176.988   1501
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.44 %
    Favored  : 75.88 %
  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 aren not related in a simple way.
  whole: -0.58 (0.31), residues: 769
  helix:  0.97 (0.29), residues: 331
  sheet: -0.19 (0.49), residues: 113
  loop : -1.94 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 607 
 TYR   0.034   0.002   TYR A 308 
 PHE   0.025   0.002   PHE A 571 
 TRP   0.033   0.003   TRP A 640 
 HIS   0.009   0.002   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7434)
  covalent geometry    : angle       0.74991 (10191)
  hydrogen bonds       : bond        0.04716 (  358)
  hydrogen bonds       : angle       4.97802 ( 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
  148 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.277 
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    7 SER cc_start: 0.8791 (t) cc_final: 0.8534 (m)
REVERT: A   64 PHE cc_start: 0.8215 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  343 ASP cc_start: 0.8822 (m-30) cc_final: 0.8270 (p0)
REVERT: A  391 TRP cc_start: 0.8481 (t-100) cc_final: 0.8241 (t-100)
REVERT: A  438 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8565 (p0)
REVERT: A  548 LYS cc_start: 0.8901 (tttt) cc_final: 0.8477 (tttm)
REVERT: A  735 ASN cc_start: 0.8916 (p0) cc_final: 0.8658 (p0)
REVERT: A  799 ARG cc_start: 0.8728 (tpt90) cc_final: 0.8493 (mmm160)
REVERT: A  869 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8690 (tp30)
  outliers start: 25
  outliers final: 11
  residues processed: 136
  average time/residue: 0.1110
  time to fit residues: 19.2314
Evaluate side-chains
  114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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  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  581 GLU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  730 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:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 48 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 689 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.085518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.070500 restraints weight = 31797.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.072979 restraints weight = 16699.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.074632 restraints weight = 10429.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.075747 restraints weight = 7380.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.076493 restraints weight = 5665.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7434  Z= 0.138
  Angle     :  0.680   9.379  10191  Z= 0.348
  Chirality :  0.041   0.188   1134
  Planarity :  0.005   0.054   1181
  Dihedral  : 17.216 177.128   1497
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 20.00 %
    Favored  : 75.59 %
  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 aren not related in a simple way.
  whole: -0.29 (0.31), residues: 769
  helix:  1.17 (0.29), residues: 327
  sheet: -0.28 (0.46), residues: 123
  loop : -1.61 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 615 
 TYR   0.027   0.002   TYR A 308 
 PHE   0.015   0.002   PHE A  64 
 TRP   0.017   0.002   TRP A 640 
 HIS   0.011   0.001   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7434)
  covalent geometry    : angle       0.67992 (10191)
  hydrogen bonds       : bond        0.04053 (  358)
  hydrogen bonds       : angle       4.57547 ( 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
  145 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.254 
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    7 SER cc_start: 0.8759 (t) cc_final: 0.8461 (m)
REVERT: A   34 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7552 (mmt90)
REVERT: A   64 PHE cc_start: 0.8287 (m-80) cc_final: 0.7591 (m-80)
REVERT: A  229 TRP cc_start: 0.8598 (t60) cc_final: 0.8368 (t60)
REVERT: A  328 TRP cc_start: 0.9137 (t60) cc_final: 0.8857 (t60)
REVERT: A  343 ASP cc_start: 0.8765 (m-30) cc_final: 0.8276 (p0)
REVERT: A  345 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8524 (p)
REVERT: A  383 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8444 (t)
REVERT: A  391 TRP cc_start: 0.8518 (t-100) cc_final: 0.8317 (t-100)
REVERT: A  405 ILE cc_start: 0.9250 (pt) cc_final: 0.8993 (mp)
REVERT: A  426 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8850 (tt)
REVERT: A  548 LYS cc_start: 0.8889 (tttt) cc_final: 0.8373 (tttm)
REVERT: A  658 ASP cc_start: 0.6658 (m-30) cc_final: 0.6068 (t0)
REVERT: A  661 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7916 (pttm)
REVERT: A  730 GLU cc_start: 0.9054 (tt0) cc_final: 0.8559 (pp20)
REVERT: A  735 ASN cc_start: 0.8810 (p0) cc_final: 0.8542 (p0)
  outliers start: 30
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1226
  time to fit residues: 20.5163
Evaluate side-chains
  128 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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  216 LYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  426 LEU
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  501 SER
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  637 LEU
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  827 LEU
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 69 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   overall best weight:    2.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.078813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.064163 restraints weight = 34159.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.066397 restraints weight = 18045.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.067878 restraints weight = 11302.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.068948 restraints weight = 7997.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.069660 restraints weight = 6189.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7434  Z= 0.236
  Angle     :  0.737   8.803  10191  Z= 0.380
  Chirality :  0.043   0.174   1134
  Planarity :  0.005   0.035   1181
  Dihedral  : 17.233 174.684   1497
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 19.41 %
    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 aren not related in a simple way.
  whole: -0.55 (0.30), residues: 769
  helix:  0.99 (0.28), residues: 332
  sheet: -0.44 (0.45), residues: 125
  loop : -1.85 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 793 
 TYR   0.025   0.002   TYR A 542 
 PHE   0.021   0.002   PHE A 571 
 TRP   0.012   0.002   TRP A 741 
 HIS   0.009   0.002   HIS A  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 7434)
  covalent geometry    : angle       0.73719 (10191)
  hydrogen bonds       : bond        0.04784 (  358)
  hydrogen bonds       : angle       4.62322 ( 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
  139 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 97
  time to evaluate  : 0.305 
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: 0.8012 (mmm-85) cc_final: 0.7642 (mmt90)
REVERT: A   64 PHE cc_start: 0.8685 (m-80) cc_final: 0.8365 (m-80)
REVERT: A  328 TRP cc_start: 0.9186 (t60) cc_final: 0.8877 (t60)
REVERT: A  345 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8048 (p)
REVERT: A  391 TRP cc_start: 0.8759 (t-100) cc_final: 0.8414 (t-100)
REVERT: A  658 ASP cc_start: 0.7135 (m-30) cc_final: 0.6343 (t0)
REVERT: A  661 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8105 (pttm)
REVERT: A  672 MET cc_start: 0.7893 (tpp) cc_final: 0.7679 (tpp)
REVERT: A  730 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8551 (pp20)
REVERT: A  735 ASN cc_start: 0.8834 (p0) cc_final: 0.8563 (p0)
REVERT: A  793 ARG cc_start: 0.9211 (mtt180) cc_final: 0.8727 (mtt180)
  outliers start: 42
  outliers final: 27
  residues processed: 124
  average time/residue: 0.1189
  time to fit residues: 18.7641
Evaluate side-chains
  121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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   37 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  269 LEU
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  501 SER
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  661 LYS
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 48 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.080395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.065606 restraints weight = 33651.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.067891 restraints weight = 17897.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.069367 restraints weight = 11294.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.070402 restraints weight = 8023.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.071161 restraints weight = 6270.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7434  Z= 0.167
  Angle     :  0.679  10.556  10191  Z= 0.342
  Chirality :  0.041   0.277   1134
  Planarity :  0.004   0.032   1181
  Dihedral  : 17.276 178.511   1497
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 20.15 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.31), residues: 769
  helix:  1.09 (0.28), residues: 337
  sheet: -0.04 (0.48), residues: 115
  loop : -1.76 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 793 
 TYR   0.024   0.002   TYR A 308 
 PHE   0.014   0.002   PHE A  32 
 TRP   0.010   0.001   TRP A 229 
 HIS   0.010   0.002   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7434)
  covalent geometry    : angle       0.67857 (10191)
  hydrogen bonds       : bond        0.04025 (  358)
  hydrogen bonds       : angle       4.42605 ( 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
  138 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.327 
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  216 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8369 (mtpt)
REVERT: A  328 TRP cc_start: 0.9194 (t60) cc_final: 0.8890 (t60)
REVERT: A  391 TRP cc_start: 0.8695 (t-100) cc_final: 0.8422 (t-100)
REVERT: A  672 MET cc_start: 0.7809 (tpp) cc_final: 0.7597 (tpp)
REVERT: A  696 MET cc_start: 0.9233 (ptp) cc_final: 0.8627 (pmm)
REVERT: A  730 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8477 (pp20)
REVERT: A  735 ASN cc_start: 0.8736 (p0) cc_final: 0.8517 (p0)
  outliers start: 38
  outliers final: 26
  residues processed: 120
  average time/residue: 0.1256
  time to fit residues: 18.9327
Evaluate side-chains
  121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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   37 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  320 PHE
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  405 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  501 SER
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  661 LYS
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  908 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0670
   chunk 58 optimal weight:    0.6980
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
A 641 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.082042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.067382 restraints weight = 32471.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.069754 restraints weight = 16911.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.071298 restraints weight = 10553.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.072327 restraints weight = 7449.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.072867 restraints weight = 5742.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.5419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7434  Z= 0.130
  Angle     :  0.651   7.562  10191  Z= 0.327
  Chirality :  0.040   0.207   1134
  Planarity :  0.004   0.038   1181
  Dihedral  : 17.095 177.879   1497
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.44 %
    Favored  : 75.00 %
  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 aren not related in a simple way.
  whole: -0.04 (0.31), residues: 769
  helix:  1.40 (0.28), residues: 327
  sheet: -0.16 (0.48), residues: 117
  loop : -1.49 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 615 
 TYR   0.019   0.001   TYR A 308 
 PHE   0.015   0.001   PHE A 571 
 TRP   0.010   0.001   TRP A 720 
 HIS   0.010   0.001   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7434)
  covalent geometry    : angle       0.65082 (10191)
  hydrogen bonds       : bond        0.03688 (  358)
  hydrogen bonds       : angle       4.34478 ( 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
  139 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.278 
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   34 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7523 (mmt90)
REVERT: A  328 TRP cc_start: 0.9190 (t60) cc_final: 0.8896 (t60)
REVERT: A  391 TRP cc_start: 0.8641 (t-100) cc_final: 0.8411 (t-100)
REVERT: A  571 PHE cc_start: 0.5610 (t80) cc_final: 0.5335 (t80)
REVERT: A  641 ASN cc_start: 0.8825 (t0) cc_final: 0.8369 (t0)
REVERT: A  672 MET cc_start: 0.7746 (tpp) cc_final: 0.7488 (tpp)
REVERT: A  696 MET cc_start: 0.9201 (ptp) cc_final: 0.8615 (pmm)
REVERT: A  730 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8297 (pp20)
REVERT: A  735 ASN cc_start: 0.8585 (p0) cc_final: 0.8348 (p0)
REVERT: A  743 VAL cc_start: 0.8884 (t) cc_final: 0.8654 (p)
  outliers start: 31
  outliers final: 23
  residues processed: 122
  average time/residue: 0.1207
  time to fit residues: 18.6508
Evaluate side-chains
  122 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  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  216 LYS
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  405 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  501 SER
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
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  730 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.079599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.064739 restraints weight = 33805.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.066924 restraints weight = 18168.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.068525 restraints weight = 11691.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.069606 restraints weight = 8279.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.070364 restraints weight = 6395.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7434  Z= 0.200
  Angle     :  0.701   7.423  10191  Z= 0.355
  Chirality :  0.042   0.224   1134
  Planarity :  0.004   0.038   1181
  Dihedral  : 17.193 178.029   1497
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 21.62 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.31), residues: 769
  helix:  1.36 (0.28), residues: 327
  sheet: -0.58 (0.44), residues: 132
  loop : -1.53 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 326 
 TYR   0.018   0.002   TYR A 542 
 PHE   0.011   0.002   PHE A 571 
 TRP   0.010   0.001   TRP A 229 
 HIS   0.010   0.001   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7434)
  covalent geometry    : angle       0.70090 (10191)
  hydrogen bonds       : bond        0.04001 (  358)
  hydrogen bonds       : angle       4.46713 ( 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
  123 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.8797 (m-30) cc_final: 0.8307 (p0)
REVERT: A  391 TRP cc_start: 0.8742 (t-100) cc_final: 0.8481 (t-100)
REVERT: A  506 MET cc_start: 0.9020 (mmm) cc_final: 0.8763 (mmt)
REVERT: A  641 ASN cc_start: 0.8890 (t0) cc_final: 0.8427 (t0)
REVERT: A  672 MET cc_start: 0.7922 (tpp) cc_final: 0.7652 (tpp)
REVERT: A  730 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8456 (pp20)
REVERT: A  735 ASN cc_start: 0.8579 (p0) cc_final: 0.8364 (p0)
  outliers start: 28
  outliers final: 23
  residues processed: 111
  average time/residue: 0.1178
  time to fit residues: 16.8536
Evaluate side-chains
  114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  216 LYS
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  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  827 LEU
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.081419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.066290 restraints weight = 33653.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.068687 restraints weight = 17652.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.070259 restraints weight = 11091.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.071419 restraints weight = 7877.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.072234 restraints weight = 6052.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.5925

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= 0.141
  Angle     :  0.688   9.575  10191  Z= 0.344
  Chirality :  0.042   0.285   1134
  Planarity :  0.004   0.038   1181
  Dihedral  : 17.136 178.322   1497
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.53 %
    Favored  : 73.38 %
  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 aren not related in a simple way.
  whole:  0.04 (0.31), residues: 769
  helix:  1.47 (0.29), residues: 327
  sheet: -0.22 (0.47), residues: 122
  loop : -1.41 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 326 
 TYR   0.015   0.001   TYR A 542 
 PHE   0.036   0.002   PHE A 202 
 TRP   0.008   0.001   TRP A 720 
 HIS   0.011   0.001   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7434)
  covalent geometry    : angle       0.68771 (10191)
  hydrogen bonds       : bond        0.03737 (  358)
  hydrogen bonds       : angle       4.40618 ( 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
  119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 TRP cc_start: 0.9200 (t60) cc_final: 0.8909 (t60)
REVERT: A  343 ASP cc_start: 0.8780 (m-30) cc_final: 0.8219 (p0)
REVERT: A  426 LEU cc_start: 0.9107 (tt) cc_final: 0.8748 (pp)
REVERT: A  477 ILE cc_start: 0.9410 (mm) cc_final: 0.9137 (mp)
REVERT: A  497 ASP cc_start: 0.8035 (t0) cc_final: 0.7652 (p0)
REVERT: A  506 MET cc_start: 0.9016 (mmm) cc_final: 0.8763 (mmt)
REVERT: A  641 ASN cc_start: 0.8831 (t0) cc_final: 0.8367 (t0)
REVERT: A  672 MET cc_start: 0.7841 (tpp) cc_final: 0.7573 (tpp)
REVERT: A  696 MET cc_start: 0.9186 (ptp) cc_final: 0.8483 (pmm)
REVERT: A  730 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8266 (pp20)
REVERT: A  735 ASN cc_start: 0.8485 (p0) cc_final: 0.8259 (p0)
  outliers start: 21
  outliers final: 20
  residues processed: 107
  average time/residue: 0.1066
  time to fit residues: 14.9468
Evaluate side-chains
  113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
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  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  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.081119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.066011 restraints weight = 33068.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.068296 restraints weight = 17531.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.069893 restraints weight = 11180.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.070956 restraints weight = 7973.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.071693 restraints weight = 6198.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.6132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7434  Z= 0.145
  Angle     :  0.694  10.578  10191  Z= 0.345
  Chirality :  0.042   0.309   1134
  Planarity :  0.005   0.074   1181
  Dihedral  : 17.079 178.222   1497
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.82 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.31), residues: 769
  helix:  1.34 (0.28), residues: 338
  sheet: -0.21 (0.47), residues: 122
  loop : -1.45 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 793 
 TYR   0.014   0.001   TYR A 308 
 PHE   0.031   0.002   PHE A 202 
 TRP   0.010   0.001   TRP A 229 
 HIS   0.011   0.001   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7434)
  covalent geometry    : angle       0.69379 (10191)
  hydrogen bonds       : bond        0.03682 (  358)
  hydrogen bonds       : angle       4.38145 ( 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
  114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 TRP cc_start: 0.9219 (t60) cc_final: 0.8922 (t60)
REVERT: A  343 ASP cc_start: 0.8782 (m-30) cc_final: 0.8234 (p0)
REVERT: A  426 LEU cc_start: 0.9115 (tt) cc_final: 0.8752 (pp)
REVERT: A  477 ILE cc_start: 0.9414 (mm) cc_final: 0.9103 (mp)
REVERT: A  497 ASP cc_start: 0.8014 (t0) cc_final: 0.7652 (p0)
REVERT: A  506 MET cc_start: 0.9021 (mmm) cc_final: 0.8707 (mmp)
REVERT: A  641 ASN cc_start: 0.8812 (t0) cc_final: 0.8358 (t0)
REVERT: A  672 MET cc_start: 0.7883 (tpp) cc_final: 0.7612 (tpp)
REVERT: A  696 MET cc_start: 0.9160 (ptp) cc_final: 0.8478 (pmm)
REVERT: A  730 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8263 (pp20)
REVERT: A  735 ASN cc_start: 0.8403 (p0) cc_final: 0.8174 (p0)
  outliers start: 21
  outliers final: 20
  residues processed: 101
  average time/residue: 0.1008
  time to fit residues: 13.5675
Evaluate side-chains
  113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  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  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  682 ILE
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.078396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.063124 restraints weight = 34625.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.065474 restraints weight = 18504.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.067095 restraints weight = 11644.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.068105 restraints weight = 8236.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.068877 restraints weight = 6429.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.6357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7434  Z= 0.202
  Angle     :  0.731  10.004  10191  Z= 0.369
  Chirality :  0.042   0.301   1134
  Planarity :  0.005   0.076   1181
  Dihedral  : 17.224 178.342   1497
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.53 %
    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 aren not related in a simple way.
  whole: -0.21 (0.31), residues: 769
  helix:  1.11 (0.28), residues: 347
  sheet: -0.24 (0.44), residues: 128
  loop : -1.61 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 793 
 TYR   0.020   0.002   TYR A 542 
 PHE   0.025   0.002   PHE A 202 
 TRP   0.011   0.002   TRP A 229 
 HIS   0.011   0.002   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 7434)
  covalent geometry    : angle       0.73105 (10191)
  hydrogen bonds       : bond        0.04101 (  358)
  hydrogen bonds       : angle       4.53086 ( 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
  115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.8874 (m-30) cc_final: 0.8342 (p0)
REVERT: A  426 LEU cc_start: 0.9175 (tt) cc_final: 0.8794 (pp)
REVERT: A  477 ILE cc_start: 0.9426 (mm) cc_final: 0.9199 (mp)
REVERT: A  497 ASP cc_start: 0.7915 (t0) cc_final: 0.7590 (p0)
REVERT: A  641 ASN cc_start: 0.8929 (t0) cc_final: 0.8490 (t0)
REVERT: A  730 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8362 (pp20)
REVERT: A  735 ASN cc_start: 0.8430 (p0) cc_final: 0.8185 (p0)
  outliers start: 22
  outliers final: 18
  residues processed: 103
  average time/residue: 0.1067
  time to fit residues: 14.3034
Evaluate side-chains
  111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  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  534 ASP
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  730 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  829 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    2.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.077913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.062716 restraints weight = 34473.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.065033 restraints weight = 18113.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.066660 restraints weight = 11480.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.067682 restraints weight = 8072.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.068325 restraints weight = 6291.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.6559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7434  Z= 0.214
  Angle     :  0.755  10.819  10191  Z= 0.378
  Chirality :  0.043   0.297   1134
  Planarity :  0.005   0.080   1181
  Dihedral  : 17.240 178.863   1497
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 24.71 %
    Favored  : 72.21 %
  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 aren not related in a simple way.
  whole: -0.33 (0.30), residues: 769
  helix:  0.97 (0.28), residues: 351
  sheet: -0.22 (0.46), residues: 118
  loop : -1.66 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 775 
 TYR   0.041   0.002   TYR A 760 
 PHE   0.024   0.002   PHE A 202 
 TRP   0.016   0.002   TRP A 741 
 HIS   0.012   0.002   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 7434)
  covalent geometry    : angle       0.75513 (10191)
  hydrogen bonds       : bond        0.04114 (  358)
  hydrogen bonds       : angle       4.58168 ( 1008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1547.01 seconds
wall clock time: 27 minutes 32.42 seconds (1652.42 seconds total)