Starting phenix.real_space_refine
on Wed Feb  4 18:52:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hco_52050/02_2026/9hco_52050_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hco_52050/02_2026/9hco_52050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hco_52050/02_2026/9hco_52050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hco_52050/02_2026/9hco_52050.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hco_52050/02_2026/9hco_52050_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hco_52050/02_2026/9hco_52050_trim.cif"
  }
  resolution = 2.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
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: 7
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Cl      1      4.86       5
     Na      2      4.78       5
     C    4014      2.51       5
     N     967      2.21       5
     O    1089      1.98       5
     H    6012      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12119
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 8633
          Classifications: {'peptide': 541}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
    Chain: "H"
      Number of atoms: 1792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 1792
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 1624
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 67
          Unusual residues: {' CL': 1, ' NA': 2, 'YG7': 1}
          Classifications: {'undetermined': 4, 'water': 11}
          Link IDs: {None: 14}
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
  Time building chain proxies: 1.94, per 1000 atoms: 0.16
  Number of scatterers: 12119
  At special positions: 0
  Unit cell: (73.216, 74.048, 119.808, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      34     16.00
     Na      2     11.00
     O    1089      8.00
     N     967      7.00
     C    4014      6.00
     H    6012      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " distance=2.03

  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: 1.04
  Conformation dependent library (CDL) restraints added in 396.3 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1402

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      58.5% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.624A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 112
      removed outlier: 3.808A  pdb=" N   VAL A 102 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 117 through 144
      removed outlier: 4.733A  pdb=" N   ILE A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      Proline residue:  A 131  - end of helix
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 3.984A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.218A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.926A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 271
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.543A  pdb=" N   SER A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 302
    Processing helix  chain 'A' and resid 304 through 314
      removed outlier: 3.675A  pdb=" N   GLY A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.258A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 349
    Processing helix  chain 'A' and resid 356 through 391
      removed outlier: 3.784A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 417
      removed outlier: 3.507A  pdb=" N   ASN A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 454
      removed outlier: 4.183A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 4.404A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.826A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 534 through 543
    Processing helix  chain 'A' and resid 543 through 559
      removed outlier: 3.526A  pdb=" N   MET A 558 " --> pdb=" O   CYS A 554 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 587
    Processing helix  chain 'A' and resid 588 through 600
    Processing helix  chain 'A' and resid 603 through 613
    Processing helix  chain 'H' and resid 47 through 51
    Processing helix  chain 'H' and resid 106 through 110
      removed outlier: 3.763A  pdb=" N   SER H 110 " --> pdb=" O   SER H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 120 through 124
    Processing helix  chain 'L' and resid 103 through 107
      removed outlier: 3.544A  pdb=" N   ASP L 106 " --> pdb=" O   GLU L 103 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   THR L 107 " --> pdb=" O   GLU L 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 103 through 107'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 25
    Processing sheet with id=AA2, first strand: chain 'H' and resid 29 through 30
      removed outlier: 6.583A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 137 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP H  55 " --> pdb=" O   ILE H  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 29 through 30
      removed outlier: 6.583A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 137 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TYR H 129 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 24 through 25
      removed outlier: 3.515A  pdb=" N   ILE L  41 " --> pdb=" O   LEU L  97 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR L  94 " --> pdb=" O   SER L  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 32
      removed outlier: 5.839A  pdb=" N   LEU L  31 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   TYR L  73 " --> pdb=" O   LEU L  57 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51

    345 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.81

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        0.84 -     1.90: 12287
        1.90 -     2.96: 0
        2.96 -     4.02: 0
        4.02 -     5.08: 0
        5.08 -     6.14: 1
  Warning: very large bond lengths.
  Bond restraints: 12288
  Sorted by residual:
  bond pdb=" CH2 TRP A 103 "
       pdb=" HH2 TRP A 103 "
    ideal  model  delta    sigma   weight residual
    0.930  6.141 -5.211 2.00e-02 2.50e+03 6.79e+04
  bond pdb=" O   HOH A 801 "
       pdb=" H2  HOH A 801 "
    ideal  model  delta    sigma   weight residual
    0.850  1.338 -0.488 2.00e-02 2.50e+03 5.96e+02
  bond pdb=" C15 YG7 A 701 "
       pdb=" C18 YG7 A 701 "
    ideal  model  delta    sigma   weight residual
    1.391  1.599 -0.208 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" C23 YG7 A 701 "
       pdb=" O01 YG7 A 701 "
    ideal  model  delta    sigma   weight residual
    1.351  1.552 -0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" C32 YG7 A 701 "
       pdb=" N06 YG7 A 701 "
    ideal  model  delta    sigma   weight residual
    1.340  1.526 -0.186 2.00e-02 2.50e+03 8.70e+01
  ... (remaining 12283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.14: 22084
       21.14 -    42.28: 0
       42.28 -    63.42: 0
       63.42 -    84.56: 0
       84.56 -   105.70: 1
  Bond angle restraints: 22085
  Sorted by residual:
  angle pdb=" CZ2 TRP A 103 "
        pdb=" CH2 TRP A 103 "
        pdb=" HH2 TRP A 103 "
      ideal   model   delta    sigma   weight residual
     119.25   13.55  105.70 3.00e+00 1.11e-01 1.24e+03
  angle pdb=" N   LEU A 248 "
        pdb=" CA  LEU A 248 "
        pdb=" C   LEU A 248 "
      ideal   model   delta    sigma   weight residual
     110.70  101.80    8.90 1.55e+00 4.16e-01 3.29e+01
  angle pdb=" C27 YG7 A 701 "
        pdb=" C30 YG7 A 701 "
        pdb=" C31 YG7 A 701 "
      ideal   model   delta    sigma   weight residual
     121.65  137.02  -15.37 3.00e+00 1.11e-01 2.62e+01
  angle pdb=" C21 YG7 A 701 "
        pdb=" C26 YG7 A 701 "
        pdb=" C29 YG7 A 701 "
      ideal   model   delta    sigma   weight residual
     106.02  121.04  -15.02 3.00e+00 1.11e-01 2.51e+01
  angle pdb=" CA  LEU A 436 "
        pdb=" C   LEU A 436 "
        pdb=" O   LEU A 436 "
      ideal   model   delta    sigma   weight residual
     120.55  115.35    5.20 1.06e+00 8.90e-01 2.40e+01
  ... (remaining 22080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.89: 5619
       35.89 -    71.78: 191
       71.78 -   107.67: 23
      107.67 -   143.56: 2
      143.56 -   179.45: 2
  Dihedral angle restraints: 5837
    sinusoidal: 3026
      harmonic: 2811
  Sorted by residual:
  dihedral pdb=" CE3 TRP A 103 "
           pdb=" CZ3 TRP A 103 "
           pdb=" CH2 TRP A 103 "
           pdb=" HH2 TRP A 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   16.20  163.80     0      5.00e+00 4.00e-02 1.07e+03
  dihedral pdb=" N   LEU A 248 "
           pdb=" C   LEU A 248 "
           pdb=" CA  LEU A 248 "
           pdb=" CB  LEU A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.03   11.77     0      2.50e+00 1.60e-01 2.22e+01
  dihedral pdb=" C13 YG7 A 701 "
           pdb=" C14 YG7 A 701 "
           pdb=" C16 YG7 A 701 "
           pdb=" C17 YG7 A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     297.39  117.94  179.45     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 5834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 843
       0.071 -    0.142: 84
       0.142 -    0.213: 6
       0.213 -    0.284: 0
       0.284 -    0.354: 1
  Chirality restraints: 934
  Sorted by residual:
  chirality pdb=" CA  LEU A 248 "
            pdb=" N   LEU A 248 "
            pdb=" C   LEU A 248 "
            pdb=" CB  LEU A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.14e+00
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CA  ILE A 251 "
            pdb=" N   ILE A 251 "
            pdb=" C   ILE A 251 "
            pdb=" CB  ILE A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.85e-01
  ... (remaining 931 not shown)

  Planarity restraints: 1785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 246 "   -0.062 2.00e-02 2.50e+03   4.40e-01 2.90e+03
        pdb=" CD  GLN A 246 "    0.006 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 246 "    0.060 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 246 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN A 246 "   -0.761 2.00e-02 2.50e+03
        pdb="HE22 GLN A 246 "    0.757 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 111 "    0.068 2.00e-02 2.50e+03   4.39e-01 2.89e+03
        pdb=" CD  GLN A 111 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 111 "   -0.066 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 111 "    0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN A 111 "   -0.753 2.00e-02 2.50e+03
        pdb="HE22 GLN A 111 "    0.762 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 112 "   -0.116 2.00e-02 2.50e+03   4.34e-01 2.83e+03
        pdb=" CG  ASN A 112 "    0.013 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 112 "    0.113 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 112 "   -0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN A 112 "    0.739 2.00e-02 2.50e+03
        pdb="HD22 ASN A 112 "   -0.748 2.00e-02 2.50e+03
  ... (remaining 1782 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.40: 5247
        2.40 -     2.95: 28158
        2.95 -     3.50: 33688
        3.50 -     4.05: 45204
        4.05 -     4.60: 66981
  Nonbonded interactions: 179278
  Sorted by model distance:
  nonbonded pdb=" HD2 TYR A 570 "
            pdb=" HG  SER A 574 "
     model   vdw
     1.853 2.100
  nonbonded pdb=" HH  TYR A 350 "
            pdb=" HG1 THR A 448 "
     model   vdw
     1.865 2.100
  nonbonded pdb=" HG  SER H 118 "
            pdb=" HZ3 TRP L 120 "
     model   vdw
     1.879 2.100
  nonbonded pdb=" HZ3 LYS A  85 "
            pdb="HD22 ASN A 355 "
     model   vdw
     1.890 2.100
  nonbonded pdb=" H   GLN H  25 "
            pdb="HE22 GLN H 132 "
     model   vdw
     1.895 2.100
  ... (remaining 179273 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 individual isotropic
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:             1.980
  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:             0.100
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.320
  Find NCS groups from input model:        0.040
  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:7.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
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      :  0.009   0.208   6279  Z= 0.491
  Angle     :  0.866  15.368   8551  Z= 0.492
  Chirality :  0.044   0.354    934
  Planarity :  0.004   0.048   1051
  Dihedral  : 18.150 179.451   2164
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 20.78 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.31), residues: 763
  helix:  0.53 (0.25), residues: 378
  sheet: -1.07 (0.49), residues: 116
  loop : -1.43 (0.41), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  38 
 TYR   0.016   0.001   TYR A 592 
 PHE   0.019   0.001   PHE A 287 
 TRP   0.024   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00900 ( 6276)
  covalent geometry    : angle       0.86659 ( 8545)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.67416 (    6)
  hydrogen bonds       : bond        0.17876 (  343)
  hydrogen bonds       : angle       7.76816 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7783 (tp)
REVERT: A  127 PHE cc_start: 0.7990 (m-10) cc_final: 0.7674 (m-80)
REVERT: A  358 TYR cc_start: 0.8275 (t80) cc_final: 0.7960 (t80)
REVERT: A  493 GLU cc_start: 0.8443 (tt0) cc_final: 0.7824 (tt0)
REVERT: A  494 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6850 (mp0)
REVERT: A  551 PHE cc_start: 0.7293 (m-10) cc_final: 0.6894 (t80)
REVERT: A  579 TYR cc_start: 0.7508 (m-80) cc_final: 0.6690 (m-80)
REVERT: H   65 GLU cc_start: 0.8244 (tt0) cc_final: 0.7560 (tm-30)
REVERT: L  102 MET cc_start: 0.6933 (ttm) cc_final: 0.6660 (mmt)
  outliers start: 8
  outliers final: 4
  residues processed: 97
  average time/residue: 0.8145
  time to fit residues: 84.8294
Evaluate side-chains
  87 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 GLU
Chi-restraints excluded: chain H residue  115 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.140828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121717 restraints weight = 20387.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.96
r_work: 0.3337 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.0856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6279  Z= 0.170
  Angle     :  0.550   5.204   8551  Z= 0.301
  Chirality :  0.040   0.145    934
  Planarity :  0.004   0.066   1051
  Dihedral  : 12.262 163.938    858
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.53 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.31), residues: 763
  helix:  0.88 (0.26), residues: 370
  sheet: -0.76 (0.50), residues: 117
  loop : -1.40 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 461 
 TYR   0.015   0.001   TYR A 592 
 PHE   0.012   0.001   PHE A 105 
 TRP   0.026   0.001   TRP A 103 
 HIS   0.003   0.001   HIS L 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6276)
  covalent geometry    : angle       0.55022 ( 8545)
  SS BOND              : bond        0.00272 (    3)
  SS BOND              : angle       0.73497 (    6)
  hydrogen bonds       : bond        0.05247 (  343)
  hydrogen bonds       : angle       5.65068 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7850 (m-10) cc_final: 0.7543 (m-80)
REVERT: A  243 LYS cc_start: 0.8404 (pttm) cc_final: 0.8154 (pmtt)
REVERT: A  275 LYS cc_start: 0.7704 (pttp) cc_final: 0.7025 (mptm)
REVERT: A  319 LYS cc_start: 0.7291 (mttt) cc_final: 0.7013 (mtpt)
REVERT: A  358 TYR cc_start: 0.8242 (t80) cc_final: 0.7921 (t80)
REVERT: A  391 ASN cc_start: 0.7775 (t0) cc_final: 0.7567 (t0)
REVERT: A  438 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (m)
REVERT: A  493 GLU cc_start: 0.8266 (tt0) cc_final: 0.7785 (tt0)
REVERT: A  579 TYR cc_start: 0.7454 (m-80) cc_final: 0.6596 (m-80)
REVERT: A  611 SER cc_start: 0.8802 (m) cc_final: 0.8494 (p)
REVERT: L   38 ARG cc_start: 0.7598 (ptm160) cc_final: 0.7364 (ptm160)
  outliers start: 15
  outliers final: 7
  residues processed: 95
  average time/residue: 0.9907
  time to fit residues: 99.8768
Evaluate side-chains
  91 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain L residue   48 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.139216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120246 restraints weight = 20484.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.93
r_work: 0.3325 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6279  Z= 0.167
  Angle     :  0.536   4.977   8551  Z= 0.291
  Chirality :  0.040   0.144    934
  Planarity :  0.004   0.066   1051
  Dihedral  : 11.830 166.358    849
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.38 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.30), residues: 763
  helix:  0.89 (0.26), residues: 378
  sheet: -0.68 (0.50), residues: 117
  loop : -1.55 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 461 
 TYR   0.015   0.001   TYR A 592 
 PHE   0.013   0.001   PHE A 105 
 TRP   0.020   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6276)
  covalent geometry    : angle       0.53586 ( 8545)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.57503 (    6)
  hydrogen bonds       : bond        0.04862 (  343)
  hydrogen bonds       : angle       5.29886 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7913 (m-10) cc_final: 0.7610 (m-80)
REVERT: A  243 LYS cc_start: 0.8417 (pttm) cc_final: 0.8180 (pmtt)
REVERT: A  275 LYS cc_start: 0.7746 (pttp) cc_final: 0.7050 (mptm)
REVERT: A  358 TYR cc_start: 0.8276 (t80) cc_final: 0.7930 (t80)
REVERT: A  391 ASN cc_start: 0.7851 (t0) cc_final: 0.7539 (t0)
REVERT: A  438 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8565 (m)
REVERT: A  493 GLU cc_start: 0.8286 (tt0) cc_final: 0.7822 (tt0)
REVERT: A  579 TYR cc_start: 0.7558 (m-80) cc_final: 0.6782 (m-80)
REVERT: H   42 LYS cc_start: 0.7759 (tttp) cc_final: 0.7211 (mmmt)
REVERT: L  106 ASP cc_start: 0.8016 (p0) cc_final: 0.7814 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 101
  average time/residue: 0.9347
  time to fit residues: 100.4118
Evaluate side-chains
  97 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   48 SER
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0970
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.140104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.121238 restraints weight = 20250.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.92
r_work: 0.3334 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6279  Z= 0.131
  Angle     :  0.508   5.145   8551  Z= 0.276
  Chirality :  0.039   0.141    934
  Planarity :  0.004   0.059   1051
  Dihedral  : 11.737 160.377    849
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.38 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.31), residues: 763
  helix:  1.06 (0.26), residues: 377
  sheet: -0.53 (0.50), residues: 116
  loop : -1.63 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.014   0.001   TYR A 592 
 PHE   0.010   0.001   PHE A 105 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6276)
  covalent geometry    : angle       0.50777 ( 8545)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       0.56539 (    6)
  hydrogen bonds       : bond        0.04483 (  343)
  hydrogen bonds       : angle       5.11858 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7975 (m-80) cc_final: 0.7659 (m-80)
REVERT: A  243 LYS cc_start: 0.8395 (pttm) cc_final: 0.8155 (pmtt)
REVERT: A  358 TYR cc_start: 0.8282 (t80) cc_final: 0.7938 (t80)
REVERT: A  391 ASN cc_start: 0.7820 (t0) cc_final: 0.7494 (t0)
REVERT: A  493 GLU cc_start: 0.8292 (tt0) cc_final: 0.7830 (tt0)
REVERT: A  579 TYR cc_start: 0.7632 (m-80) cc_final: 0.6848 (m-80)
REVERT: H   42 LYS cc_start: 0.7792 (tttp) cc_final: 0.7264 (mmmt)
  outliers start: 17
  outliers final: 11
  residues processed: 98
  average time/residue: 0.8741
  time to fit residues: 91.2690
Evaluate side-chains
  99 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   47 GLU
Chi-restraints excluded: chain L residue   48 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 61 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0270
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.121589 restraints weight = 20571.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.93
r_work: 0.3337 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6279  Z= 0.121
  Angle     :  0.498   4.977   8551  Z= 0.269
  Chirality :  0.039   0.137    934
  Planarity :  0.004   0.056   1051
  Dihedral  : 11.615 157.855    848
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.38 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.31), residues: 763
  helix:  1.18 (0.26), residues: 376
  sheet: -0.51 (0.49), residues: 116
  loop : -1.63 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.017   0.001   TYR A 110 
 PHE   0.013   0.001   PHE A 531 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6276)
  covalent geometry    : angle       0.49825 ( 8545)
  SS BOND              : bond        0.00178 (    3)
  SS BOND              : angle       0.52041 (    6)
  hydrogen bonds       : bond        0.04313 (  343)
  hydrogen bonds       : angle       4.98694 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7959 (m-80) cc_final: 0.7618 (m-80)
REVERT: A  243 LYS cc_start: 0.8414 (pttm) cc_final: 0.8175 (pmtt)
REVERT: A  358 TYR cc_start: 0.8233 (t80) cc_final: 0.7882 (t80)
REVERT: A  391 ASN cc_start: 0.7703 (t0) cc_final: 0.7351 (t0)
REVERT: A  438 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8533 (m)
REVERT: A  493 GLU cc_start: 0.8280 (tt0) cc_final: 0.7867 (tt0)
REVERT: A  579 TYR cc_start: 0.7623 (m-80) cc_final: 0.6833 (m-80)
REVERT: A  607 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7254 (mtt90)
REVERT: H   42 LYS cc_start: 0.7799 (tttp) cc_final: 0.7262 (mmmt)
  outliers start: 17
  outliers final: 10
  residues processed: 98
  average time/residue: 0.8934
  time to fit residues: 93.2882
Evaluate side-chains
  100 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   48 SER
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.139288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.120514 restraints weight = 20356.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.91
r_work: 0.3333 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6279  Z= 0.142
  Angle     :  0.506   4.925   8551  Z= 0.274
  Chirality :  0.039   0.139    934
  Planarity :  0.004   0.054   1051
  Dihedral  : 11.594 155.043    848
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.00 %
    Favored  : 77.21 %
  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 are not related in a simple way.
  whole: -0.06 (0.31), residues: 763
  helix:  1.19 (0.26), residues: 378
  sheet: -0.47 (0.49), residues: 116
  loop : -1.59 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.017   0.001   TYR A 110 
 PHE   0.012   0.001   PHE A 105 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6276)
  covalent geometry    : angle       0.50645 ( 8545)
  SS BOND              : bond        0.00239 (    3)
  SS BOND              : angle       0.53220 (    6)
  hydrogen bonds       : bond        0.04380 (  343)
  hydrogen bonds       : angle       4.91555 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7911 (m-80) cc_final: 0.7596 (m-80)
REVERT: A  358 TYR cc_start: 0.8260 (t80) cc_final: 0.7908 (t80)
REVERT: A  391 ASN cc_start: 0.7700 (t0) cc_final: 0.7336 (t0)
REVERT: A  493 GLU cc_start: 0.8254 (tt0) cc_final: 0.7835 (tt0)
REVERT: A  579 TYR cc_start: 0.7593 (m-80) cc_final: 0.6874 (m-80)
REVERT: A  607 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7280 (mtt90)
REVERT: H   42 LYS cc_start: 0.7833 (tttp) cc_final: 0.7245 (mmmt)
  outliers start: 18
  outliers final: 14
  residues processed: 100
  average time/residue: 0.9224
  time to fit residues: 98.5231
Evaluate side-chains
  102 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   47 GLU
Chi-restraints excluded: chain L residue   48 SER
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.139215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120477 restraints weight = 20331.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.92
r_work: 0.3331 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6279  Z= 0.136
  Angle     :  0.503   4.894   8551  Z= 0.273
  Chirality :  0.039   0.137    934
  Planarity :  0.004   0.054   1051
  Dihedral  : 11.565 152.500    848
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.16 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.31), residues: 763
  helix:  1.22 (0.26), residues: 378
  sheet: -0.46 (0.49), residues: 116
  loop : -1.53 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.019   0.001   TYR A 110 
 PHE   0.013   0.001   PHE A 311 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6276)
  covalent geometry    : angle       0.50259 ( 8545)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       0.48388 (    6)
  hydrogen bonds       : bond        0.04317 (  343)
  hydrogen bonds       : angle       4.86416 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7909 (m-80) cc_final: 0.7596 (m-80)
REVERT: A  243 LYS cc_start: 0.8412 (pttm) cc_final: 0.8158 (pmtt)
REVERT: A  358 TYR cc_start: 0.8274 (t80) cc_final: 0.7908 (t80)
REVERT: A  391 ASN cc_start: 0.7688 (t0) cc_final: 0.7342 (t0)
REVERT: A  493 GLU cc_start: 0.8230 (tt0) cc_final: 0.7811 (tt0)
REVERT: A  579 TYR cc_start: 0.7617 (m-80) cc_final: 0.6908 (m-80)
REVERT: H   42 LYS cc_start: 0.7848 (tttp) cc_final: 0.7257 (mmmt)
  outliers start: 19
  outliers final: 13
  residues processed: 98
  average time/residue: 0.9474
  time to fit residues: 99.0913
Evaluate side-chains
  97 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain H residue   54 ASN
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   47 GLU
Chi-restraints excluded: chain L residue   48 SER
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  102 MET
Chi-restraints excluded: chain L residue  107 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0980
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 69 optimal weight:    0.1980
   chunk 62 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.140958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.122257 restraints weight = 20371.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 1.91
r_work: 0.3355 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.099   6279  Z= 0.116
  Angle     :  0.494   4.936   8551  Z= 0.268
  Chirality :  0.038   0.136    934
  Planarity :  0.004   0.054   1051
  Dihedral  : 11.474 148.050    848
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 20.78 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.31), residues: 763
  helix:  1.31 (0.26), residues: 377
  sheet: -0.40 (0.50), residues: 115
  loop : -1.47 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 152 
 TYR   0.021   0.001   TYR A 110 
 PHE   0.011   0.001   PHE A 311 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6276)
  covalent geometry    : angle       0.49446 ( 8545)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.51043 (    6)
  hydrogen bonds       : bond        0.04096 (  343)
  hydrogen bonds       : angle       4.76716 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7888 (m-80) cc_final: 0.7462 (m-80)
REVERT: A  243 LYS cc_start: 0.8433 (pttm) cc_final: 0.8149 (pmtt)
REVERT: A  358 TYR cc_start: 0.8244 (t80) cc_final: 0.7884 (t80)
REVERT: A  391 ASN cc_start: 0.7665 (t0) cc_final: 0.7303 (t0)
REVERT: A  493 GLU cc_start: 0.8158 (tt0) cc_final: 0.7777 (pt0)
REVERT: A  579 TYR cc_start: 0.7623 (m-80) cc_final: 0.6897 (m-80)
REVERT: H   42 LYS cc_start: 0.7834 (tttp) cc_final: 0.7592 (tttm)
  outliers start: 15
  outliers final: 11
  residues processed: 99
  average time/residue: 0.7727
  time to fit residues: 81.7962
Evaluate side-chains
  98 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain H residue   54 ASN
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.137827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118882 restraints weight = 20410.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.96
r_work: 0.3309 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   6279  Z= 0.163
  Angle     :  0.519   4.943   8551  Z= 0.282
  Chirality :  0.040   0.140    934
  Planarity :  0.004   0.053   1051
  Dihedral  : 11.507 148.135    848
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.24 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.30), residues: 763
  helix:  1.12 (0.26), residues: 384
  sheet: -0.36 (0.50), residues: 115
  loop : -1.58 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 607 
 TYR   0.020   0.002   TYR A 110 
 PHE   0.013   0.001   PHE A 105 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6276)
  covalent geometry    : angle       0.51865 ( 8545)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       0.48337 (    6)
  hydrogen bonds       : bond        0.04412 (  343)
  hydrogen bonds       : angle       4.82354 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7835 (m-80) cc_final: 0.7524 (m-80)
REVERT: A  391 ASN cc_start: 0.7629 (t0) cc_final: 0.7270 (t0)
REVERT: A  493 GLU cc_start: 0.8198 (tt0) cc_final: 0.7772 (tt0)
REVERT: A  579 TYR cc_start: 0.7529 (m-80) cc_final: 0.6771 (m-80)
REVERT: H   42 LYS cc_start: 0.7817 (tttp) cc_final: 0.7573 (tttm)
  outliers start: 15
  outliers final: 12
  residues processed: 101
  average time/residue: 0.7952
  time to fit residues: 86.0395
Evaluate side-chains
  98 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain H residue   54 ASN
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
H  22 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.137355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118324 restraints weight = 20599.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.97
r_work: 0.3301 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6279  Z= 0.163
  Angle     :  0.529   6.522   8551  Z= 0.287
  Chirality :  0.040   0.139    934
  Planarity :  0.004   0.057   1051
  Dihedral  : 11.570 147.941    848
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.93 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.30), residues: 763
  helix:  1.07 (0.26), residues: 384
  sheet: -0.32 (0.50), residues: 115
  loop : -1.59 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 607 
 TYR   0.021   0.002   TYR A 107 
 PHE   0.013   0.001   PHE A 105 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6276)
  covalent geometry    : angle       0.52931 ( 8545)
  SS BOND              : bond        0.00229 (    3)
  SS BOND              : angle       0.53586 (    6)
  hydrogen bonds       : bond        0.04495 (  343)
  hydrogen bonds       : angle       4.84736 (  951)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7847 (m-80) cc_final: 0.7553 (m-80)
REVERT: A  391 ASN cc_start: 0.7663 (t0) cc_final: 0.7300 (t0)
REVERT: A  438 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8157 (m)
REVERT: A  493 GLU cc_start: 0.8213 (tt0) cc_final: 0.7778 (tt0)
REVERT: A  579 TYR cc_start: 0.7529 (m-80) cc_final: 0.6765 (m-80)
REVERT: H   42 LYS cc_start: 0.7870 (tttp) cc_final: 0.7634 (tttm)
REVERT: H   82 LYS cc_start: 0.8112 (mppt) cc_final: 0.7738 (mttp)
  outliers start: 19
  outliers final: 16
  residues processed: 100
  average time/residue: 0.8721
  time to fit residues: 93.3562
Evaluate side-chains
  103 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain H residue   54 ASN
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue  115 CYS
Chi-restraints excluded: chain L residue   38 ARG
Chi-restraints excluded: chain L residue   47 GLU
Chi-restraints excluded: chain L residue   48 SER
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.138891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120030 restraints weight = 20545.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.96
r_work: 0.3323 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.133   6279  Z= 0.131
  Angle     :  0.513   5.261   8551  Z= 0.278
  Chirality :  0.039   0.136    934
  Planarity :  0.004   0.054   1051
  Dihedral  : 11.491 144.461    848
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.71 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.30), residues: 763
  helix:  1.16 (0.26), residues: 383
  sheet: -0.33 (0.50), residues: 115
  loop : -1.57 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 607 
 TYR   0.021   0.001   TYR A 110 
 PHE   0.011   0.001   PHE A 311 
 TRP   0.013   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6276)
  covalent geometry    : angle       0.51313 ( 8545)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       0.56311 (    6)
  hydrogen bonds       : bond        0.04240 (  343)
  hydrogen bonds       : angle       4.77232 (  951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3953.12 seconds
wall clock time: 67 minutes 41.31 seconds (4061.31 seconds total)