Starting phenix.real_space_refine
on Fri Jul  3 06:13:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hco_52050/07_2026/9hco_52050_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hco_52050/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hco_52050/07_2026/9hco_52050_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hco_52050/07_2026/9hco_52050_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hco_52050/07_2026/9hco_52050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hco_52050/07_2026/9hco_52050.map"
  }
  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-dev-6108/lib/python3.11/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, 64
          Ad-hoc single atom residues: {' NA': 2, ' CL': 1}
          Unusual residues: {'YG7': 1}
          Classifications: {'undetermined': 1, 'water': 11}
          Link IDs: {None: 10}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.18
  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: 0.98
  Conformation dependent library (CDL) restraints added in 193.3 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: 0.28
  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: 2.69

  Time building geometry restraints manager: 1.22 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:             1.640
  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:             0.090
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.750
  Find NCS groups from input model:        0.020
  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:6.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
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/Z
  covalent geometry    : bond        0.00900 /  0.49 ( 6276)
  covalent geometry    : angle       0.86659 /  0.49 ( 8545)
  SS BOND              : bond        0.00230 /  0.12 (    3)
  SS BOND              : angle       0.67416 /  0.31 (    6)
  hydrogen bonds       : bond        0.17876 / 11.58 (  343)
  hydrogen bonds       : angle       7.76816 /  5.53 (  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  : 0.350 
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: 0.7565
  time to fit residues: 79.2720
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  : 0.298 
-------------------------------------------------------------------------------
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...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.141054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.122249 restraints weight = 20399.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.91
r_work: 0.3344 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.0824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6279  Z= 0.166
  Angle     :  0.550   5.762   8551  Z= 0.302
  Chirality :  0.040   0.145    934
  Planarity :  0.004   0.066   1051
  Dihedral  : 12.308 166.012    858
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.69 %
    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: -0.31 (0.31), residues: 763
  helix:  0.90 (0.26), residues: 370
  sheet: -0.75 (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   0.019   0.001   TRP A 103 
 HIS   0.003   0.001   HIS L 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.17 ( 6276)
  covalent geometry    : angle       0.55006 /  0.30 ( 8545)
  SS BOND              : bond        0.00249 /  0.13 (    3)
  SS BOND              : angle       0.74874 /  0.38 (    6)
  hydrogen bonds       : bond        0.05437 /  3.48 (  343)
  hydrogen bonds       : angle       5.71988 /  4.09 (  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
  103 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7942 (m-10) cc_final: 0.7626 (m-80)
REVERT: A  243 LYS cc_start: 0.8411 (pttm) cc_final: 0.8168 (pmtt)
REVERT: A  275 LYS cc_start: 0.7716 (pttp) cc_final: 0.7081 (mptm)
REVERT: A  319 LYS cc_start: 0.7316 (mttt) cc_final: 0.7078 (mtpt)
REVERT: A  358 TYR cc_start: 0.8284 (t80) cc_final: 0.7954 (t80)
REVERT: A  438 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8593 (m)
REVERT: A  493 GLU cc_start: 0.8306 (tt0) cc_final: 0.7822 (tt0)
REVERT: A  579 TYR cc_start: 0.7558 (m-80) cc_final: 0.6708 (m-80)
REVERT: A  611 SER cc_start: 0.8820 (m) cc_final: 0.8539 (p)
REVERT: L   38 ARG cc_start: 0.7632 (ptm160) cc_final: 0.7401 (ptm160)
  outliers start: 14
  outliers final: 7
  residues processed: 94
  average time/residue: 0.7845
  time to fit residues: 78.8604
Evaluate side-chains
  90 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120687 restraints weight = 20589.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.93
r_work: 0.3333 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6279  Z= 0.156
  Angle     :  0.529   5.009   8551  Z= 0.287
  Chirality :  0.040   0.143    934
  Planarity :  0.004   0.066   1051
  Dihedral  : 11.870 166.690    849
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.22 %
    Favored  : 77.83 %
  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: -0.22 (0.31), residues: 763
  helix:  1.01 (0.26), residues: 371
  sheet: -0.66 (0.50), residues: 117
  loop : -1.47 (0.39), residues: 275

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   0.012   0.001   PHE A 105 
 TRP   0.017   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.16 ( 6276)
  covalent geometry    : angle       0.52921 /  0.29 ( 8545)
  SS BOND              : bond        0.00212 /  0.11 (    3)
  SS BOND              : angle       0.59429 /  0.28 (    6)
  hydrogen bonds       : bond        0.04781 /  3.07 (  343)
  hydrogen bonds       : angle       5.28973 /  3.80 (  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
  110 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7920 (m-10) cc_final: 0.7635 (m-80)
REVERT: A  243 LYS cc_start: 0.8422 (pttm) cc_final: 0.8185 (pmtt)
REVERT: A  275 LYS cc_start: 0.7728 (pttp) cc_final: 0.7048 (mptm)
REVERT: A  319 LYS cc_start: 0.7470 (mttt) cc_final: 0.7192 (mtpt)
REVERT: A  358 TYR cc_start: 0.8285 (t80) cc_final: 0.7938 (t80)
REVERT: A  391 ASN cc_start: 0.7861 (t0) cc_final: 0.7578 (t0)
REVERT: A  417 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7525 (tpp)
REVERT: A  438 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8476 (m)
REVERT: A  493 GLU cc_start: 0.8301 (tt0) cc_final: 0.7835 (tt0)
REVERT: A  579 TYR cc_start: 0.7580 (m-80) cc_final: 0.6824 (m-80)
REVERT: H   42 LYS cc_start: 0.7774 (tttp) cc_final: 0.7254 (mmmt)
  outliers start: 19
  outliers final: 12
  residues processed: 102
  average time/residue: 0.8104
  time to fit residues: 88.3619
Evaluate side-chains
  98 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
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  417 MET
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  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:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   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:    0.6980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.121235 restraints weight = 20342.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.91
r_work: 0.3332 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6279  Z= 0.141
  Angle     :  0.514   5.035   8551  Z= 0.280
  Chirality :  0.039   0.141    934
  Planarity :  0.004   0.059   1051
  Dihedral  : 11.816 161.022    849
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.07 %
    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: -0.18 (0.31), residues: 763
  helix:  1.08 (0.26), residues: 377
  sheet: -0.50 (0.50), residues: 116
  loop : -1.65 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.015   0.001   TYR A 110 
 PHE   0.010   0.001   PHE A 105 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 6276)
  covalent geometry    : angle       0.51409 /  0.28 ( 8545)
  SS BOND              : bond        0.00196 /  0.10 (    3)
  SS BOND              : angle       0.53964 /  0.27 (    6)
  hydrogen bonds       : bond        0.04527 /  2.91 (  343)
  hydrogen bonds       : angle       5.13461 /  3.69 (  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: 18
    poor density    : 90
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7971 (m-10) cc_final: 0.7658 (m-80)
REVERT: A  243 LYS cc_start: 0.8442 (pttm) cc_final: 0.8209 (pmtt)
REVERT: A  319 LYS cc_start: 0.7404 (mttt) cc_final: 0.7142 (mttm)
REVERT: A  358 TYR cc_start: 0.8288 (t80) cc_final: 0.7947 (t80)
REVERT: A  391 ASN cc_start: 0.7850 (t0) cc_final: 0.7509 (t0)
REVERT: A  493 GLU cc_start: 0.8320 (tt0) cc_final: 0.7846 (tt0)
REVERT: A  579 TYR cc_start: 0.7637 (m-80) cc_final: 0.6854 (m-80)
REVERT: H   42 LYS cc_start: 0.7797 (tttp) cc_final: 0.7264 (mmmt)
  outliers start: 18
  outliers final: 11
  residues processed: 98
  average time/residue: 0.7441
  time to fit residues: 78.1491
Evaluate side-chains
  96 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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  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 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:    0.9990
   chunk 32 optimal weight:    0.0270
   chunk 66 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 69 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.5238

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.140083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.121065 restraints weight = 20612.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.97
r_work: 0.3334 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6279  Z= 0.125
  Angle     :  0.501   4.948   8551  Z= 0.272
  Chirality :  0.039   0.139    934
  Planarity :  0.004   0.055   1051
  Dihedral  : 11.647 158.824    848
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.76 %
    Favored  : 78.45 %
  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: -0.12 (0.31), residues: 763
  helix:  1.14 (0.26), residues: 378
  sheet: -0.47 (0.49), residues: 116
  loop : -1.64 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.018   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/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 6276)
  covalent geometry    : angle       0.50078 /  0.27 ( 8545)
  SS BOND              : bond        0.00177 /  0.09 (    3)
  SS BOND              : angle       0.52654 /  0.27 (    6)
  hydrogen bonds       : bond        0.04340 /  2.79 (  343)
  hydrogen bonds       : angle       5.00995 /  3.60 (  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
  107 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7833 (m-80) cc_final: 0.7502 (m-80)
REVERT: A  243 LYS cc_start: 0.8393 (pttm) cc_final: 0.8152 (pmtt)
REVERT: A  358 TYR cc_start: 0.8177 (t80) cc_final: 0.7837 (t80)
REVERT: A  391 ASN cc_start: 0.7744 (t0) cc_final: 0.7389 (t0)
REVERT: A  493 GLU cc_start: 0.8236 (tt0) cc_final: 0.7773 (tt0)
REVERT: A  579 TYR cc_start: 0.7489 (m-80) cc_final: 0.6676 (m-80)
REVERT: A  607 ARG cc_start: 0.7356 (mtt90) cc_final: 0.7138 (mtt90)
REVERT: H   42 LYS cc_start: 0.7690 (tttp) cc_final: 0.7095 (mmmt)
  outliers start: 18
  outliers final: 11
  residues processed: 100
  average time/residue: 0.7523
  time to fit residues: 80.8202
Evaluate side-chains
  97 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 69 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.5980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.140093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121558 restraints weight = 20373.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.90
r_work: 0.3342 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6279  Z= 0.130
  Angle     :  0.501   4.943   8551  Z= 0.273
  Chirality :  0.039   0.138    934
  Planarity :  0.004   0.052   1051
  Dihedral  : 11.603 156.393    848
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.84 %
    Favored  : 77.36 %
  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 (0.31), residues: 763
  helix:  1.19 (0.26), residues: 378
  sheet: -0.45 (0.49), residues: 116
  loop : -1.60 (0.37), residues: 269

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   0.012   0.001   PHE A 105 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 6276)
  covalent geometry    : angle       0.50119 /  0.27 ( 8545)
  SS BOND              : bond        0.00215 /  0.11 (    3)
  SS BOND              : angle       0.52310 /  0.27 (    6)
  hydrogen bonds       : bond        0.04280 /  2.75 (  343)
  hydrogen bonds       : angle       4.93033 /  3.55 (  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
  106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7932 (m-80) cc_final: 0.7532 (m-80)
REVERT: A  243 LYS cc_start: 0.8472 (pttm) cc_final: 0.8173 (pmtt)
REVERT: A  358 TYR cc_start: 0.8260 (t80) cc_final: 0.7911 (t80)
REVERT: A  391 ASN cc_start: 0.7824 (t0) cc_final: 0.7475 (t0)
REVERT: A  493 GLU cc_start: 0.8272 (tt0) cc_final: 0.7868 (tt0)
REVERT: A  579 TYR cc_start: 0.7672 (m-80) cc_final: 0.6959 (m-80)
REVERT: A  607 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7322 (mtt90)
REVERT: H   42 LYS cc_start: 0.7843 (tttp) cc_final: 0.7283 (mmmt)
  outliers start: 18
  outliers final: 14
  residues processed: 100
  average time/residue: 0.7302
  time to fit residues: 78.7398
Evaluate side-chains
  100 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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   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  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:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.139141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.120392 restraints weight = 20376.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.94
r_work: 0.3328 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6279  Z= 0.149
  Angle     :  0.507   4.925   8551  Z= 0.276
  Chirality :  0.039   0.141    934
  Planarity :  0.004   0.052   1051
  Dihedral  : 11.602 154.280    848
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.00 %
    Favored  : 76.74 %
  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 (0.31), residues: 763
  helix:  1.17 (0.26), residues: 377
  sheet: -0.43 (0.49), residues: 116
  loop : -1.58 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.022   0.001   TYR A 110 
 PHE   0.012   0.001   PHE A 105 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 6276)
  covalent geometry    : angle       0.50710 /  0.28 ( 8545)
  SS BOND              : bond        0.00229 /  0.12 (    3)
  SS BOND              : angle       0.48477 /  0.25 (    6)
  hydrogen bonds       : bond        0.04376 /  2.82 (  343)
  hydrogen bonds       : angle       4.92200 /  3.54 (  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
  108 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  127 PHE cc_start: 0.7812 (m-80) cc_final: 0.7500 (m-80)
REVERT: A  358 TYR cc_start: 0.8243 (t80) cc_final: 0.7886 (t80)
REVERT: A  391 ASN cc_start: 0.7659 (t0) cc_final: 0.7298 (t0)
REVERT: A  493 GLU cc_start: 0.8202 (tt0) cc_final: 0.7745 (tt0)
REVERT: A  579 TYR cc_start: 0.7534 (m-80) cc_final: 0.6800 (m-80)
REVERT: H   42 LYS cc_start: 0.7757 (tttp) cc_final: 0.7126 (mmmt)
  outliers start: 21
  outliers final: 13
  residues processed: 102
  average time/residue: 0.7856
  time to fit residues: 86.2068
Evaluate side-chains
  99 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  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  107 THR
Chi-restraints excluded: chain L residue  119 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.140026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121308 restraints weight = 20356.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.94
r_work: 0.3340 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   6279  Z= 0.129
  Angle     :  0.503   4.937   8551  Z= 0.274
  Chirality :  0.039   0.137    934
  Planarity :  0.004   0.049   1051
  Dihedral  : 11.650 156.520    848
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.78 %
    Favored  : 76.59 %
  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 are not related in a simple way.
  whole: -0.01 (0.31), residues: 763
  helix:  1.21 (0.26), residues: 377
  sheet: -0.39 (0.49), residues: 115
  loop : -1.55 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.022   0.001   TYR A 110 
 PHE   0.010   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/Z
  covalent geometry    : bond        0.00314 /  0.13 ( 6276)
  covalent geometry    : angle       0.50338 /  0.27 ( 8545)
  SS BOND              : bond        0.00210 /  0.11 (    3)
  SS BOND              : angle       0.50528 /  0.26 (    6)
  hydrogen bonds       : bond        0.04230 /  2.72 (  343)
  hydrogen bonds       : angle       4.87293 /  3.50 (  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
  106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7801 (m-80) cc_final: 0.7398 (m-80)
REVERT: A  358 TYR cc_start: 0.8239 (t80) cc_final: 0.7861 (t80)
REVERT: A  391 ASN cc_start: 0.7715 (t0) cc_final: 0.7336 (t0)
REVERT: A  493 GLU cc_start: 0.8172 (tt0) cc_final: 0.7734 (tt0)
REVERT: A  579 TYR cc_start: 0.7534 (m-80) cc_final: 0.6798 (m-80)
REVERT: H   42 LYS cc_start: 0.7722 (tttp) cc_final: 0.7035 (mmmt)
  outliers start: 17
  outliers final: 13
  residues processed: 102
  average time/residue: 0.7283
  time to fit residues: 80.4905
Evaluate side-chains
  100 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  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  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:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.138695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.120194 restraints weight = 20358.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.90
r_work: 0.3325 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   6279  Z= 0.150
  Angle     :  0.514   4.905   8551  Z= 0.280
  Chirality :  0.039   0.137    934
  Planarity :  0.004   0.049   1051
  Dihedral  : 11.720 159.393    848
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.09 %
    Favored  : 76.28 %
  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: -0.17 (0.30), residues: 763
  helix:  1.04 (0.26), residues: 384
  sheet: -0.44 (0.49), residues: 116
  loop : -1.65 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 607 
 TYR   0.021   0.001   TYR A 110 
 PHE   0.011   0.001   PHE A 105 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.15 ( 6276)
  covalent geometry    : angle       0.51357 /  0.28 ( 8545)
  SS BOND              : bond        0.00231 /  0.12 (    3)
  SS BOND              : angle       0.50208 /  0.25 (    6)
  hydrogen bonds       : bond        0.04343 /  2.80 (  343)
  hydrogen bonds       : angle       4.88455 /  3.51 (  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
  105 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7907 (m-80) cc_final: 0.7592 (m-80)
REVERT: A  243 LYS cc_start: 0.8448 (pttm) cc_final: 0.8223 (pmtt)
REVERT: A  391 ASN cc_start: 0.7708 (t0) cc_final: 0.7311 (t0)
REVERT: A  493 GLU cc_start: 0.8226 (tt0) cc_final: 0.7819 (tt0)
REVERT: A  579 TYR cc_start: 0.7640 (m-80) cc_final: 0.6891 (m-80)
REVERT: H   42 LYS cc_start: 0.7890 (tttp) cc_final: 0.7664 (tttm)
  outliers start: 17
  outliers final: 15
  residues processed: 100
  average time/residue: 0.8167
  time to fit residues: 87.9100
Evaluate side-chains
  101 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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 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  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:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.120097 restraints weight = 20531.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.97
r_work: 0.3322 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.132   6279  Z= 0.148
  Angle     :  0.514   4.915   8551  Z= 0.281
  Chirality :  0.039   0.137    934
  Planarity :  0.004   0.049   1051
  Dihedral  : 11.739 158.858    848
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.09 %
    Favored  : 76.28 %
  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: -0.15 (0.30), residues: 763
  helix:  1.04 (0.26), residues: 384
  sheet: -0.35 (0.49), residues: 115
  loop : -1.66 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.021   0.001   TYR A 110 
 PHE   0.011   0.001   PHE A 311 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.15 ( 6276)
  covalent geometry    : angle       0.51389 /  0.28 ( 8545)
  SS BOND              : bond        0.00231 /  0.12 (    3)
  SS BOND              : angle       0.53608 /  0.27 (    6)
  hydrogen bonds       : bond        0.04327 /  2.79 (  343)
  hydrogen bonds       : angle       4.86486 /  3.50 (  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
  106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.7807 (m-80) cc_final: 0.7502 (m-80)
REVERT: A  391 ASN cc_start: 0.7732 (t0) cc_final: 0.7380 (t0)
REVERT: A  493 GLU cc_start: 0.8178 (tt0) cc_final: 0.7743 (tt0)
REVERT: A  579 TYR cc_start: 0.7531 (m-80) cc_final: 0.6774 (m-80)
REVERT: H   42 LYS cc_start: 0.7819 (tttp) cc_final: 0.7575 (tttm)
REVERT: H   82 LYS cc_start: 0.8096 (mppt) cc_final: 0.7731 (mttp)
  outliers start: 17
  outliers final: 15
  residues processed: 100
  average time/residue: 0.8319
  time to fit residues: 89.5502
Evaluate side-chains
  103 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  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  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 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  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:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.139069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.120172 restraints weight = 20513.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.97
r_work: 0.3324 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.128   6279  Z= 0.143
  Angle     :  0.509   4.910   8551  Z= 0.277
  Chirality :  0.039   0.137    934
  Planarity :  0.004   0.048   1051
  Dihedral  : 11.730 158.198    848
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.09 %
    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: -0.14 (0.30), residues: 763
  helix:  1.05 (0.26), residues: 384
  sheet: -0.34 (0.49), residues: 115
  loop : -1.66 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.020   0.001   TYR A 110 
 PHE   0.010   0.001   PHE A 105 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.14 ( 6276)
  covalent geometry    : angle       0.50870 /  0.28 ( 8545)
  SS BOND              : bond        0.00227 /  0.12 (    3)
  SS BOND              : angle       0.55232 /  0.27 (    6)
  hydrogen bonds       : bond        0.04282 /  2.76 (  343)
  hydrogen bonds       : angle       4.84481 /  3.49 (  951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3669.59 seconds
wall clock time: 62 minutes 58.34 seconds (3778.34 seconds total)