Starting phenix.real_space_refine
on Tue Feb  3 18:31:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yq5_73324/02_2026/9yq5_73324.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yq5_73324/02_2026/9yq5_73324.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yq5_73324/02_2026/9yq5_73324.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yq5_73324/02_2026/9yq5_73324.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yq5_73324/02_2026/9yq5_73324.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yq5_73324/02_2026/9yq5_73324.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.094
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       2      5.49       5
     S      35      5.16       5
     C    3894      2.51       5
     N     991      2.21       5
     O    1110      1.98       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: 6034
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4064
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 497, 4053
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 13, 'TRANS': 483}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 497, 4053
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 13, 'TRANS': 483}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4152
    Chain: "B"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 950
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "C"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "A"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 74
          Unusual residues: {' MN': 2, 'UGA': 1, 'Y01': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 341 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 341 " occ=0.50
  Time building chain proxies: 1.62, per 1000 atoms: 0.27
  Number of scatterers: 6034
  At special positions: 0
  Unit cell: (71.28, 93.96, 141.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      35     16.00
     P       2     15.00
     O    1110      8.00
     N     991      7.00
     C    3894      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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: 0.57
  Conformation dependent library (CDL) restraints added in 260.9 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      48.7% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 51
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.764A  pdb=" N   LEU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 107
    Processing helix  chain 'A' and resid 124 through 126
      No H-bonds generated for 'chain 'A' and resid 124 through 126'
    Processing helix  chain 'A' and resid 127 through 138
      removed outlier: 3.656A  pdb=" N   ALA A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 133 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.572A  pdb=" N   SER A 152 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 217 through 220
    Processing helix  chain 'A' and resid 238 through 262
      removed outlier: 3.710A  pdb=" N   TRP A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 3.547A  pdb=" N   GLU A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   ASP A 285 " --> pdb=" O   ASN A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 300 through 311
    Processing helix  chain 'A' and resid 331 through 356
      removed outlier: 4.652A  pdb=" N   TRP A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   TYR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.518A  pdb=" N   HIS A 360 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY A 361 " --> pdb=" O   TRP A 358 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 357 through 361'
    Processing helix  chain 'A' and resid 364 through 391
      removed outlier: 3.969A  pdb=" N   PHE A 378 " --> pdb=" O   GLN A 374 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   PHE A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 420
    Processing helix  chain 'A' and resid 421 through 428
      removed outlier: 3.640A  pdb=" N   ALA A 424 " --> pdb=" O   ASN A 421 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 428 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 450
      removed outlier: 3.816A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
    Processing helix  chain 'A' and resid 470 through 474
    Processing helix  chain 'A' and resid 476 through 497
    Processing helix  chain 'A' and resid 504 through 534
    Processing helix  chain 'A' and resid 539 through 551
      removed outlier: 3.590A  pdb=" N   GLU A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 107 through 111
      removed outlier: 3.681A  pdb=" N   TYR B 111 " --> pdb=" O   THR B 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 64
      removed outlier: 4.019A  pdb=" N   LYS C  64 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 113
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 7.787A  pdb=" N   VAL A  84 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   LEU A 116 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   CYS A 118 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ILE A  88 " --> pdb=" O   CYS A 118 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   ILE A 120 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLY A  90 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ALA A  89 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 10.749A  pdb=" N   TYR A 318 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 10.959A  pdb=" N   ALA A 226 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 10.596A  pdb=" N   ALA A 228 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ALA A 322 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501
      removed outlier: 6.201A  pdb=" N   PHE A 500 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.801A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET B  82 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
      removed outlier: 7.937A  pdb=" N   VAL B  12 " --> pdb=" O   GLN B 119 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   THR B 121 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   TRP B 114 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   ALA B  97 " --> pdb=" O   TRP B 114 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   GLN B 116 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   CYS B  95 " --> pdb=" O   GLN B 116 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B  92 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   SER B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 52
      removed outlier: 6.620A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ALA C  50 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU C  34 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    892 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1865
        1.34 -     1.46: 1655
        1.46 -     1.58: 2613
        1.58 -     1.70: 1
        1.70 -     1.81: 55
  Bond restraints: 6189
  Sorted by residual:
  bond pdb=" O5D UGA A 601 "
       pdb=" PA  UGA A 601 "
    ideal  model  delta    sigma   weight residual
    1.645  1.749 -0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" CAI Y01 A 602 "
       pdb=" CAK Y01 A 602 "
    ideal  model  delta    sigma   weight residual
    1.492  1.407  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" O3A UGA A 601 "
       pdb=" PA  UGA A 601 "
    ideal  model  delta    sigma   weight residual
    1.652  1.569  0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" O3B UGA A 601 "
       pdb=" PB  UGA A 601 "
    ideal  model  delta    sigma   weight residual
    1.646  1.713 -0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" CAI Y01 A 602 "
       pdb=" CAZ Y01 A 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.383 -0.051 2.00e-02 2.50e+03 6.48e+00
  ... (remaining 6184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.70: 8394
        4.70 -     9.40: 15
        9.40 -    14.10: 4
       14.10 -    18.80: 0
       18.80 -    23.50: 1
  Bond angle restraints: 8414
  Sorted by residual:
  angle pdb=" PA  UGA A 601 "
        pdb=" O3A UGA A 601 "
        pdb=" PB  UGA A 601 "
      ideal   model   delta    sigma   weight residual
     123.32  146.82  -23.50 3.00e+00 1.11e-01 6.14e+01
  angle pdb=" OAG Y01 A 602 "
        pdb=" CAY Y01 A 602 "
        pdb=" OAW Y01 A 602 "
      ideal   model   delta    sigma   weight residual
     123.38  111.47   11.91 3.00e+00 1.11e-01 1.58e+01
  angle pdb=" CAM Y01 A 602 "
        pdb=" CAY Y01 A 602 "
        pdb=" OAW Y01 A 602 "
      ideal   model   delta    sigma   weight residual
     111.19  122.88  -11.69 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" O2A UGA A 601 "
        pdb=" PA  UGA A 601 "
        pdb=" O5D UGA A 601 "
      ideal   model   delta    sigma   weight residual
     109.54   98.27   11.27 3.00e+00 1.11e-01 1.41e+01
  angle pdb=" CAV Y01 A 602 "
        pdb=" CAZ Y01 A 602 "
        pdb=" CBH Y01 A 602 "
      ideal   model   delta    sigma   weight residual
     116.96  126.60   -9.64 3.00e+00 1.11e-01 1.03e+01
  ... (remaining 8409 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3193
       17.77 -    35.53: 349
       35.53 -    53.29: 104
       53.29 -    71.06: 22
       71.06 -    88.82: 5
  Dihedral angle restraints: 3673
    sinusoidal: 1506
      harmonic: 2167
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.13   39.87     1      1.00e+01 1.00e-02 2.23e+01
  dihedral pdb=" CA  ASP C  59 "
           pdb=" CB  ASP C  59 "
           pdb=" CG  ASP C  59 "
           pdb=" OD1 ASP C  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.65   58.65     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  PRO B  41 "
           pdb=" C   PRO B  41 "
           pdb=" N   GLY B  42 "
           pdb=" CA  GLY B  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.81  -16.19     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 3670 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 853
       0.082 -    0.164: 61
       0.164 -    0.246: 2
       0.246 -    0.328: 1
       0.328 -    0.409: 2
  Chirality restraints: 919
  Sorted by residual:
  chirality pdb=" C2' UGA A 601 "
            pdb=" C1' UGA A 601 "
            pdb=" C3' UGA A 601 "
            pdb=" O2' UGA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.23   -2.64    0.41 2.00e-01 2.50e+01 4.19e+00
  chirality pdb=" C1D UGA A 601 "
            pdb=" C2D UGA A 601 "
            pdb=" N1  UGA A 601 "
            pdb=" O4D UGA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.55   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" C5' UGA A 601 "
            pdb=" C4' UGA A 601 "
            pdb=" C6' UGA A 601 "
            pdb=" O5' UGA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.74    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 916 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 270 "   -0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO A 271 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 252 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   PHE A 252 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   PHE A 252 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASN A 253 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 434 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.14e+00
        pdb=" C   TYR A 434 "    0.025 2.00e-02 2.50e+03
        pdb=" O   TYR A 434 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   PHE A 435 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 150
        2.71 -     3.26: 5625
        3.26 -     3.80: 9735
        3.80 -     4.35: 12597
        4.35 -     4.90: 21695
  Nonbonded interactions: 49802
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  93 "
            pdb="MN    MN A 603 "
     model   vdw
     2.159 2.320
  nonbonded pdb=" OE2 GLU A 207 "
            pdb=" NE1 TRP A 325 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OE1 GLN A 172 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   LYS A 155 "
            pdb=" NE2 GLN A 186 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OH  TYR A 377 "
            pdb=" OAH Y01 A 602 "
     model   vdw
     2.324 3.040
  ... (remaining 49797 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=0.50 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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.520
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   6191  Z= 0.175
  Angle     :  0.647  23.499   8418  Z= 0.283
  Chirality :  0.047   0.409    919
  Planarity :  0.003   0.043   1038
  Dihedral  : 16.311  88.823   2289
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 15.62 %
    Favored  : 83.60 %
  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:  0.81 (0.31), residues: 737
  helix:  1.58 (0.29), residues: 325
  sheet:  0.39 (0.43), residues: 148
  loop : -0.64 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  52 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.010   0.001   PHE A  49 
 TRP   0.010   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6189)
  covalent geometry    : angle       0.64727 ( 8414)
  SS BOND              : bond        0.00111 (    2)
  SS BOND              : angle       0.22985 (    4)
  hydrogen bonds       : bond        0.12216 (  323)
  hydrogen bonds       : angle       5.06073 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7568 (t80) cc_final: 0.7245 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 70
  average time/residue: 0.2739
  time to fit residues: 20.6981
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  505 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
C  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.128866 restraints weight = 11348.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.29
r_work: 0.3290 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.0657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6191  Z= 0.135
  Angle     :  0.495  10.742   8418  Z= 0.262
  Chirality :  0.041   0.146    919
  Planarity :  0.004   0.043   1038
  Dihedral  :  7.456  76.864    969
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.46 %
    Favored  : 83.60 %
  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:  0.78 (0.31), residues: 737
  helix:  1.57 (0.29), residues: 326
  sheet:  0.45 (0.42), residues: 148
  loop : -0.73 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  98 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.012   0.001   PHE A  49 
 TRP   0.013   0.001   TRP A 287 
 HIS   0.002   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6189)
  covalent geometry    : angle       0.49462 ( 8414)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       0.29081 (    4)
  hydrogen bonds       : bond        0.04247 (  323)
  hydrogen bonds       : angle       4.37208 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.167 
Fit side-chains
REVERT: B   82 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6915 (mtp)
  outliers start: 6
  outliers final: 1
  residues processed: 71
  average time/residue: 0.3214
  time to fit residues: 24.4492
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.173612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129785 restraints weight = 13924.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.94
r_work: 0.3284 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.0751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6191  Z= 0.115
  Angle     :  0.471  11.577   8418  Z= 0.248
  Chirality :  0.040   0.142    919
  Planarity :  0.003   0.043   1038
  Dihedral  :  6.533  71.217    960
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 15.30 %
    Favored  : 83.60 %
  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:  0.79 (0.31), residues: 737
  helix:  1.59 (0.29), residues: 326
  sheet:  0.43 (0.42), residues: 148
  loop : -0.73 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.011   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6189)
  covalent geometry    : angle       0.47090 ( 8414)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.30080 (    4)
  hydrogen bonds       : bond        0.03966 (  323)
  hydrogen bonds       : angle       4.23920 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7872 (t80) cc_final: 0.7516 (t80)
REVERT: A  129 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7296 (mttm)
REVERT: B   82 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6836 (mtp)
  outliers start: 7
  outliers final: 1
  residues processed: 74
  average time/residue: 0.4128
  time to fit residues: 32.4184
Evaluate side-chains
  70 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 50 optimal weight:   20.0000
   chunk 37 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   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 = 0.3944 r_free = 0.3944 target = 0.172898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.127359 restraints weight = 11801.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.55
r_work: 0.3277 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6191  Z= 0.129
  Angle     :  0.485  12.074   8418  Z= 0.255
  Chirality :  0.040   0.141    919
  Planarity :  0.003   0.043   1038
  Dihedral  :  6.419  70.886    959
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.46 %
    Favored  : 82.97 %
  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:  0.78 (0.30), residues: 737
  helix:  1.58 (0.29), residues: 326
  sheet:  0.45 (0.42), residues: 148
  loop : -0.76 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 348 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.012   0.001   PHE A  49 
 TRP   0.011   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6189)
  covalent geometry    : angle       0.48495 ( 8414)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       0.36959 (    4)
  hydrogen bonds       : bond        0.04069 (  323)
  hydrogen bonds       : angle       4.23632 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7864 (t80) cc_final: 0.7516 (t80)
REVERT: A  144 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7969 (ttmt)
REVERT: A  438 MET cc_start: 0.7966 (mmm) cc_final: 0.7586 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 71
  average time/residue: 0.4075
  time to fit residues: 30.7814
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  505 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0070
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0050
   chunk 69 optimal weight:    0.2980
   chunk 13 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.3612

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.174803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131912 restraints weight = 16504.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 3.58
r_work: 0.3312 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6191  Z= 0.090
  Angle     :  0.441  10.820   8418  Z= 0.233
  Chirality :  0.039   0.137    919
  Planarity :  0.003   0.042   1038
  Dihedral  :  6.061  69.342    959
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 16.25 %
    Favored  : 83.28 %
  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:  0.95 (0.31), residues: 737
  helix:  1.74 (0.29), residues: 326
  sheet:  0.54 (0.42), residues: 148
  loop : -0.69 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  66 
 TYR   0.013   0.001   TYR A 414 
 PHE   0.010   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 246 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 ( 6189)
  covalent geometry    : angle       0.44080 ( 8414)
  SS BOND              : bond        0.00133 (    2)
  SS BOND              : angle       0.23222 (    4)
  hydrogen bonds       : bond        0.03469 (  323)
  hydrogen bonds       : angle       4.05401 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7717 (t80) cc_final: 0.7356 (t80)
REVERT: A  129 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7239 (mttm)
  outliers start: 3
  outliers final: 0
  residues processed: 72
  average time/residue: 0.3374
  time to fit residues: 26.1451
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3921 r_free = 0.3921 target = 0.170791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125641 restraints weight = 13690.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.86
r_work: 0.3249 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   6191  Z= 0.190
  Angle     :  0.548  14.131   8418  Z= 0.284
  Chirality :  0.043   0.148    919
  Planarity :  0.004   0.045   1038
  Dihedral  :  6.457  70.204    959
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.25 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.30), residues: 737
  helix:  1.43 (0.29), residues: 326
  sheet:  0.48 (0.42), residues: 148
  loop : -0.80 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 348 
 TYR   0.018   0.002   TYR A 528 
 PHE   0.014   0.002   PHE A 252 
 TRP   0.013   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6189)
  covalent geometry    : angle       0.54759 ( 8414)
  SS BOND              : bond        0.00312 (    2)
  SS BOND              : angle       0.59097 (    4)
  hydrogen bonds       : bond        0.04689 (  323)
  hydrogen bonds       : angle       4.34825 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7854 (t80) cc_final: 0.7524 (t80)
REVERT: A  125 GLU cc_start: 0.7226 (tt0) cc_final: 0.6199 (mp0)
REVERT: A  129 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7348 (mttp)
REVERT: A  144 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7997 (ttmt)
REVERT: A  255 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7495 (mt-10)
REVERT: A  438 MET cc_start: 0.8022 (mmm) cc_final: 0.7634 (mmm)
REVERT: B   82 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6720 (mtp)
REVERT: C  113 TYR cc_start: 0.8732 (m-80) cc_final: 0.8435 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 72
  average time/residue: 0.3663
  time to fit residues: 28.0437
Evaluate side-chains
  75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue   82 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0050
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 52 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0770
   overall best weight:    0.4352

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.174571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.129672 restraints weight = 13640.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 3.01
r_work: 0.3293 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6191  Z= 0.096
  Angle     :  0.457  12.294   8418  Z= 0.240
  Chirality :  0.039   0.137    919
  Planarity :  0.003   0.043   1038
  Dihedral  :  6.064  69.202    959
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 16.56 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.31), residues: 737
  helix:  1.65 (0.29), residues: 326
  sheet:  0.53 (0.42), residues: 148
  loop : -0.71 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 178 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.010   0.001   PHE A  49 
 TRP   0.010   0.001   TRP A 246 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6189)
  covalent geometry    : angle       0.45752 ( 8414)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.32294 (    4)
  hydrogen bonds       : bond        0.03642 (  323)
  hydrogen bonds       : angle       4.08829 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7793 (t80) cc_final: 0.7454 (t80)
REVERT: A  129 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7239 (mttm)
REVERT: A  255 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7490 (mt-10)
REVERT: C  113 TYR cc_start: 0.8616 (m-80) cc_final: 0.8364 (m-80)
  outliers start: 5
  outliers final: 1
  residues processed: 72
  average time/residue: 0.3227
  time to fit residues: 24.8926
Evaluate side-chains
  70 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  449 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 62 optimal weight:    0.0470
   chunk 66 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 61 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.7280

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.173609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.131189 restraints weight = 16360.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 3.46
r_work: 0.3285 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.0935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6191  Z= 0.115
  Angle     :  0.477  13.072   8418  Z= 0.249
  Chirality :  0.041   0.139    919
  Planarity :  0.003   0.043   1038
  Dihedral  :  6.070  69.179    959
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.56 %
    Favored  : 82.33 %
  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:  0.88 (0.31), residues: 737
  helix:  1.63 (0.29), residues: 326
  sheet:  0.56 (0.43), residues: 148
  loop : -0.70 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 348 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.011   0.001   TRP A 287 
 HIS   0.004   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6189)
  covalent geometry    : angle       0.47744 ( 8414)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       0.36418 (    4)
  hydrogen bonds       : bond        0.03873 (  323)
  hydrogen bonds       : angle       4.12618 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7671 (t80) cc_final: 0.7305 (t80)
REVERT: A  129 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7174 (mttm)
REVERT: C  113 TYR cc_start: 0.8535 (m-80) cc_final: 0.8236 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 73
  average time/residue: 0.3218
  time to fit residues: 25.0681
Evaluate side-chains
  72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  505 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0980
   chunk 55 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.174108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.131317 restraints weight = 14700.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 3.21
r_work: 0.3306 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6191  Z= 0.109
  Angle     :  0.469  13.030   8418  Z= 0.245
  Chirality :  0.040   0.138    919
  Planarity :  0.003   0.042   1038
  Dihedral  :  6.002  68.877    959
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 17.03 %
    Favored  : 82.49 %
  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:  0.92 (0.31), residues: 737
  helix:  1.68 (0.29), residues: 326
  sheet:  0.57 (0.43), residues: 148
  loop : -0.68 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 348 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.011   0.001   TRP A 246 
 HIS   0.004   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6189)
  covalent geometry    : angle       0.46921 ( 8414)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.34595 (    4)
  hydrogen bonds       : bond        0.03771 (  323)
  hydrogen bonds       : angle       4.08560 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7647 (t80) cc_final: 0.7277 (t80)
REVERT: A  129 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7195 (mttp)
REVERT: C  113 TYR cc_start: 0.8540 (m-80) cc_final: 0.8220 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 70
  average time/residue: 0.3373
  time to fit residues: 25.1343
Evaluate side-chains
  72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  505 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    0.0470
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.174094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.132131 restraints weight = 20318.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 4.03
r_work: 0.3241 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.0953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6191  Z= 0.108
  Angle     :  0.470  13.218   8418  Z= 0.245
  Chirality :  0.040   0.139    919
  Planarity :  0.003   0.042   1038
  Dihedral  :  5.952  68.528    959
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 17.35 %
    Favored  : 82.18 %
  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:  0.91 (0.31), residues: 737
  helix:  1.67 (0.29), residues: 326
  sheet:  0.57 (0.43), residues: 148
  loop : -0.69 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 348 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.010   0.001   PHE A  49 
 TRP   0.011   0.001   TRP A 246 
 HIS   0.005   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6189)
  covalent geometry    : angle       0.46981 ( 8414)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       0.35278 (    4)
  hydrogen bonds       : bond        0.03770 (  323)
  hydrogen bonds       : angle       4.08394 (  892)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   49 PHE cc_start: 0.7784 (t80) cc_final: 0.7384 (t80)
REVERT: A  129 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7285 (mttm)
REVERT: C  113 TYR cc_start: 0.8544 (m-80) cc_final: 0.8229 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 70
  average time/residue: 0.3415
  time to fit residues: 25.5664
Evaluate side-chains
  73 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  505 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 1 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.7458

-------------------------------------------------------------------------------
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 = 0.3952 r_free = 0.3952 target = 0.173672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.131522 restraints weight = 17986.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 4.18
r_work: 0.3255 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.0950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6191  Z= 0.116
  Angle     :  0.477  13.671   8418  Z= 0.248
  Chirality :  0.040   0.139    919
  Planarity :  0.003   0.043   1038
  Dihedral  :  5.963  68.249    959
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 16.88 %
    Favored  : 82.49 %
  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:  0.90 (0.31), residues: 737
  helix:  1.66 (0.29), residues: 326
  sheet:  0.56 (0.43), residues: 148
  loop : -0.70 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 348 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.011   0.001   TRP A 246 
 HIS   0.005   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6189)
  covalent geometry    : angle       0.47731 ( 8414)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.38296 (    4)
  hydrogen bonds       : bond        0.03862 (  323)
  hydrogen bonds       : angle       4.09219 (  892)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.41 seconds
wall clock time: 35 minutes 58.17 seconds (2158.17 seconds total)