Starting phenix.real_space_refine
on Thu Jul  2 07:27:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yq2_73321/07_2026/9yq2_73321.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yq2_73321/07_2026/9yq2_73321.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yq2_73321/07_2026/9yq2_73321.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yq2_73321/07_2026/9yq2_73321.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yq2_73321/07_2026/9yq2_73321.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yq2_73321/07_2026/9yq2_73321.cif"
  }
  resolution = 2.9
  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=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1812 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     S      34      5.16       5
     C    3838      2.51       5
     N     978      2.21       5
     O    1087      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 5939
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3981
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 487, 3970
          Classifications: {'peptide': 487}
          Link IDs: {'PTRANS': 13, 'TRANS': 473}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 487, 3970
          Classifications: {'peptide': 487}
          Link IDs: {'PTRANS': 13, 'TRANS': 473}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4065
    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: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 70
          Ad-hoc single atom residues: {' MN': 2}
          Unusual residues: {'LMT': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Chain breaks: 2
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 341 " occ=0.63
      ... (20 atoms not shown)
      pdb=" NH2BARG A 341 " occ=0.37
  Time building chain proxies: 2.20, per 1000 atoms: 0.37
  Number of scatterers: 5939
  At special positions: 0
  Unit cell: (86.064, 136.92, 99.756, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      2     24.99
     S      34     16.00
     O    1087      8.00
     N     978      7.00
     C    3838      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: 0.52
  Conformation dependent library (CDL) restraints added in 475.8 milliseconds
  

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1358

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 7 sheets defined
      48.0% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 74
      removed outlier: 4.167A  pdb=" N   PHE A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A  55 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 3.721A  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 127 through 138
      removed outlier: 4.024A  pdb=" N   ALA A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.754A  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: 3.705A  pdb=" N   TRP A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLN A 259 " --> pdb=" O   GLU A 255 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 5.357A  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 302 through 311
    Processing helix  chain 'A' and resid 331 through 349
    Processing helix  chain 'A' and resid 350 through 357
    Processing helix  chain 'A' and resid 364 through 392
      removed outlier: 3.651A  pdb=" N   ILE A 375 " --> pdb=" O   CYS A 371 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ALA A 392 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 420
    Processing helix  chain 'A' and resid 421 through 428
    Processing helix  chain 'A' and resid 429 through 448
      removed outlier: 3.830A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 4.769A  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 472 through 497
      removed outlier: 6.699A  pdb=" N   ILE A 478 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   THR A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 534
    Processing helix  chain 'A' and resid 539 through 552
      removed outlier: 4.001A  pdb=" N   LEU A 551 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.658A  pdb=" N   THR B  31 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 107 through 111
      removed outlier: 3.585A  pdb=" N   TYR B 111 " --> pdb=" O   THR B 108 " (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: 8.195A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU A 116 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   ILE A 170 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   CYS A 118 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   GLN A 172 " --> pdb=" O   CYS A 118 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ILE A 120 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   VAL A  84 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LEU A 116 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   CYS A 118 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A  88 " --> pdb=" O   CYS A 118 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   ILE A 120 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   GLY A  90 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA A  89 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   LEU A 272 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 10.478A  pdb=" N   TYR A 318 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 11.006A  pdb=" N   ALA A 226 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 10.477A  pdb=" N   ALA A 228 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 6.629A  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: 6.169A  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 4 through 6
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12
      removed outlier: 5.929A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 5.929A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 59
      removed outlier: 6.676A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ALA C  50 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU C  34 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    877 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: 1.01

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1837
        1.35 -     1.46: 1656
        1.46 -     1.58: 2543
        1.58 -     1.70: 0
        1.70 -     1.82: 52
  Bond restraints: 6088
  Sorted by residual:
  bond pdb=" CAI Y01 A 601 "
       pdb=" CAK Y01 A 601 "
    ideal  model  delta    sigma   weight residual
    1.492  1.407  0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" CAI Y01 A 601 "
       pdb=" CAZ Y01 A 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.382 -0.050 2.00e-02 2.50e+03 6.32e+00
  bond pdb=" CAY Y01 A 601 "
       pdb=" OAG Y01 A 601 "
    ideal  model  delta    sigma   weight residual
    1.207  1.251 -0.044 2.00e-02 2.50e+03 4.79e+00
  bond pdb=" C4' LMT A 603 "
       pdb=" C5' LMT A 603 "
    ideal  model  delta    sigma   weight residual
    1.530  1.571 -0.041 2.00e-02 2.50e+03 4.15e+00
  bond pdb=" C2B LMT A 603 "
       pdb=" O2B LMT A 603 "
    ideal  model  delta    sigma   weight residual
    1.410  1.371  0.039 2.00e-02 2.50e+03 3.71e+00
  ... (remaining 6083 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 8180
        2.37 -     4.73: 67
        4.73 -     7.10: 14
        7.10 -     9.46: 2
        9.46 -    11.83: 4
  Bond angle restraints: 8267
  Sorted by residual:
  angle pdb=" N   TRP A 358 "
        pdb=" CA  TRP A 358 "
        pdb=" C   TRP A 358 "
      ideal   model   delta    sigma   weight residual
     114.75  108.41    6.34 1.26e+00 6.30e-01 2.53e+01
  angle pdb=" OAG Y01 A 601 "
        pdb=" CAY Y01 A 601 "
        pdb=" OAW Y01 A 601 "
      ideal   model   delta    sigma   weight residual
     123.38  111.55   11.83 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CAM Y01 A 601 "
        pdb=" CAY Y01 A 601 "
        pdb=" OAW Y01 A 601 "
      ideal   model   delta    sigma   weight residual
     111.19  122.62  -11.43 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" C4B LMT A 603 "
        pdb=" C5B LMT A 603 "
        pdb=" C6B LMT A 603 "
      ideal   model   delta    sigma   weight residual
     114.23  104.33    9.90 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CAV Y01 A 601 "
        pdb=" CAZ Y01 A 601 "
        pdb=" CBH Y01 A 601 "
      ideal   model   delta    sigma   weight residual
     116.96  126.68   -9.72 3.00e+00 1.11e-01 1.05e+01
  ... (remaining 8262 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.64: 3086
       14.64 -    29.29: 379
       29.29 -    43.93: 117
       43.93 -    58.57: 37
       58.57 -    73.22: 7
  Dihedral angle restraints: 3626
    sinusoidal: 1492
      harmonic: 2134
  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   58.80   34.20     1      1.00e+01 1.00e-02 1.66e+01
  dihedral pdb=" CA  PHE A 362 "
           pdb=" C   PHE A 362 "
           pdb=" N   SER A 363 "
           pdb=" CA  SER A 363 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.84   19.16     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  THR C  90 "
           pdb=" C   THR C  90 "
           pdb=" N   ALA C  91 "
           pdb=" CA  ALA C  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.61  -16.39     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 3623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 803
       0.066 -    0.132: 95
       0.132 -    0.198: 4
       0.198 -    0.264: 2
       0.264 -    0.330: 3
  Chirality restraints: 907
  Sorted by residual:
  chirality pdb=" C1' LMT A 603 "
            pdb=" C2' LMT A 603 "
            pdb=" O1' LMT A 603 "
            pdb=" O5' LMT A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.64   -0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" C3B LMT A 603 "
            pdb=" C2B LMT A 603 "
            pdb=" C4B LMT A 603 "
            pdb=" O3B LMT A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.82   -0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" C4' LMT A 603 "
            pdb=" C3' LMT A 603 "
            pdb=" C5' LMT A 603 "
            pdb=" O1B LMT A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.83    0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 904 not shown)

  Planarity restraints: 1019
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 252 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   PHE A 252 "    0.028 2.00e-02 2.50e+03
        pdb=" O   PHE A 252 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ASN A 253 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "   -0.023 5.00e-02 4.00e+02   3.47e-02 1.92e+00
        pdb=" N   PRO A  95 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  86 "    0.018 5.00e-02 4.00e+02   2.72e-02 1.19e+00
        pdb=" N   PRO C  87 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO C  87 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C  87 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1016 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 101
        2.67 -     3.23: 5442
        3.23 -     3.79: 9336
        3.79 -     4.34: 13228
        4.34 -     4.90: 22266
  Nonbonded interactions: 50373
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  93 "
            pdb="MN    MN A 602 "
     model   vdw
     2.113 3.060
  nonbonded pdb=" OD2 ASP B 104 "
            pdb=" OG1 THR B 107 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" NH1 ARG B  66 "
            pdb=" O   SER B  84 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ASP A 496 "
            pdb=" NZ  LYS B  30 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   LEU A 518 "
            pdb=" OG  SER A 522 "
     model   vdw
     2.286 3.040
  ... (remaining 50368 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=0.37 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:             4.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.420
  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:             0.010
  Load rotamer database and sin/cos tables:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   6090  Z= 0.159
  Angle     :  0.609  11.826   8271  Z= 0.295
  Chirality :  0.047   0.330    907
  Planarity :  0.003   0.035   1019
  Dihedral  : 14.726  73.216   2262
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  9.79 %
    Favored  : 90.05 %
  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:  0.48 (0.31), residues: 724
  helix:  1.49 (0.30), residues: 319
  sheet:  0.15 (0.44), residues: 153
  loop : -1.05 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  66 
 TYR   0.011   0.001   TYR A 414 
 PHE   0.011   0.001   PHE A 385 
 TRP   0.010   0.001   TRP A 536 
 HIS   0.001   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.16 ( 6088)
  covalent geometry    : angle       0.60947 /  0.29 ( 8267)
  SS BOND              : bond        0.00257 /  0.12 (    2)
  SS BOND              : angle       0.50390 /  0.22 (    4)
  hydrogen bonds       : bond        0.14192 /  9.87 (  315)
  hydrogen bonds       : angle       5.53414 /  4.06 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.144 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.5130
  time to fit residues: 39.4954
Evaluate side-chains
  68 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 HIS
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.148360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.118557 restraints weight = 6100.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.01
r_work: 0.3270 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.0625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6090  Z= 0.158
  Angle     :  0.516   5.897   8271  Z= 0.281
  Chirality :  0.043   0.165    907
  Planarity :  0.004   0.037   1019
  Dihedral  :  6.834  57.956    953
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.47 %
    Favored  : 89.57 %
  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:  0.45 (0.31), residues: 724
  helix:  1.47 (0.29), residues: 322
  sheet:  0.11 (0.43), residues: 148
  loop : -1.06 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 549 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.012   0.001   PHE A  49 
 TRP   0.010   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.16 ( 6088)
  covalent geometry    : angle       0.51568 /  0.28 ( 8267)
  SS BOND              : bond        0.00155 /  0.07 (    2)
  SS BOND              : angle       0.32064 /  0.16 (    4)
  hydrogen bonds       : bond        0.04341 /  2.90 (  315)
  hydrogen bonds       : angle       4.45037 /  3.33 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.246 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7866 (m) cc_final: 0.7586 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 79
  average time/residue: 0.4836
  time to fit residues: 40.3576
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain C residue    5 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0870
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 HIS
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.117784 restraints weight = 9032.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.46
r_work: 0.3252 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6090  Z= 0.122
  Angle     :  0.465   5.211   8271  Z= 0.255
  Chirality :  0.041   0.144    907
  Planarity :  0.003   0.030   1019
  Dihedral  :  6.212  59.920    951
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.95 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.31), residues: 724
  helix:  1.55 (0.30), residues: 322
  sheet:  0.12 (0.44), residues: 147
  loop : -1.08 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  52 
 TYR   0.011   0.001   TYR A 414 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 536 
 HIS   0.002   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 6088)
  covalent geometry    : angle       0.46555 /  0.26 ( 8267)
  SS BOND              : bond        0.00181 /  0.09 (    2)
  SS BOND              : angle       0.30754 /  0.14 (    4)
  hydrogen bonds       : bond        0.03862 /  2.59 (  315)
  hydrogen bonds       : angle       4.24508 /  3.16 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.146 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7826 (m) cc_final: 0.7546 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 80
  average time/residue: 0.4623
  time to fit residues: 39.1657
Evaluate side-chains
  75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 71 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0070
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 HIS
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.151220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.118890 restraints weight = 9338.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.49
r_work: 0.3259 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6090  Z= 0.115
  Angle     :  0.465   5.248   8271  Z= 0.253
  Chirality :  0.041   0.140    907
  Planarity :  0.003   0.030   1019
  Dihedral  :  6.024  58.993    951
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.08 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 724
  helix:  1.60 (0.30), residues: 322
  sheet:  0.13 (0.43), residues: 147
  loop : -1.10 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 536 
 HIS   0.002   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 6088)
  covalent geometry    : angle       0.46499 /  0.25 ( 8267)
  SS BOND              : bond        0.00191 /  0.09 (    2)
  SS BOND              : angle       0.36824 /  0.17 (    4)
  hydrogen bonds       : bond        0.03713 /  2.48 (  315)
  hydrogen bonds       : angle       4.16661 /  3.09 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.225 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 80
  average time/residue: 0.4462
  time to fit residues: 37.9469
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain C residue    5 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 HIS
A 542 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.150567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119774 restraints weight = 10387.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.44
r_work: 0.3241 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6090  Z= 0.128
  Angle     :  0.474   5.382   8271  Z= 0.257
  Chirality :  0.041   0.139    907
  Planarity :  0.003   0.028   1019
  Dihedral  :  5.947  57.916    951
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.72 %
    Favored  : 87.32 %
  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:  0.51 (0.31), residues: 724
  helix:  1.57 (0.30), residues: 322
  sheet:  0.12 (0.43), residues: 147
  loop : -1.11 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.012   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 536 
 HIS   0.002   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 6088)
  covalent geometry    : angle       0.47428 /  0.26 ( 8267)
  SS BOND              : bond        0.00203 /  0.10 (    2)
  SS BOND              : angle       0.37320 /  0.18 (    4)
  hydrogen bonds       : bond        0.03788 /  2.54 (  315)
  hydrogen bonds       : angle       4.17331 /  3.10 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.154 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 79
  average time/residue: 0.3472
  time to fit residues: 29.1659
Evaluate side-chains
  74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain C residue    5 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.117038 restraints weight = 16382.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 3.16
r_work: 0.3189 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6090  Z= 0.147
  Angle     :  0.490   6.607   8271  Z= 0.266
  Chirality :  0.042   0.142    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.967  57.060    951
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.72 %
    Favored  : 87.16 %
  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:  0.49 (0.31), residues: 724
  helix:  1.58 (0.30), residues: 317
  sheet:  0.18 (0.44), residues: 145
  loop : -1.13 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.013   0.001   PHE C  47 
 TRP   0.010   0.001   TRP A 536 
 HIS   0.002   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 6088)
  covalent geometry    : angle       0.49048 /  0.27 ( 8267)
  SS BOND              : bond        0.00225 /  0.11 (    2)
  SS BOND              : angle       0.44495 /  0.21 (    4)
  hydrogen bonds       : bond        0.03925 /  2.62 (  315)
  hydrogen bonds       : angle       4.23398 /  3.14 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  390 ILE cc_start: 0.7890 (pt) cc_final: 0.7685 (mt)
REVERT: B  107 THR cc_start: 0.7750 (m) cc_final: 0.7486 (p)
  outliers start: 7
  outliers final: 4
  residues processed: 81
  average time/residue: 0.3829
  time to fit residues: 33.1276
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain C residue    5 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 156 ASN
A 360 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.152323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120835 restraints weight = 13242.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.83
r_work: 0.3223 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6090  Z= 0.136
  Angle     :  0.485   7.323   8271  Z= 0.262
  Chirality :  0.042   0.141    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.909  56.382    951
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.56 %
    Favored  : 87.32 %
  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:  0.51 (0.31), residues: 724
  helix:  1.60 (0.30), residues: 317
  sheet:  0.16 (0.44), residues: 145
  loop : -1.12 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  66 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.012   0.001   PHE C  47 
 TRP   0.010   0.001   TRP A 536 
 HIS   0.002   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.14 ( 6088)
  covalent geometry    : angle       0.48466 /  0.26 ( 8267)
  SS BOND              : bond        0.00215 /  0.10 (    2)
  SS BOND              : angle       0.40491 /  0.19 (    4)
  hydrogen bonds       : bond        0.03852 /  2.57 (  315)
  hydrogen bonds       : angle       4.20236 /  3.12 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.175 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7714 (m) cc_final: 0.7443 (p)
REVERT: C   28 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7672 (mm)
  outliers start: 7
  outliers final: 4
  residues processed: 76
  average time/residue: 0.3628
  time to fit residues: 29.2943
Evaluate side-chains
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0060
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 156 ASN
A 360 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.150314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.118055 restraints weight = 16197.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 3.11
r_work: 0.3211 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6090  Z= 0.127
  Angle     :  0.475   8.148   8271  Z= 0.259
  Chirality :  0.041   0.141    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.858  55.903    951
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.88 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 724
  helix:  1.64 (0.30), residues: 317
  sheet:  0.13 (0.43), residues: 148
  loop : -1.11 (0.34), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.012   0.001   PHE C  47 
 TRP   0.010   0.001   TRP A 536 
 HIS   0.002   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 6088)
  covalent geometry    : angle       0.47530 /  0.26 ( 8267)
  SS BOND              : bond        0.00211 /  0.10 (    2)
  SS BOND              : angle       0.39202 /  0.18 (    4)
  hydrogen bonds       : bond        0.03787 /  2.53 (  315)
  hydrogen bonds       : angle       4.17665 /  3.10 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.162 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7690 (m) cc_final: 0.7423 (p)
REVERT: C   28 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7652 (mm)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.3803
  time to fit residues: 31.4542
Evaluate side-chains
  78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0770
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 156 ASN
A 360 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.150603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.119152 restraints weight = 7785.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.28
r_work: 0.3267 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6090  Z= 0.126
  Angle     :  0.480   8.536   8271  Z= 0.260
  Chirality :  0.041   0.141    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.818  55.391    951
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.52 %
    Favored  : 86.68 %
  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:  0.56 (0.31), residues: 724
  helix:  1.65 (0.30), residues: 317
  sheet:  0.15 (0.43), residues: 148
  loop : -1.10 (0.34), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.012   0.001   PHE C  47 
 TRP   0.010   0.001   TRP A 536 
 HIS   0.002   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 6088)
  covalent geometry    : angle       0.48006 /  0.26 ( 8267)
  SS BOND              : bond        0.00216 /  0.10 (    2)
  SS BOND              : angle       0.40095 /  0.18 (    4)
  hydrogen bonds       : bond        0.03758 /  2.51 (  315)
  hydrogen bonds       : angle       4.16842 /  3.09 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.215 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7688 (m) cc_final: 0.7402 (p)
REVERT: C   28 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7667 (mm)
  outliers start: 5
  outliers final: 4
  residues processed: 75
  average time/residue: 0.3813
  time to fit residues: 30.4593
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 60 optimal weight:    0.0980
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.3780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 156 ASN
A 360 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.153403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.122263 restraints weight = 10355.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.50
r_work: 0.3263 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6090  Z= 0.109
  Angle     :  0.466   8.893   8271  Z= 0.253
  Chirality :  0.041   0.141    907
  Planarity :  0.003   0.028   1019
  Dihedral  :  5.725  54.792    951
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 12.68 %
    Favored  : 86.68 %
  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:  0.64 (0.31), residues: 724
  helix:  1.72 (0.30), residues: 317
  sheet:  0.22 (0.43), residues: 146
  loop : -1.06 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  66 
 TYR   0.011   0.001   TYR A 414 
 PHE   0.012   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 536 
 HIS   0.001   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 6088)
  covalent geometry    : angle       0.46616 /  0.25 ( 8267)
  SS BOND              : bond        0.00213 /  0.10 (    2)
  SS BOND              : angle       0.40891 /  0.18 (    4)
  hydrogen bonds       : bond        0.03624 /  2.42 (  315)
  hydrogen bonds       : angle       4.11359 /  3.05 (  877)

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

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

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1448 Ramachandran restraints generated.
    724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.172 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 74
  average time/residue: 0.4095
  time to fit residues: 31.9310
Evaluate side-chains
  72 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain C residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0050
   chunk 57 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0470
   overall best weight:    0.4892

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 156 ASN
A 360 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.153060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.121197 restraints weight = 13188.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.87
r_work: 0.3239 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6090  Z= 0.117
  Angle     :  0.470   8.568   8271  Z= 0.255
  Chirality :  0.041   0.139    907
  Planarity :  0.003   0.028   1019
  Dihedral  :  5.677  53.837    951
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.52 %
    Favored  : 86.52 %
  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:  0.64 (0.31), residues: 724
  helix:  1.70 (0.30), residues: 317
  sheet:  0.22 (0.43), residues: 148
  loop : -1.04 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  66 
 TYR   0.012   0.001   TYR B 111 
 PHE   0.012   0.001   PHE C  47 
 TRP   0.011   0.001   TRP A 536 
 HIS   0.002   0.000   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 6088)
  covalent geometry    : angle       0.46984 /  0.25 ( 8267)
  SS BOND              : bond        0.00219 /  0.11 (    2)
  SS BOND              : angle       0.44714 /  0.20 (    4)
  hydrogen bonds       : bond        0.03687 /  2.46 (  315)
  hydrogen bonds       : angle       4.11807 /  3.05 (  877)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2253.60 seconds
wall clock time: 39 minutes 4.76 seconds (2344.76 seconds total)