Starting phenix.real_space_refine
on Tue Feb  3 22:30:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yq2_73321/02_2026/9yq2_73321.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yq2_73321/02_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yq2_73321/02_2026/9yq2_73321.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yq2_73321/02_2026/9yq2_73321.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yq2_73321/02_2026/9yq2_73321.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yq2_73321/02_2026/9yq2_73321.map"
  }
  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): 0.00s

  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: 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, 72
          Unusual residues: {' MN': 2, 'LMT': 1, 'Y01': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 341 " occ=0.63
      ... (20 atoms not shown)
      pdb=" NH2BARG A 341 " occ=0.37
  Time building chain proxies: 1.78, per 1000 atoms: 0.30
  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: 0.54
  Conformation dependent library (CDL) restraints added in 363.8 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: 0.20
  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: 0.94

  Time building geometry restraints manager: 0.71 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 2.320
  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:             4.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.410
  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:7.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
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
  covalent geometry    : bond        0.00326 ( 6088)
  covalent geometry    : angle       0.60947 ( 8267)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       0.50390 (    4)
  hydrogen bonds       : bond        0.14192 (  315)
  hydrogen bonds       : angle       5.53414 (  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  : 0.146 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.5001
  time to fit residues: 38.4155
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  : 0.212 
-------------------------------------------------------------------------------
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:    1.9990
   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:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.150612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.120720 restraints weight = 6023.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.01
r_work: 0.3279 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    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 = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.0660

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= 0.159
  Angle     :  0.514   5.860   8271  Z= 0.280
  Chirality :  0.043   0.160    907
  Planarity :  0.004   0.035   1019
  Dihedral  :  6.775  57.937    953
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.63 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.31), residues: 724
  helix:  1.46 (0.29), residues: 322
  sheet:  0.11 (0.43), residues: 148
  loop : -1.05 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  52 
 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
  covalent geometry    : bond        0.00364 ( 6088)
  covalent geometry    : angle       0.51365 ( 8267)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.36332 (    4)
  hydrogen bonds       : bond        0.04348 (  315)
  hydrogen bonds       : angle       4.43948 (  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
  80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7860 (m) cc_final: 0.7582 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 77
  average time/residue: 0.4628
  time to fit residues: 37.5822
Evaluate side-chains
  74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0270
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 360 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.149838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.117649 restraints weight = 8980.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.44
r_work: 0.3249 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
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 = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.0788

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= 0.124
  Angle     :  0.470   5.275   8271  Z= 0.258
  Chirality :  0.041   0.143    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  6.252  59.857    951
  Min Nonbonded Distance : 2.464

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:  0.50 (0.31), residues: 724
  helix:  1.55 (0.30), residues: 322
  sheet:  0.10 (0.44), residues: 147
  loop : -1.07 (0.34), residues: 255

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   0.011   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 246 
 HIS   0.002   0.000   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6088)
  covalent geometry    : angle       0.46999 ( 8267)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.30219 (    4)
  hydrogen bonds       : bond        0.03911 (  315)
  hydrogen bonds       : angle       4.26148 (  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
  82 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.238 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7877 (m) cc_final: 0.7598 (p)
  outliers start: 6
  outliers final: 0
  residues processed: 79
  average time/residue: 0.5112
  time to fit residues: 42.6995
Evaluate side-chains
  72 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.5980
   chunk 28 optimal weight:    0.0170
   chunk 71 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 360 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.150585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.118047 restraints weight = 9260.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.50
r_work: 0.3252 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.0889

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= 0.126
  Angle     :  0.474   5.398   8271  Z= 0.258
  Chirality :  0.041   0.141    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  6.068  59.029    951
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.59 %
    Favored  : 88.44 %
  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:  0.50 (0.31), residues: 724
  helix:  1.56 (0.30), residues: 322
  sheet:  0.11 (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   0.012   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 246 
 HIS   0.002   0.000   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6088)
  covalent geometry    : angle       0.47404 ( 8267)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.38781 (    4)
  hydrogen bonds       : bond        0.03809 (  315)
  hydrogen bonds       : angle       4.20494 (  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
  81 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7715 (m) cc_final: 0.7453 (p)
  outliers start: 6
  outliers final: 3
  residues processed: 79
  average time/residue: 0.5158
  time to fit residues: 43.0655
Evaluate side-chains
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   chunk 44 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 360 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.150155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119320 restraints weight = 10348.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.42
r_work: 0.3243 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    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 = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.0931

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= 0.133
  Angle     :  0.479   5.444   8271  Z= 0.260
  Chirality :  0.041   0.141    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.990  58.058    951
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.24 %
    Favored  : 87.80 %
  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:  1.55 (0.30), residues: 322
  sheet:  0.11 (0.43), residues: 147
  loop : -1.10 (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 246 
 HIS   0.002   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6088)
  covalent geometry    : angle       0.47925 ( 8267)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       0.37799 (    4)
  hydrogen bonds       : bond        0.03842 (  315)
  hydrogen bonds       : angle       4.20714 (  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
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.223 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 77
  average time/residue: 0.5049
  time to fit residues: 41.1712
Evaluate side-chains
  75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0570
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0570
   chunk 68 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
A 360 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.151099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.118760 restraints weight = 16348.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.18
r_work: 0.3226 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    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 = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6090  Z= 0.107
  Angle     :  0.457   6.105   8271  Z= 0.249
  Chirality :  0.041   0.140    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.869  57.364    951
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.72 %
    Favored  : 87.48 %
  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:  1.74 (0.30), residues: 317
  sheet:  0.19 (0.43), residues: 145
  loop : -1.07 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.011   0.001   TYR A 414 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.009   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6088)
  covalent geometry    : angle       0.45709 ( 8267)
  SS BOND              : bond        0.00197 (    2)
  SS BOND              : angle       0.41840 (    4)
  hydrogen bonds       : bond        0.03627 (  315)
  hydrogen bonds       : angle       4.11654 (  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
  78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.176 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 78
  average time/residue: 0.4866
  time to fit residues: 40.2894
Evaluate side-chains
  73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3696 r_free = 0.3696 target = 0.146821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.114897 restraints weight = 13389.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.80
r_work: 0.3191 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6090  Z= 0.193
  Angle     :  0.534   6.931   8271  Z= 0.288
  Chirality :  0.044   0.145    907
  Planarity :  0.004   0.041   1019
  Dihedral  :  6.106  56.935    951
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.40 %
    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:  0.35 (0.31), residues: 724
  helix:  1.44 (0.30), residues: 317
  sheet:  0.06 (0.44), residues: 147
  loop : -1.14 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  98 
 TYR   0.014   0.002   TYR A 528 
 PHE   0.016   0.002   PHE B  47 
 TRP   0.011   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 6088)
  covalent geometry    : angle       0.53448 ( 8267)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       0.51381 (    4)
  hydrogen bonds       : bond        0.04257 (  315)
  hydrogen bonds       : angle       4.35707 (  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
  84 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.206 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7740 (m) cc_final: 0.7484 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 81
  average time/residue: 0.4701
  time to fit residues: 40.3814
Evaluate side-chains
  79 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3749 r_free = 0.3749 target = 0.151286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.118838 restraints weight = 16033.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 3.09
r_work: 0.3181 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.104         |
| 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) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1091

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= 0.150
  Angle     :  0.502   7.944   8271  Z= 0.272
  Chirality :  0.042   0.142    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  6.020  56.376    951
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.88 %
    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:  0.40 (0.31), residues: 724
  helix:  1.47 (0.30), residues: 317
  sheet:  0.06 (0.44), residues: 147
  loop : -1.10 (0.34), residues: 260

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 B  47 
 TRP   0.012   0.001   TRP A 536 
 HIS   0.002   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6088)
  covalent geometry    : angle       0.50195 ( 8267)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       0.35681 (    4)
  hydrogen bonds       : bond        0.03980 (  315)
  hydrogen bonds       : angle       4.27726 (  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
  80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7782 (m) cc_final: 0.7534 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 79
  average time/residue: 0.4774
  time to fit residues: 39.9562
Evaluate side-chains
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.4980
   chunk 36 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3756 r_free = 0.3756 target = 0.151947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.121149 restraints weight = 7714.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.25
r_work: 0.3254 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1098

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= 0.139
  Angle     :  0.494   8.287   8271  Z= 0.268
  Chirality :  0.042   0.142    907
  Planarity :  0.003   0.029   1019
  Dihedral  :  5.932  55.672    951
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  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:  0.43 (0.31), residues: 724
  helix:  1.52 (0.30), residues: 317
  sheet:  0.15 (0.44), residues: 148
  loop : -1.16 (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   0.012   0.001   TRP A 536 
 HIS   0.002   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6088)
  covalent geometry    : angle       0.49424 ( 8267)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.45027 (    4)
  hydrogen bonds       : bond        0.03890 (  315)
  hydrogen bonds       : angle       4.25085 (  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
  79 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7802 (m) cc_final: 0.7528 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 79
  average time/residue: 0.4856
  time to fit residues: 40.7479
Evaluate side-chains
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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 17 optimal weight:    0.2980
   chunk 6 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0000
   chunk 11 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0670
   chunk 69 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.2922

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3787 r_free = 0.3787 target = 0.154849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.123277 restraints weight = 10322.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.60
r_work: 0.3274 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6090  Z= 0.098
  Angle     :  0.449   7.405   8271  Z= 0.245
  Chirality :  0.040   0.141    907
  Planarity :  0.003   0.028   1019
  Dihedral  :  5.565  53.903    951
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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:  0.67 (0.31), residues: 724
  helix:  1.76 (0.30), residues: 316
  sheet:  0.35 (0.44), residues: 144
  loop : -1.13 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  66 
 TYR   0.012   0.001   TYR A 414 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.012   0.001   TRP A 536 
 HIS   0.001   0.000   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6088)
  covalent geometry    : angle       0.44895 ( 8267)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       0.38732 (    4)
  hydrogen bonds       : bond        0.03470 (  315)
  hydrogen bonds       : angle       4.07469 (  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
  73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B  107 THR cc_start: 0.7566 (m) cc_final: 0.7324 (t)
  outliers start: 4
  outliers final: 3
  residues processed: 72
  average time/residue: 0.5129
  time to fit residues: 39.1353
Evaluate side-chains
  69 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    0.1980
   chunk 7 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 49 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.153170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121360 restraints weight = 13169.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.86
r_work: 0.3240 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    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 = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
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   0.025   6090  Z= 0.122
  Angle     :  0.476   8.448   8271  Z= 0.257
  Chirality :  0.041   0.141    907
  Planarity :  0.003   0.028   1019
  Dihedral  :  5.559  53.276    951
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 12.84 %
    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:  0.65 (0.31), residues: 724
  helix:  1.70 (0.30), residues: 317
  sheet:  0.35 (0.44), residues: 146
  loop : -1.11 (0.34), residues: 261

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   0.013   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
  covalent geometry    : bond        0.00273 ( 6088)
  covalent geometry    : angle       0.47619 ( 8267)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.53292 (    4)
  hydrogen bonds       : bond        0.03701 (  315)
  hydrogen bonds       : angle       4.11798 (  877)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2521.94 seconds
wall clock time: 43 minutes 51.29 seconds (2631.29 seconds total)