Starting phenix.real_space_refine
on Tue Feb  3 19:07:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i94_52751/02_2026/9i94_52751_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i94_52751/02_2026/9i94_52751.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i94_52751/02_2026/9i94_52751_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i94_52751/02_2026/9i94_52751_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i94_52751/02_2026/9i94_52751.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i94_52751/02_2026/9i94_52751.map"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3872      2.51       5
     N    1016      2.21       5
     O    1222      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6135
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4546
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 553, 4538
          Classifications: {'peptide': 553}
          Link IDs: {'PTRANS': 20, 'TRANS': 532}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 553, 4538
          Classifications: {'peptide': 553}
          Link IDs: {'PTRANS': 20, 'TRANS': 532}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4652
    Chain: "C"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 139
          Classifications: {'peptide': 17}
          Link IDs: {'TRANS': 16}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1195
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 8, 'TRANS': 143}
    Chain: "A"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 245
          Unusual residues: {'LMT': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'KZ0': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 6
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASN A 367 " occ=0.53
      ... (14 atoms not shown)
      pdb=" ND2BASN A 367 " occ=0.47
  Time building chain proxies: 2.33, per 1000 atoms: 0.38
  Number of scatterers: 6135
  At special positions: 0
  Unit cell: (85.293, 76.545, 93.312, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1222      8.00
     N    1016      7.00
     C    3872      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 341.6 milliseconds
  

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 3 sheets defined
      15.1% alpha, 50.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 295 through 302
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.588A  pdb=" N   ARG A 542 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 669 through 673
    Processing helix  chain 'A' and resid 675 through 680
      removed outlier: 4.388A  pdb=" N   ASN A 680 " --> pdb=" O   GLU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 774
      removed outlier: 3.684A  pdb=" N   MET A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 17
    Processing helix  chain 'B' and resid 1025 through 1038
    Processing helix  chain 'B' and resid 1109 through 1111
      No H-bonds generated for 'chain 'B' and resid 1109 through 1111'
    Processing helix  chain 'B' and resid 1112 through 1138
      removed outlier: 4.178A  pdb=" N   ASP B1129 " --> pdb=" O   LYS B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1138 through 1150
      removed outlier: 3.618A  pdb=" N   ILE B1147 " --> pdb=" O   ARG B1143 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ASP B1150 " --> pdb=" O   ASP B1146 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249
      removed outlier: 3.598A  pdb=" N   ASN A 232 " --> pdb=" O   TYR A 244 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   HIS A 745 " --> pdb=" O   TRP A 739 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   TRP A 739 " --> pdb=" O   HIS A 745 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 13.069A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 13.089A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TYR A 704 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   SER A 715 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ALA A 702 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU A 717 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL A 700 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   VAL A 719 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER A 698 " --> pdb=" O   VAL A 719 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE A 693 " --> pdb=" O   TRP A 697 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLN A 627 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER A 638 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   GLY A 625 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   SER A 640 " --> pdb=" O   ARG A 623 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ARG A 623 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ILE A 642 " --> pdb=" O   GLY A 621 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLY A 621 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL A 607 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   PHE A 575 " --> pdb=" O   ILE A 566 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249
      removed outlier: 4.744A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 9.142A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 11.304A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASP A 402 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 1041 through 1043
      removed outlier: 4.070A  pdb=" N   LEU B1018 " --> pdb=" O   LEU B1043 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   LEU B1055 " --> pdb=" O   VAL B1015 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE B1017 " --> pdb=" O   LEU B1055 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   LEU B1057 " --> pdb=" O   ILE B1017 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ASP B1019 " --> pdb=" O   LEU B1057 " (cutoff:3.500A)
      removed outlier: 9.276A  pdb=" N   LYS B1059 " --> pdb=" O   ASP B1019 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   ASN B1085 " --> pdb=" O   GLY B1058 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   VAL B1060 " --> pdb=" O   THR B1083 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   THR B1083 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ILE B1062 " --> pdb=" O   ILE B1081 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE B1081 " --> pdb=" O   ILE B1062 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   LYS B1064 " --> pdb=" O   GLN B1079 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   GLN B1079 " --> pdb=" O   LYS B1064 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   THR B1066 " --> pdb=" O   GLU B1077 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   GLU B1077 " --> pdb=" O   THR B1066 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   SER B1068 " --> pdb=" O   THR B1075 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   THR B1075 " --> pdb=" O   SER B1068 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    879 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: 1.12

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 994
        1.30 -     1.43: 1834
        1.43 -     1.56: 3410
        1.56 -     1.68: 5
        1.68 -     1.81: 44
  Bond restraints: 6287
  Sorted by residual:
  bond pdb=" N   ASP A 536 "
       pdb=" CA  ASP A 536 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.034 1.27e-02 6.20e+03 7.25e+00
  bond pdb=" C   ALA C  17 "
       pdb=" O   ALA C  17 "
    ideal  model  delta    sigma   weight residual
    1.231  1.179  0.052 2.00e-02 2.50e+03 6.76e+00
  bond pdb=" N   ASP A 695 "
       pdb=" CA  ASP A 695 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.29e-02 6.01e+03 5.91e+00
  bond pdb=" C3' LMT A 801 "
       pdb=" O3' LMT A 801 "
    ideal  model  delta    sigma   weight residual
    1.404  1.358  0.046 2.00e-02 2.50e+03 5.27e+00
  bond pdb=" C2B LMT A 801 "
       pdb=" O2B LMT A 801 "
    ideal  model  delta    sigma   weight residual
    1.410  1.365  0.045 2.00e-02 2.50e+03 5.02e+00
  ... (remaining 6282 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 8116
        1.96 -     3.91: 301
        3.91 -     5.87: 80
        5.87 -     7.83: 11
        7.83 -     9.78: 21
  Bond angle restraints: 8529
  Sorted by residual:
  angle pdb=" C   ASN A 401 "
        pdb=" N   ASP A 402 "
        pdb=" CA  ASP A 402 "
      ideal   model   delta    sigma   weight residual
     121.54  131.20   -9.66 1.91e+00 2.74e-01 2.56e+01
  angle pdb=" C   LYS B1050 "
        pdb=" N   ASP B1051 "
        pdb=" CA  ASP B1051 "
      ideal   model   delta    sigma   weight residual
     122.46  129.31   -6.85 1.41e+00 5.03e-01 2.36e+01
  angle pdb=" N   ARG A 696 "
        pdb=" CA  ARG A 696 "
        pdb=" C   ARG A 696 "
      ideal   model   delta    sigma   weight residual
     114.62  109.41    5.21 1.14e+00 7.69e-01 2.09e+01
  angle pdb=" C   ALA A 694 "
        pdb=" N   ASP A 695 "
        pdb=" CA  ASP A 695 "
      ideal   model   delta    sigma   weight residual
     121.54  129.00   -7.46 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" CA  ASP A 695 "
        pdb=" CB  ASP A 695 "
        pdb=" CG  ASP A 695 "
      ideal   model   delta    sigma   weight residual
     112.60  116.35   -3.75 1.00e+00 1.00e+00 1.40e+01
  ... (remaining 8524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.27: 3638
       25.27 -    50.53: 222
       50.53 -    75.80: 54
       75.80 -   101.07: 35
      101.07 -   126.34: 42
  Dihedral angle restraints: 3991
    sinusoidal: 1855
      harmonic: 2136
  Sorted by residual:
  dihedral pdb=" CA  GLU A 391 "
           pdb=" C   GLU A 391 "
           pdb=" N   PRO A 392 "
           pdb=" CA  PRO A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.03   22.97     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  GLU A 301 "
           pdb=" C   GLU A 301 "
           pdb=" N   HIS A 302 "
           pdb=" CA  HIS A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.43   21.57     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" C1' LMT A 807 "
           pdb=" C5' LMT A 807 "
           pdb=" O5' LMT A 807 "
           pdb=" C4' LMT A 807 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.78   63.56 -126.34     1      3.00e+01 1.11e-03 1.70e+01
  ... (remaining 3988 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 792
       0.074 -    0.147: 103
       0.147 -    0.221: 22
       0.221 -    0.294: 7
       0.294 -    0.368: 1
  Chirality restraints: 925
  Sorted by residual:
  chirality pdb=" C5' LMT A 807 "
            pdb=" C4' LMT A 807 "
            pdb=" C6' LMT A 807 "
            pdb=" O5' LMT A 807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.14   -0.37 2.00e-01 2.50e+01 3.38e+00
  chirality pdb=" C5' LMT A 803 "
            pdb=" C4' LMT A 803 "
            pdb=" C6' LMT A 803 "
            pdb=" O5' LMT A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.27   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C5' LMT A 804 "
            pdb=" C4' LMT A 804 "
            pdb=" C6' LMT A 804 "
            pdb=" O5' LMT A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.27   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 922 not shown)

  Planarity restraints: 1078
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 391 "   -0.068 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO A 392 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 438 "    0.062 5.00e-02 4.00e+02   9.44e-02 1.43e+01
        pdb=" N   PRO A 439 "   -0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO A 439 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 439 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 260 "    0.052 5.00e-02 4.00e+02   7.88e-02 9.93e+00
        pdb=" N   PRO A 261 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 261 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 261 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1075 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 175
        2.70 -     3.25: 5700
        3.25 -     3.80: 9334
        3.80 -     4.35: 12725
        4.35 -     4.90: 22192
  Nonbonded interactions: 50126
  Sorted by model distance:
  nonbonded pdb=" O6' LMT A 803 "
            pdb=" O6B LMT A 803 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O6B LMT A 801 "
            pdb=" O6' LMT A 802 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OD1 ASN A 239 "
            pdb=" NH1 ARG A 267 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG1 THR A 238 "
            pdb=" OD1 ASP A 749 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   GLN A 534 "
            pdb=" NH2 ARG A 542 "
     model   vdw
     2.238 3.120
  ... (remaining 50121 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=0.47 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:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.650
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
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      :  0.007   0.077   6291  Z= 0.350
  Angle     :  0.984   9.785   8529  Z= 0.467
  Chirality :  0.059   0.368    925
  Planarity :  0.008   0.105   1078
  Dihedral  : 23.468 126.336   2627
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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: -0.29 (0.30), residues: 717
  helix:  0.39 (0.56), residues: 83
  sheet:  0.27 (0.26), residues: 361
  loop : -0.90 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 267 
 TYR   0.038   0.002   TYR A 628 
 PHE   0.035   0.002   PHE B1107 
 TRP   0.017   0.001   TRP A 697 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 6287)
  covalent geometry    : angle       0.98380 ( 8529)
  hydrogen bonds       : bond        0.14707 (  312)
  hydrogen bonds       : angle       6.88868 (  879)
  Misc. bond           : bond        0.04604 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: A  330 ASP cc_start: 0.8828 (t0) cc_final: 0.8437 (t0)
REVERT: A  344 ASP cc_start: 0.8162 (p0) cc_final: 0.7892 (p0)
REVERT: A  500 LEU cc_start: 0.9137 (mm) cc_final: 0.8735 (mt)
REVERT: A  670 LYS cc_start: 0.8855 (tptt) cc_final: 0.8630 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.6416
  time to fit residues: 60.8314
Evaluate side-chains
  59 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 317 HIS
A 323 GLN
A 345 ASN
A 393 GLN
** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 513 GLN
A 720 GLN
B1033 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.085615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.066912 restraints weight = 24343.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.95
r_work: 0.2771 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   6291  Z= 0.270
  Angle     :  0.793   7.951   8529  Z= 0.392
  Chirality :  0.052   0.281    925
  Planarity :  0.007   0.093   1078
  Dihedral  : 13.985  96.598   1245
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.36 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  7.09 %
    Favored  : 91.02 %
  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: -0.02 (0.30), residues: 717
  helix:  1.20 (0.55), residues: 88
  sheet:  0.30 (0.26), residues: 362
  loop : -0.77 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 267 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.011   0.002   PHE A 377 
 TRP   0.018   0.001   TRP A 697 
 HIS   0.002   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 ( 6287)
  covalent geometry    : angle       0.79348 ( 8529)
  hydrogen bonds       : bond        0.04456 (  312)
  hydrogen bonds       : angle       5.74032 (  879)
  Misc. bond           : bond        0.00070 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: A  330 ASP cc_start: 0.8717 (t0) cc_final: 0.8346 (t0)
REVERT: A  344 ASP cc_start: 0.8100 (p0) cc_final: 0.7852 (p0)
REVERT: A  670 LYS cc_start: 0.8638 (tptt) cc_final: 0.8429 (tppt)
REVERT: B 1125 LYS cc_start: 0.8459 (mppt) cc_final: 0.8135 (mppt)
  outliers start: 12
  outliers final: 5
  residues processed: 69
  average time/residue: 0.7103
  time to fit residues: 51.0509
Evaluate side-chains
  59 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain C residue    9 LEU
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1048 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    0.2980
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.086637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.068855 restraints weight = 16620.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 3.27
r_work: 0.2837 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6291  Z= 0.158
  Angle     :  0.661   7.554   8529  Z= 0.338
  Chirality :  0.048   0.285    925
  Planarity :  0.006   0.074   1078
  Dihedral  : 10.586  71.877   1245
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.52 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.92 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.30), residues: 717
  helix:  1.60 (0.55), residues: 88
  sheet:  0.35 (0.26), residues: 362
  loop : -0.70 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1049 
 TYR   0.012   0.001   TYR A 705 
 PHE   0.010   0.001   PHE B1103 
 TRP   0.009   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6287)
  covalent geometry    : angle       0.66115 ( 8529)
  hydrogen bonds       : bond        0.03735 (  312)
  hydrogen bonds       : angle       5.38661 (  879)
  Misc. bond           : bond        0.00033 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7922 (tm-30)
REVERT: A  330 ASP cc_start: 0.8772 (t0) cc_final: 0.8393 (t0)
REVERT: A  716 MET cc_start: 0.9252 (pp-130) cc_final: 0.9008 (pp-130)
REVERT: B 1138 LYS cc_start: 0.8998 (mttm) cc_final: 0.8712 (mttt)
  outliers start: 7
  outliers final: 3
  residues processed: 64
  average time/residue: 0.6547
  time to fit residues: 43.8767
Evaluate side-chains
  61 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 ASN
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.087704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.068991 restraints weight = 26013.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 4.06
r_work: 0.2809 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6291  Z= 0.135
  Angle     :  0.634   7.637   8529  Z= 0.324
  Chirality :  0.046   0.247    925
  Planarity :  0.006   0.067   1078
  Dihedral  :  8.889  57.696   1245
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.87 %
    Favored  : 87.87 %
  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:  0.29 (0.30), residues: 717
  helix:  1.91 (0.56), residues: 88
  sheet:  0.45 (0.26), residues: 358
  loop : -0.65 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 734 
 TYR   0.011   0.001   TYR A 705 
 PHE   0.008   0.001   PHE A 377 
 TRP   0.008   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6287)
  covalent geometry    : angle       0.63369 ( 8529)
  hydrogen bonds       : bond        0.03427 (  312)
  hydrogen bonds       : angle       5.19866 (  879)
  Misc. bond           : bond        0.00023 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: A  330 ASP cc_start: 0.8705 (t0) cc_final: 0.8294 (t0)
REVERT: A  670 LYS cc_start: 0.8226 (tppt) cc_final: 0.7977 (tppt)
REVERT: B 1125 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8020 (mppt)
  outliers start: 8
  outliers final: 2
  residues processed: 63
  average time/residue: 0.6226
  time to fit residues: 41.1054
Evaluate side-chains
  58 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 LEU
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 41 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 67 optimal weight:    0.3980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.087366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.068341 restraints weight = 29228.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 4.28
r_work: 0.2794 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6291  Z= 0.146
  Angle     :  0.625   8.398   8529  Z= 0.319
  Chirality :  0.045   0.180    925
  Planarity :  0.005   0.065   1078
  Dihedral  :  8.229  59.784   1245
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.50 %
    Favored  : 87.09 %
  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:  0.37 (0.31), residues: 717
  helix:  2.00 (0.55), residues: 88
  sheet:  0.48 (0.27), residues: 358
  loop : -0.58 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 734 
 TYR   0.011   0.001   TYR A 705 
 PHE   0.007   0.001   PHE A 377 
 TRP   0.007   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6287)
  covalent geometry    : angle       0.62491 ( 8529)
  hydrogen bonds       : bond        0.03431 (  312)
  hydrogen bonds       : angle       5.14855 (  879)
  Misc. bond           : bond        0.00025 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7753 (tm-30)
REVERT: A  330 ASP cc_start: 0.8690 (t0) cc_final: 0.8297 (t0)
REVERT: A  670 LYS cc_start: 0.8193 (tppt) cc_final: 0.7914 (tppt)
REVERT: B 1099 SER cc_start: 0.9174 (p) cc_final: 0.8865 (m)
REVERT: B 1125 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7954 (mppt)
  outliers start: 9
  outliers final: 4
  residues processed: 63
  average time/residue: 0.6441
  time to fit residues: 42.3182
Evaluate side-chains
  59 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain C residue    9 LEU
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 ASN
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.087286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.068601 restraints weight = 24101.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 3.92
r_work: 0.2807 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2816
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2816
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6291  Z= 0.131
  Angle     :  0.593   7.077   8529  Z= 0.306
  Chirality :  0.044   0.154    925
  Planarity :  0.005   0.062   1078
  Dihedral  :  7.944  59.955   1245
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.28 %
    Favored  : 86.61 %
  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:  0.46 (0.31), residues: 717
  helix:  2.11 (0.55), residues: 88
  sheet:  0.53 (0.27), residues: 358
  loop : -0.52 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 734 
 TYR   0.011   0.001   TYR A 705 
 PHE   0.007   0.001   PHE A 417 
 TRP   0.006   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6287)
  covalent geometry    : angle       0.59272 ( 8529)
  hydrogen bonds       : bond        0.03303 (  312)
  hydrogen bonds       : angle       5.06278 (  879)
  Misc. bond           : bond        0.00021 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: A  330 ASP cc_start: 0.8777 (t0) cc_final: 0.8392 (t0)
REVERT: A  497 MET cc_start: 0.8212 (mtp) cc_final: 0.7986 (ttp)
REVERT: A  670 LYS cc_start: 0.8251 (tppt) cc_final: 0.7945 (tppt)
REVERT: B 1099 SER cc_start: 0.9240 (p) cc_final: 0.8956 (m)
REVERT: B 1125 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8111 (mppt)
  outliers start: 7
  outliers final: 4
  residues processed: 65
  average time/residue: 0.6650
  time to fit residues: 45.1463
Evaluate side-chains
  61 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain C residue   15 ASP
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.084909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.065676 restraints weight = 30437.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 4.33
r_work: 0.2735 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   6291  Z= 0.237
  Angle     :  0.672   7.503   8529  Z= 0.345
  Chirality :  0.047   0.161    925
  Planarity :  0.005   0.061   1078
  Dihedral  :  8.290  56.366   1245
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.13 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.31), residues: 717
  helix:  1.94 (0.54), residues: 88
  sheet:  0.42 (0.27), residues: 362
  loop : -0.59 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 734 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.009   0.001   PHE A 417 
 TRP   0.008   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 6287)
  covalent geometry    : angle       0.67228 ( 8529)
  hydrogen bonds       : bond        0.03893 (  312)
  hydrogen bonds       : angle       5.37778 (  879)
  Misc. bond           : bond        0.00038 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7852 (tm-30)
REVERT: A  670 LYS cc_start: 0.8263 (tppt) cc_final: 0.7956 (tppt)
REVERT: B 1125 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8056 (mppt)
  outliers start: 10
  outliers final: 5
  residues processed: 57
  average time/residue: 0.7211
  time to fit residues: 42.8371
Evaluate side-chains
  58 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain C residue    9 LEU
Chi-restraints excluded: chain C residue   15 ASP
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    0.2980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
A 513 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.085760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.068673 restraints weight = 14025.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.98
r_work: 0.2840 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6291  Z= 0.170
  Angle     :  0.622   8.030   8529  Z= 0.322
  Chirality :  0.045   0.157    925
  Planarity :  0.005   0.060   1078
  Dihedral  :  8.086  59.095   1245
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.23 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.31), residues: 717
  helix:  2.01 (0.54), residues: 88
  sheet:  0.45 (0.27), residues: 362
  loop : -0.56 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 734 
 TYR   0.012   0.001   TYR A 705 
 PHE   0.008   0.001   PHE A 417 
 TRP   0.007   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 6287)
  covalent geometry    : angle       0.62217 ( 8529)
  hydrogen bonds       : bond        0.03554 (  312)
  hydrogen bonds       : angle       5.25116 (  879)
  Misc. bond           : bond        0.00028 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: A  330 ASP cc_start: 0.8728 (t0) cc_final: 0.8346 (t0)
REVERT: A  648 GLU cc_start: 0.8412 (pm20) cc_final: 0.8025 (pt0)
REVERT: A  670 LYS cc_start: 0.8188 (tppt) cc_final: 0.7892 (tppt)
REVERT: B 1125 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8079 (mppt)
  outliers start: 7
  outliers final: 5
  residues processed: 60
  average time/residue: 0.6320
  time to fit residues: 39.5529
Evaluate side-chains
  60 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain C residue   15 ASP
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0470
   chunk 61 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.5860

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.087922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.069940 restraints weight = 19073.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 3.53
r_work: 0.2843 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6291  Z= 0.123
  Angle     :  0.621   8.864   8529  Z= 0.318
  Chirality :  0.044   0.153    925
  Planarity :  0.005   0.060   1078
  Dihedral  :  7.788  57.128   1245
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.91 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.31), residues: 717
  helix:  2.07 (0.55), residues: 88
  sheet:  0.58 (0.27), residues: 356
  loop : -0.56 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.011   0.001   TYR A 705 
 PHE   0.007   0.001   PHE A 754 
 TRP   0.006   0.001   TRP A 697 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6287)
  covalent geometry    : angle       0.62072 ( 8529)
  hydrogen bonds       : bond        0.03201 (  312)
  hydrogen bonds       : angle       5.02370 (  879)
  Misc. bond           : bond        0.00022 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: A  330 ASP cc_start: 0.8669 (t0) cc_final: 0.8276 (t0)
REVERT: A  648 GLU cc_start: 0.8406 (pm20) cc_final: 0.7951 (pt0)
REVERT: A  670 LYS cc_start: 0.8097 (tppt) cc_final: 0.7792 (tppt)
REVERT: B 1099 SER cc_start: 0.9138 (p) cc_final: 0.8857 (m)
REVERT: B 1125 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7911 (mppt)
  outliers start: 8
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5928
  time to fit residues: 39.6509
Evaluate side-chains
  61 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 ASN
A 513 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.085705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.066882 restraints weight = 29128.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 4.19
r_work: 0.2759 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6291  Z= 0.185
  Angle     :  0.632   8.887   8529  Z= 0.326
  Chirality :  0.045   0.158    925
  Planarity :  0.005   0.060   1078
  Dihedral  :  7.823  54.848   1245
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 13.39 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.31), residues: 717
  helix:  2.01 (0.55), residues: 88
  sheet:  0.50 (0.27), residues: 358
  loop : -0.56 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 734 
 TYR   0.012   0.001   TYR A 705 
 PHE   0.008   0.001   PHE A 417 
 TRP   0.006   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6287)
  covalent geometry    : angle       0.63180 ( 8529)
  hydrogen bonds       : bond        0.03568 (  312)
  hydrogen bonds       : angle       5.18642 (  879)
  Misc. bond           : bond        0.00035 (    4)

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: A  648 GLU cc_start: 0.8495 (pm20) cc_final: 0.7915 (pp20)
REVERT: A  670 LYS cc_start: 0.8214 (tppt) cc_final: 0.7961 (tppt)
REVERT: B 1099 SER cc_start: 0.9255 (p) cc_final: 0.8971 (m)
REVERT: B 1125 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8178 (mppt)
  outliers start: 5
  outliers final: 4
  residues processed: 58
  average time/residue: 0.6559
  time to fit residues: 39.7169
Evaluate side-chains
  60 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 ASN
A 513 GLN
B1033 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.086136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.068343 restraints weight = 16879.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 3.27
r_work: 0.2835 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6291  Z= 0.150
  Angle     :  0.638   9.223   8529  Z= 0.325
  Chirality :  0.044   0.155    925
  Planarity :  0.005   0.059   1078
  Dihedral  :  7.714  54.624   1245
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.07 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.31), residues: 717
  helix:  2.00 (0.55), residues: 88
  sheet:  0.53 (0.27), residues: 358
  loop : -0.53 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 734 
 TYR   0.011   0.001   TYR A 705 
 PHE   0.007   0.001   PHE A 417 
 TRP   0.006   0.001   TRP A 697 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6287)
  covalent geometry    : angle       0.63841 ( 8529)
  hydrogen bonds       : bond        0.03396 (  312)
  hydrogen bonds       : angle       5.11689 (  879)
  Misc. bond           : bond        0.00022 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2031.09 seconds
wall clock time: 35 minutes 28.60 seconds (2128.60 seconds total)