Starting phenix.real_space_refine
on Sun Aug 24 04:04:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r1f_18809/08_2025/8r1f_18809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r1f_18809/08_2025/8r1f_18809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r1f_18809/08_2025/8r1f_18809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r1f_18809/08_2025/8r1f_18809.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r1f_18809/08_2025/8r1f_18809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r1f_18809/08_2025/8r1f_18809.cif"
  }
  resolution = 3.67
  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=   0.059
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     S      56      5.16       5
     C    5305      2.51       5
     N    1431      2.21       5
     O    1571      1.98       5
     H    8263      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16629
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 11110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 681, 11110
          Classifications: {'peptide': 681}
          Link IDs: {'PTRANS': 28, 'TRANS': 652}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2365
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 7, 'TRANS': 134}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "C"
      Number of atoms: 3151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 3151
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 15, 'TRANS': 186}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12835  SG  CYS B 110      56.475  36.607  79.155  1.00176.24           S
  ATOM  12878  SG  CYS B 113      55.532  34.457  81.709  1.00179.11           S
  ATOM  13405  SG  CYS B 143      55.194  38.288  82.316  1.00194.25           S
  ATOM  13429  SG  CYS B 146      58.574  36.731  82.368  1.00210.49           S
  ATOM  11605  SG  CYS B  37      56.648  19.590  79.458  1.00183.23           S
  ATOM  11652  SG  CYS B  40      59.322  17.617  80.885  1.00176.19           S
  ATOM  12158  SG  CYS B  70      58.332  21.223  82.276  1.00180.55           S
  ATOM  12202  SG  CYS B  73      60.186  20.867  79.074  1.00173.90           S
  ATOM  14814  SG  CYS C 176      16.452  40.292  92.297  1.00246.45           S
  ATOM  15777  SG  CYS C 238      18.788  39.517  89.134  1.00228.58           S
  ATOM  15823  SG  CYS C 242      20.345  40.437  92.437  1.00243.62           S

  Time building chain proxies: 3.21, per 1000 atoms: 0.19
  Number of scatterers: 16629
  At special positions: 0
  Unit cell: (118.44, 109.62, 109.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      3     29.99
     S      56     16.00
     O    1571      8.00
     N    1431      7.00
     C    5305      6.00
     H    8263      1.00
    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=0, symmetry=0
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 386.4 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 201 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B 110 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B 113 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B 143 "
        pdb="ZN    ZN B 201 " - pdb=" SG  CYS B 146 "
      pdb="  ZN B 202 "
        pdb="ZN    ZN B 202 " - pdb=" SG  CYS B  37 "
        pdb="ZN    ZN B 202 " - pdb=" SG  CYS B  73 "
        pdb="ZN    ZN B 202 " - pdb=" SG  CYS B  40 "
        pdb="ZN    ZN B 202 " - pdb=" SG  CYS B  70 "
      pdb="  ZN C 401 "
        pdb="ZN    ZN C 401 " - pdb=" ND1 HIS C 179 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 238 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 242 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 176 "
      Number of angles added : 15


  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 9 sheets defined
      56.4% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 129 through 143
      removed outlier: 3.874A  pdb=" N   ILE A 136 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 139 " --> pdb=" O   GLU A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 158
    Processing helix  chain 'A' and resid 159 through 167
      removed outlier: 4.206A  pdb=" N   PHE A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 247
    Processing helix  chain 'A' and resid 249 through 274
      removed outlier: 3.536A  pdb=" N   ALA A 255 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TYR A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      Proline residue:  A 265  - end of helix
      removed outlier: 3.535A  pdb=" N   CYS A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.573A  pdb=" N   ARG A 279 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 284 through 292
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.703A  pdb=" N   LEU A 296 " --> pdb=" O   ASN A 293 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   HIS A 297 " --> pdb=" O   ARG A 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 293 through 297'
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 4.301A  pdb=" N   MET A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 314
    Processing helix  chain 'A' and resid 317 through 329
    Processing helix  chain 'A' and resid 332 through 354
      removed outlier: 3.533A  pdb=" N   LEU A 346 " --> pdb=" O   THR A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 364
    Processing helix  chain 'A' and resid 365 through 386
    Processing helix  chain 'A' and resid 403 through 413
    Processing helix  chain 'A' and resid 426 through 433
    Processing helix  chain 'A' and resid 435 through 437
      No H-bonds generated for 'chain 'A' and resid 435 through 437'
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 451 through 458
    Processing helix  chain 'A' and resid 459 through 469
    Processing helix  chain 'A' and resid 476 through 484
      Proline residue:  A 481  - end of helix
    Processing helix  chain 'A' and resid 485 through 516
    Processing helix  chain 'A' and resid 531 through 547
    Processing helix  chain 'A' and resid 549 through 553
    Processing helix  chain 'A' and resid 568 through 584
    Processing helix  chain 'A' and resid 585 through 588
    Processing helix  chain 'A' and resid 608 through 625
      removed outlier: 3.982A  pdb=" N   PHE A 612 " --> pdb=" O   THR A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 642
      removed outlier: 4.114A  pdb=" N   TYR A 638 " --> pdb=" O   PRO A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 650 through 655
      removed outlier: 3.815A  pdb=" N   SER A 654 " --> pdb=" O   ASP A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 668
      removed outlier: 3.592A  pdb=" N   SER A 661 " --> pdb=" O   VAL A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 677
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 709 through 723
    Processing helix  chain 'A' and resid 726 through 742
      removed outlier: 3.684A  pdb=" N   ALA A 732 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL A 740 " --> pdb=" O   GLY A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 750
    Processing helix  chain 'A' and resid 751 through 761
      removed outlier: 3.656A  pdb=" N   LEU A 757 " --> pdb=" O   GLU A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 774
    Processing helix  chain 'A' and resid 784 through 797
    Processing helix  chain 'A' and resid 798 through 811
    Processing helix  chain 'A' and resid 819 through 823
    Processing helix  chain 'A' and resid 854 through 869
    Processing helix  chain 'B' and resid 18 through 26
    Processing helix  chain 'B' and resid 45 through 55
    Processing helix  chain 'B' and resid 70 through 85
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 102 through 106
    Processing helix  chain 'B' and resid 118 through 128
    Processing helix  chain 'B' and resid 143 through 148
    Processing helix  chain 'C' and resid 104 through 108
      removed outlier: 3.873A  pdb=" N   TYR C 107 " --> pdb=" O   GLN C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 169
    Processing helix  chain 'C' and resid 176 through 181
    Processing helix  chain 'C' and resid 277 through 292
    Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388
      removed outlier: 6.553A  pdb=" N   GLU A 387 " --> pdb=" O   ARG A 440 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 527
    Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 593
      removed outlier: 3.673A  pdb=" N   LEU A 598 " --> pdb=" O   ASP A 593 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 685
    Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 777
      removed outlier: 6.606A  pdb=" N   GLU A 775 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LYS A 829 " --> pdb=" O   GLU A 775 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   ASP A 777 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   GLY A 831 " --> pdb=" O   ASP A 777 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE A 826 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU A 849 " --> pdb=" O   ILE A 826 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   ALA A 828 " --> pdb=" O   LEU A 849 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLU A 851 " --> pdb=" O   ALA A 828 " (cutoff:3.500A)
      removed outlier: 8.555A  pdb=" N   ASN A 830 " --> pdb=" O   GLU A 851 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37
      removed outlier: 6.334A  pdb=" N   GLU B  36 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 91
      removed outlier: 3.780A  pdb=" N   TYR B  88 " --> pdb=" O   ASN B 134 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ARG B 109 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113
      removed outlier: 4.516A  pdb=" N   HIS C 233 " --> pdb=" O   GLU C 198 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 127
      removed outlier: 4.211A  pdb=" N   ILE C 251 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA C 161 " --> pdb=" O   HIS C 214 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   HIS C 214 " --> pdb=" O   ALA C 161 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1176 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: 3.21

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 8245
        1.03 -     1.23: 29
        1.23 -     1.42: 3574
        1.42 -     1.62: 4872
        1.62 -     1.82: 83
  Bond restraints: 16803
  Sorted by residual:
  bond pdb=" N   VAL A 234 "
       pdb=" H   VAL A 234 "
    ideal  model  delta    sigma   weight residual
    0.860  0.963 -0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" N   MET B   8 "
       pdb=" CA  MET B   8 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.040 1.90e-02 2.77e+03 4.42e+00
  bond pdb=" CD  ARG A 500 "
       pdb=" NE  ARG A 500 "
    ideal  model  delta    sigma   weight residual
    1.458  1.429  0.029 1.40e-02 5.10e+03 4.18e+00
  bond pdb=" CG  ARG A 500 "
       pdb=" CD  ARG A 500 "
    ideal  model  delta    sigma   weight residual
    1.520  1.468  0.052 3.00e-02 1.11e+03 3.01e+00
  bond pdb=" CA  ASP A 389 "
       pdb=" CB  ASP A 389 "
    ideal  model  delta    sigma   weight residual
    1.526  1.552 -0.026 1.53e-02 4.27e+03 2.82e+00
  ... (remaining 16798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 28886
        1.87 -     3.75: 1380
        3.75 -     5.62: 63
        5.62 -     7.49: 12
        7.49 -     9.37: 3
  Bond angle restraints: 30344
  Sorted by residual:
  angle pdb=" CB  ARG A 500 "
        pdb=" CG  ARG A 500 "
        pdb=" CD  ARG A 500 "
      ideal   model   delta    sigma   weight residual
     111.30  101.93    9.37 2.30e+00 1.89e-01 1.66e+01
  angle pdb=" C   GLU A 135 "
        pdb=" CA  GLU A 135 "
        pdb=" CB  GLU A 135 "
      ideal   model   delta    sigma   weight residual
     110.46  103.06    7.40 1.94e+00 2.66e-01 1.46e+01
  angle pdb=" C   PHE A 256 "
        pdb=" CA  PHE A 256 "
        pdb=" CB  PHE A 256 "
      ideal   model   delta    sigma   weight residual
     110.88  105.73    5.15 1.57e+00 4.06e-01 1.07e+01
  angle pdb=" CA  TYR A 146 "
        pdb=" CB  TYR A 146 "
        pdb=" CG  TYR A 146 "
      ideal   model   delta    sigma   weight residual
     113.90  108.05    5.85 1.80e+00 3.09e-01 1.06e+01
  angle pdb=" N   LEU A 458 "
        pdb=" CA  LEU A 458 "
        pdb=" C   LEU A 458 "
      ideal   model   delta    sigma   weight residual
     109.76  114.44   -4.68 1.59e+00 3.96e-01 8.67e+00
  ... (remaining 30339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.96: 7143
       15.96 -    31.93: 452
       31.93 -    47.89: 157
       47.89 -    63.85: 133
       63.85 -    79.82: 31
  Dihedral angle restraints: 7916
    sinusoidal: 4351
      harmonic: 3565
  Sorted by residual:
  dihedral pdb=" CD  ARG A 500 "
           pdb=" NE  ARG A 500 "
           pdb=" CZ  ARG A 500 "
           pdb=" NH1 ARG A 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   42.03  -42.03     1      1.00e+01 1.00e-02 2.47e+01
  dihedral pdb=" CA  SER B 147 "
           pdb=" C   SER B 147 "
           pdb=" N   ARG B 148 "
           pdb=" CA  ARG B 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.95   19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" C   ASN A 699 "
           pdb=" N   ASN A 699 "
           pdb=" CA  ASN A 699 "
           pdb=" CB  ASN A 699 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.47    8.87     0      2.50e+00 1.60e-01 1.26e+01
  ... (remaining 7913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 768
       0.056 -    0.111: 353
       0.111 -    0.167: 117
       0.167 -    0.222: 18
       0.222 -    0.278: 4
  Chirality restraints: 1260
  Sorted by residual:
  chirality pdb=" CA  ASN A 699 "
            pdb=" N   ASN A 699 "
            pdb=" C   ASN A 699 "
            pdb=" CB  ASN A 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ILE B  34 "
            pdb=" N   ILE B  34 "
            pdb=" C   ILE B  34 "
            pdb=" CB  ILE B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ARG C 248 "
            pdb=" N   ARG C 248 "
            pdb=" C   ARG C 248 "
            pdb=" CB  ARG C 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1257 not shown)

  Planarity restraints: 2472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 500 "    0.874 9.50e-02 1.11e+02   2.92e-01 9.43e+01
        pdb=" NE  ARG A 500 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 500 "   -0.052 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 500 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 500 "    0.008 2.00e-02 2.50e+03
        pdb="HH11 ARG A 500 "   -0.008 2.00e-02 2.50e+03
        pdb="HH12 ARG A 500 "    0.008 2.00e-02 2.50e+03
        pdb="HH21 ARG A 500 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A 500 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 734 "   -0.426 9.50e-02 1.11e+02   1.42e-01 2.16e+01
        pdb=" NE  ARG A 734 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 734 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 734 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 734 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 734 "    0.009 2.00e-02 2.50e+03
        pdb="HH12 ARG A 734 "   -0.004 2.00e-02 2.50e+03
        pdb="HH21 ARG A 734 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 734 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 256 "   -0.045 2.00e-02 2.50e+03   1.95e-02 1.14e+01
        pdb=" CG  PHE A 256 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 256 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 256 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 256 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 256 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 256 "   -0.008 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 256 "    0.007 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 256 "    0.007 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 256 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 256 "   -0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 256 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 2469 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 1706
        2.26 -     2.85: 38212
        2.85 -     3.43: 42591
        3.43 -     4.02: 58195
        4.02 -     4.60: 90108
  Nonbonded interactions: 230812
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 130 "
            pdb=" HH  TYR A 134 "
     model   vdw
     1.677 2.450
  nonbonded pdb=" O   PRO C 152 "
            pdb=" HG1 THR C 155 "
     model   vdw
     1.693 2.450
  nonbonded pdb=" HH  TYR A 668 "
            pdb=" OD2 ASP A 675 "
     model   vdw
     1.703 2.450
  nonbonded pdb=" O   PRO B  16 "
            pdb=" HH  TYR B  61 "
     model   vdw
     1.708 2.450
  nonbonded pdb=" HG  SER C  95 "
            pdb=" O   THR C 211 "
     model   vdw
     1.726 2.450
  ... (remaining 230807 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:             0.100
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.260
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5340
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      :  0.008   0.053   8552  Z= 0.352
  Angle     :  0.998  11.951  11556  Z= 0.573
  Chirality :  0.068   0.278   1260
  Planarity :  0.016   0.377   1501
  Dihedral  : 11.490  79.816   3271
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 0.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.66 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.25), residues: 1017
  helix: -0.82 (0.20), residues: 482
  sheet: -0.21 (0.47), residues: 118
  loop :  0.21 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.001   ARG A 500 
 TYR   0.030   0.004   TYR A 494 
 PHE   0.051   0.005   PHE A 256 
 TRP   0.019   0.004   TRP A 791 
 HIS   0.013   0.003   HIS C 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00757 ( 8540)
  covalent geometry    : angle       0.97879 (11541)
  hydrogen bonds       : bond        0.14889 (  422)
  hydrogen bonds       : angle       7.48762 ( 1176)
  metal coordination   : bond        0.02245 (   12)
  metal coordination   : angle       5.52555 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  256 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 GLU cc_start: 0.6539 (tt0) cc_final: 0.6316 (tp30)
REVERT: A  313 MET cc_start: 0.7243 (ttm) cc_final: 0.6892 (ttm)
REVERT: A  389 ASP cc_start: 0.6868 (m-30) cc_final: 0.5337 (p0)
REVERT: A  415 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6835 (mp0)
REVERT: A  470 GLU cc_start: 0.5170 (tt0) cc_final: 0.4954 (mm-30)
REVERT: A  556 TYR cc_start: 0.7071 (t80) cc_final: 0.6333 (t80)
REVERT: A  558 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6402 (mm-30)
REVERT: A  559 PHE cc_start: 0.6303 (m-80) cc_final: 0.6008 (m-80)
REVERT: A  591 THR cc_start: 0.5311 (p) cc_final: 0.4549 (m)
REVERT: A  630 ASP cc_start: 0.6216 (p0) cc_final: 0.5757 (p0)
REVERT: A  756 GLU cc_start: 0.6405 (tt0) cc_final: 0.6121 (tm-30)
REVERT: A  757 LEU cc_start: 0.6630 (mt) cc_final: 0.6279 (tt)
REVERT: B   47 ARG cc_start: 0.7264 (tpp80) cc_final: 0.7057 (tpp80)
REVERT: B   58 CYS cc_start: 0.7062 (m) cc_final: 0.6223 (t)
REVERT: B   61 TYR cc_start: 0.6486 (m-80) cc_final: 0.5270 (m-80)
REVERT: B   72 LYS cc_start: 0.9120 (pttm) cc_final: 0.8878 (pttm)
REVERT: B   90 LEU cc_start: 0.4983 (mt) cc_final: 0.4626 (mp)
REVERT: B  129 LYS cc_start: 0.7730 (mttt) cc_final: 0.6999 (mmmt)
REVERT: C  100 GLN cc_start: 0.7958 (pt0) cc_final: 0.7681 (pt0)
REVERT: C  137 LEU cc_start: 0.7216 (tp) cc_final: 0.6625 (tp)
REVERT: C  163 TYR cc_start: 0.4948 (m-80) cc_final: 0.4123 (m-80)
REVERT: C  165 GLN cc_start: 0.8806 (mt0) cc_final: 0.8291 (mt0)
REVERT: C  171 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: C  196 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6281 (ttp-110)
REVERT: C  271 GLU cc_start: 0.7220 (tt0) cc_final: 0.6910 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 256
  average time/residue: 0.2813
  time to fit residues: 92.2213
Evaluate side-chains
  159 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 HIS
B 100 ASN
** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.218007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.183058 restraints weight = 38680.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.189174 restraints weight = 20942.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.192532 restraints weight = 12805.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.192835 restraints weight = 9482.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.193638 restraints weight = 9603.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8552  Z= 0.226
  Angle     :  0.679   8.877  11556  Z= 0.358
  Chirality :  0.042   0.141   1260
  Planarity :  0.006   0.050   1501
  Dihedral  :  5.013  56.279   1146
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  8.09 %
    Favored  : 90.10 %
  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 aren not related in a simple way.
  whole:  0.07 (0.26), residues: 1017
  helix:  0.21 (0.23), residues: 485
  sheet: -0.28 (0.47), residues: 120
  loop :  0.20 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 500 
 TYR   0.021   0.002   TYR B  86 
 PHE   0.024   0.002   PHE A 467 
 TRP   0.012   0.002   TRP A 791 
 HIS   0.004   0.001   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 8540)
  covalent geometry    : angle       0.66435 (11541)
  hydrogen bonds       : bond        0.05086 (  422)
  hydrogen bonds       : angle       5.79743 ( 1176)
  metal coordination   : bond        0.01466 (   12)
  metal coordination   : angle       3.93657 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  174 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6651 (t80)
REVERT: A  556 TYR cc_start: 0.6316 (t80) cc_final: 0.6029 (t80)
REVERT: A  559 PHE cc_start: 0.7785 (m-80) cc_final: 0.7495 (m-80)
REVERT: A  591 THR cc_start: 0.7608 (p) cc_final: 0.6037 (m)
REVERT: A  757 LEU cc_start: 0.8620 (mt) cc_final: 0.7921 (tt)
REVERT: B   58 CYS cc_start: 0.8040 (m) cc_final: 0.7248 (t)
REVERT: C  160 MET cc_start: 0.7305 (ttp) cc_final: 0.7063 (ttp)
  outliers start: 17
  outliers final: 11
  residues processed: 167
  average time/residue: 0.2404
  time to fit residues: 53.1225
Evaluate side-chains
  135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  209 ARG
Chi-restraints excluded: chain C residue  289 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 98 optimal weight:    0.6980
   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 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  10 GLN
B 100 ASN
** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.218662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.182948 restraints weight = 39026.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.189244 restraints weight = 21098.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.192240 restraints weight = 14029.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.191990 restraints weight = 10972.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.192714 restraints weight = 10285.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8552  Z= 0.140
  Angle     :  0.574   6.948  11556  Z= 0.296
  Chirality :  0.039   0.138   1260
  Planarity :  0.005   0.045   1501
  Dihedral  :  4.696  58.157   1146
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.44 %
    Favored  : 88.29 %
  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 aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1017
  helix:  0.69 (0.23), residues: 487
  sheet: -0.29 (0.48), residues: 116
  loop :  0.50 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 500 
 TYR   0.016   0.001   TYR A 502 
 PHE   0.016   0.002   PHE A 467 
 TRP   0.010   0.002   TRP B 139 
 HIS   0.003   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8540)
  covalent geometry    : angle       0.55867 (11541)
  hydrogen bonds       : bond        0.04260 (  422)
  hydrogen bonds       : angle       5.29681 ( 1176)
  metal coordination   : bond        0.00770 (   12)
  metal coordination   : angle       3.65616 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  140 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 PRO cc_start: 0.8081 (Cg_exo) cc_final: 0.7781 (Cg_endo)
REVERT: A  461 ASP cc_start: 0.7678 (p0) cc_final: 0.7415 (p0)
REVERT: A  511 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6619 (t80)
REVERT: A  556 TYR cc_start: 0.6383 (t80) cc_final: 0.6182 (t80)
REVERT: A  559 PHE cc_start: 0.7812 (m-80) cc_final: 0.7588 (m-80)
REVERT: A  591 THR cc_start: 0.7553 (p) cc_final: 0.5989 (m)
REVERT: A  757 LEU cc_start: 0.8547 (mt) cc_final: 0.7897 (tt)
REVERT: B   58 CYS cc_start: 0.7937 (m) cc_final: 0.7043 (t)
REVERT: B  127 ASP cc_start: 0.6921 (m-30) cc_final: 0.6696 (m-30)
REVERT: C  160 MET cc_start: 0.7261 (ttp) cc_final: 0.7016 (ttp)
REVERT: C  206 LEU cc_start: 0.4539 (mp) cc_final: 0.3803 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 138
  average time/residue: 0.2422
  time to fit residues: 44.3302
Evaluate side-chains
  121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain C residue  209 ARG
Chi-restraints excluded: chain C residue  289 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0670
   chunk 83 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0670
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.218117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.183653 restraints weight = 38488.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.188809 restraints weight = 20751.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.191392 restraints weight = 13799.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.192568 restraints weight = 10591.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.193190 restraints weight = 10444.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8552  Z= 0.123
  Angle     :  0.533   6.550  11556  Z= 0.272
  Chirality :  0.038   0.137   1260
  Planarity :  0.005   0.045   1501
  Dihedral  :  4.543  59.023   1146
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.29 %
    Favored  : 87.22 %
  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 aren not related in a simple way.
  whole:  0.74 (0.27), residues: 1017
  helix:  0.87 (0.23), residues: 488
  sheet: -0.34 (0.48), residues: 116
  loop :  0.52 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  84 
 TYR   0.012   0.001   TYR B  86 
 PHE   0.014   0.002   PHE C 113 
 TRP   0.009   0.001   TRP B 139 
 HIS   0.004   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8540)
  covalent geometry    : angle       0.51861 (11541)
  hydrogen bonds       : bond        0.03752 (  422)
  hydrogen bonds       : angle       5.03225 ( 1176)
  metal coordination   : bond        0.00581 (   12)
  metal coordination   : angle       3.42518 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 PRO cc_start: 0.8051 (Cg_exo) cc_final: 0.7849 (Cg_endo)
REVERT: A  464 TYR cc_start: 0.8283 (t80) cc_final: 0.7601 (t80)
REVERT: A  511 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6614 (t80)
REVERT: A  559 PHE cc_start: 0.7960 (m-80) cc_final: 0.7675 (m-80)
REVERT: A  589 MET cc_start: 0.7949 (mtp) cc_final: 0.7729 (mtp)
REVERT: A  591 THR cc_start: 0.7506 (p) cc_final: 0.5978 (m)
REVERT: A  757 LEU cc_start: 0.8431 (mt) cc_final: 0.7933 (tt)
REVERT: B   58 CYS cc_start: 0.7854 (m) cc_final: 0.7084 (t)
REVERT: B  127 ASP cc_start: 0.6834 (m-30) cc_final: 0.6477 (m-30)
REVERT: C  206 LEU cc_start: 0.4597 (mp) cc_final: 0.3709 (tt)
  outliers start: 14
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2022
  time to fit residues: 38.6082
Evaluate side-chains
  124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  209 ARG
Chi-restraints excluded: chain C residue  289 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 85 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.217718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.183875 restraints weight = 38467.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.188784 restraints weight = 22623.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.191199 restraints weight = 14512.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.191615 restraints weight = 10951.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.192059 restraints weight = 10894.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.5157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8552  Z= 0.118
  Angle     :  0.513   6.460  11556  Z= 0.262
  Chirality :  0.038   0.131   1260
  Planarity :  0.004   0.045   1501
  Dihedral  :  4.409  59.630   1146
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.50 %
    Favored  : 87.11 %
  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 aren not related in a simple way.
  whole:  0.93 (0.27), residues: 1017
  helix:  1.08 (0.23), residues: 488
  sheet: -0.37 (0.48), residues: 116
  loop :  0.56 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  84 
 TYR   0.014   0.001   TYR C 126 
 PHE   0.014   0.001   PHE A 467 
 TRP   0.009   0.001   TRP B 139 
 HIS   0.004   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8540)
  covalent geometry    : angle       0.50040 (11541)
  hydrogen bonds       : bond        0.03525 (  422)
  hydrogen bonds       : angle       4.89085 ( 1176)
  metal coordination   : bond        0.00582 (   12)
  metal coordination   : angle       3.13176 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  136 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 TYR cc_start: 0.8178 (t80) cc_final: 0.7415 (t80)
REVERT: A  511 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6512 (t80)
REVERT: A  537 LEU cc_start: 0.4718 (tt) cc_final: 0.4324 (tt)
REVERT: A  589 MET cc_start: 0.8029 (mtp) cc_final: 0.7787 (mtp)
REVERT: A  591 THR cc_start: 0.7472 (p) cc_final: 0.5965 (m)
REVERT: A  757 LEU cc_start: 0.8460 (mt) cc_final: 0.7944 (tt)
REVERT: B   58 CYS cc_start: 0.7749 (m) cc_final: 0.7134 (t)
REVERT: B  127 ASP cc_start: 0.6934 (m-30) cc_final: 0.6718 (m-30)
REVERT: C  140 THR cc_start: 0.6434 (OUTLIER) cc_final: 0.6174 (t)
REVERT: C  200 ASN cc_start: 0.7008 (m110) cc_final: 0.6746 (m-40)
REVERT: C  206 LEU cc_start: 0.4400 (mp) cc_final: 0.3566 (tt)
  outliers start: 13
  outliers final: 10
  residues processed: 133
  average time/residue: 0.2090
  time to fit residues: 38.2456
Evaluate side-chains
  128 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0040
   chunk 57 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0020
   chunk 71 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.4400

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.218514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.184411 restraints weight = 38233.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.189506 restraints weight = 20572.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.192450 restraints weight = 13460.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.193032 restraints weight = 10125.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.194020 restraints weight = 10050.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8552  Z= 0.101
  Angle     :  0.491   6.566  11556  Z= 0.249
  Chirality :  0.037   0.138   1260
  Planarity :  0.004   0.045   1501
  Dihedral  :  4.248  59.974   1146
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.71 %
    Favored  : 87.01 %
  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 aren not related in a simple way.
  whole:  1.15 (0.27), residues: 1017
  helix:  1.34 (0.23), residues: 485
  sheet: -0.30 (0.48), residues: 116
  loop :  0.60 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  84 
 TYR   0.014   0.001   TYR C 126 
 PHE   0.013   0.001   PHE A 730 
 TRP   0.009   0.001   TRP B 139 
 HIS   0.004   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8540)
  covalent geometry    : angle       0.47996 (11541)
  hydrogen bonds       : bond        0.03264 (  422)
  hydrogen bonds       : angle       4.72703 ( 1176)
  metal coordination   : bond        0.00558 (   12)
  metal coordination   : angle       2.95959 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 TYR cc_start: 0.8160 (t80) cc_final: 0.7408 (t80)
REVERT: A  511 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6466 (t80)
REVERT: A  537 LEU cc_start: 0.4667 (tt) cc_final: 0.4246 (tt)
REVERT: A  589 MET cc_start: 0.7988 (mtp) cc_final: 0.7768 (mtp)
REVERT: A  591 THR cc_start: 0.7429 (p) cc_final: 0.5929 (m)
REVERT: B   18 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7570 (mmmt)
REVERT: B   58 CYS cc_start: 0.7861 (m) cc_final: 0.7129 (t)
REVERT: B  127 ASP cc_start: 0.6886 (m-30) cc_final: 0.6667 (m-30)
REVERT: C  140 THR cc_start: 0.6563 (OUTLIER) cc_final: 0.6150 (t)
REVERT: C  206 LEU cc_start: 0.4383 (mp) cc_final: 0.3556 (tt)
  outliers start: 12
  outliers final: 10
  residues processed: 130
  average time/residue: 0.2351
  time to fit residues: 41.7524
Evaluate side-chains
  129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 11 optimal weight:    0.1980
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.213592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.178660 restraints weight = 38090.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.182613 restraints weight = 22385.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.185513 restraints weight = 14897.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.185794 restraints weight = 11342.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.186545 restraints weight = 11168.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8552  Z= 0.165
  Angle     :  0.546   7.393  11556  Z= 0.282
  Chirality :  0.039   0.139   1260
  Planarity :  0.005   0.045   1501
  Dihedral  :  4.452  59.911   1146
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.61 %
    Favored  : 86.69 %
  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 aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1017
  helix:  1.06 (0.23), residues: 485
  sheet: -0.45 (0.48), residues: 116
  loop :  0.50 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 500 
 TYR   0.018   0.002   TYR B  86 
 PHE   0.022   0.002   PHE A 467 
 TRP   0.010   0.001   TRP B 139 
 HIS   0.005   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8540)
  covalent geometry    : angle       0.53443 (11541)
  hydrogen bonds       : bond        0.03727 (  422)
  hydrogen bonds       : angle       4.95382 ( 1176)
  metal coordination   : bond        0.00737 (   12)
  metal coordination   : angle       3.14507 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  138 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6490 (t80)
REVERT: A  537 LEU cc_start: 0.5110 (tt) cc_final: 0.4700 (tt)
REVERT: A  572 LYS cc_start: 0.7546 (tttt) cc_final: 0.7202 (tptp)
REVERT: A  591 THR cc_start: 0.7430 (p) cc_final: 0.5939 (m)
REVERT: B   58 CYS cc_start: 0.7877 (m) cc_final: 0.7103 (t)
REVERT: B  127 ASP cc_start: 0.6963 (m-30) cc_final: 0.6734 (m-30)
REVERT: C  200 ASN cc_start: 0.7686 (m-40) cc_final: 0.7447 (m110)
REVERT: C  206 LEU cc_start: 0.4608 (mp) cc_final: 0.3708 (tt)
  outliers start: 16
  outliers final: 15
  residues processed: 132
  average time/residue: 0.2193
  time to fit residues: 39.4326
Evaluate side-chains
  131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.214891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.180458 restraints weight = 38114.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.186668 restraints weight = 21629.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.188336 restraints weight = 13591.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.188209 restraints weight = 11023.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.189306 restraints weight = 10451.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.5807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8552  Z= 0.139
  Angle     :  0.530   7.773  11556  Z= 0.273
  Chirality :  0.038   0.139   1260
  Planarity :  0.004   0.045   1501
  Dihedral  :  4.424  59.992   1146
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.89 %
    Favored  : 85.20 %
  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 aren not related in a simple way.
  whole:  0.96 (0.27), residues: 1017
  helix:  1.12 (0.23), residues: 481
  sheet: -0.41 (0.49), residues: 113
  loop :  0.58 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 500 
 TYR   0.016   0.001   TYR C 103 
 PHE   0.016   0.002   PHE A 467 
 TRP   0.011   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8540)
  covalent geometry    : angle       0.52028 (11541)
  hydrogen bonds       : bond        0.03535 (  422)
  hydrogen bonds       : angle       4.86426 ( 1176)
  metal coordination   : bond        0.00651 (   12)
  metal coordination   : angle       2.85009 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  140 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6524 (t80)
REVERT: A  537 LEU cc_start: 0.5166 (tt) cc_final: 0.4747 (tt)
REVERT: A  572 LYS cc_start: 0.7601 (tttt) cc_final: 0.7189 (tptp)
REVERT: A  591 THR cc_start: 0.7377 (p) cc_final: 0.5922 (m)
REVERT: B   58 CYS cc_start: 0.7903 (m) cc_final: 0.7108 (t)
REVERT: B  127 ASP cc_start: 0.6987 (m-30) cc_final: 0.6763 (m-30)
REVERT: C  200 ASN cc_start: 0.7825 (m-40) cc_final: 0.7503 (m110)
REVERT: C  206 LEU cc_start: 0.4393 (mp) cc_final: 0.3480 (tt)
  outliers start: 18
  outliers final: 14
  residues processed: 134
  average time/residue: 0.2229
  time to fit residues: 40.2563
Evaluate side-chains
  132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0050
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.215139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.181004 restraints weight = 37962.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.185049 restraints weight = 22731.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.187779 restraints weight = 14974.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.188124 restraints weight = 11445.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.188590 restraints weight = 11240.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.5933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8552  Z= 0.123
  Angle     :  0.527   8.154  11556  Z= 0.272
  Chirality :  0.038   0.140   1260
  Planarity :  0.004   0.046   1501
  Dihedral  :  4.375  59.920   1146
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.84 %
    Favored  : 84.66 %
  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 aren not related in a simple way.
  whole:  1.12 (0.27), residues: 1017
  helix:  1.26 (0.24), residues: 481
  sheet: -0.36 (0.48), residues: 114
  loop :  0.66 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 710 
 TYR   0.018   0.001   TYR C 103 
 PHE   0.013   0.001   PHE A 730 
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8540)
  covalent geometry    : angle       0.51866 (11541)
  hydrogen bonds       : bond        0.03416 (  422)
  hydrogen bonds       : angle       4.78861 ( 1176)
  metal coordination   : bond        0.00622 (   12)
  metal coordination   : angle       2.57820 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6528 (t80)
REVERT: A  572 LYS cc_start: 0.7576 (tttt) cc_final: 0.7171 (tptp)
REVERT: A  591 THR cc_start: 0.7374 (p) cc_final: 0.5898 (m)
REVERT: B   58 CYS cc_start: 0.7848 (m) cc_final: 0.7106 (t)
REVERT: B  127 ASP cc_start: 0.7000 (m-30) cc_final: 0.6774 (m-30)
REVERT: C  200 ASN cc_start: 0.7766 (m-40) cc_final: 0.7483 (m110)
REVERT: C  206 LEU cc_start: 0.4351 (mp) cc_final: 0.3481 (tt)
  outliers start: 14
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2137
  time to fit residues: 37.5321
Evaluate side-chains
  131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 68 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.213058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.178488 restraints weight = 37895.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.182476 restraints weight = 22970.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.185289 restraints weight = 15058.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.185510 restraints weight = 11537.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.186147 restraints weight = 11297.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.6083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8552  Z= 0.151
  Angle     :  0.549   7.910  11556  Z= 0.286
  Chirality :  0.039   0.141   1260
  Planarity :  0.005   0.045   1501
  Dihedral  :  4.450  59.902   1146
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.95 %
    Favored  : 84.56 %
  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 aren not related in a simple way.
  whole:  0.98 (0.27), residues: 1017
  helix:  1.09 (0.23), residues: 481
  sheet: -0.31 (0.50), residues: 111
  loop :  0.62 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 181 
 TYR   0.017   0.001   TYR C 103 
 PHE   0.013   0.002   PHE A 256 
 TRP   0.011   0.001   TRP B 139 
 HIS   0.005   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8540)
  covalent geometry    : angle       0.54047 (11541)
  hydrogen bonds       : bond        0.03606 (  422)
  hydrogen bonds       : angle       4.87954 ( 1176)
  metal coordination   : bond        0.00703 (   12)
  metal coordination   : angle       2.78854 (   15)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  144 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 TYR cc_start: 0.8294 (t80) cc_final: 0.7932 (t80)
REVERT: A  511 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6540 (t80)
REVERT: A  537 LEU cc_start: 0.5068 (tt) cc_final: 0.4658 (tt)
REVERT: A  572 LYS cc_start: 0.7631 (tttt) cc_final: 0.7180 (tptp)
REVERT: A  591 THR cc_start: 0.7410 (p) cc_final: 0.5978 (m)
REVERT: B   58 CYS cc_start: 0.7915 (m) cc_final: 0.7100 (t)
REVERT: B  127 ASP cc_start: 0.7062 (m-30) cc_final: 0.6826 (m-30)
REVERT: C  200 ASN cc_start: 0.7792 (m-40) cc_final: 0.7407 (m110)
REVERT: C  206 LEU cc_start: 0.4373 (mp) cc_final: 0.3465 (tt)
  outliers start: 14
  outliers final: 13
  residues processed: 126
  average time/residue: 0.2004
  time to fit residues: 34.3284
Evaluate side-chains
  130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  511 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  209 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 67 optimal weight:    9.9990
   chunk 34 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0050
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 64 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.214891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.180836 restraints weight = 37937.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.185195 restraints weight = 22523.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.187893 restraints weight = 14720.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.188092 restraints weight = 11388.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.188500 restraints weight = 10956.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.6163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8552  Z= 0.116
  Angle     :  0.517   7.724  11556  Z= 0.268
  Chirality :  0.038   0.140   1260
  Planarity :  0.004   0.046   1501
  Dihedral  :  4.296  59.851   1146
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.84 %
    Favored  : 84.77 %
  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 aren not related in a simple way.
  whole:  1.25 (0.27), residues: 1017
  helix:  1.35 (0.24), residues: 479
  sheet: -0.23 (0.50), residues: 111
  loop :  0.73 (0.32), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 814 
 TYR   0.018   0.001   TYR C 103 
 PHE   0.013   0.001   PHE A 730 
 TRP   0.010   0.001   TRP B 139 
 HIS   0.003   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8540)
  covalent geometry    : angle       0.51046 (11541)
  hydrogen bonds       : bond        0.03327 (  422)
  hydrogen bonds       : angle       4.72423 ( 1176)
  metal coordination   : bond        0.00595 (   12)
  metal coordination   : angle       2.31235 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2886.64 seconds
wall clock time: 49 minutes 57.41 seconds (2997.41 seconds total)